From c8689c54496769efd3196e488f80c6b10fbbdecd Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 6 Mar 2024 10:39:59 -0600 Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#259) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.9.1 → 24.2.0](https://github.com/psf/black/compare/23.9.1...24.2.0) - [github.com/pycqa/isort: 5.12.0 → 5.13.2](https://github.com/pycqa/isort/compare/5.12.0...5.13.2) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 +- .../aggregate_summary/aggregate_init.py | 43 +++++++++++-------- .../aggregate_summary/analyze_data.py | 1 + .../aggregate_summary/plotting.py | 1 + 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.../src/engines/gomc/project.py | 1 + .../src/engines/gromacs/project.py | 1 + .../src/engines/hoomd/project.py | 1 + .../src/engines/hoomd/project_rahman.py | 1 + .../src/engines/lammps-UD/example-project.py | 1 + .../src/engines/lammps-UD/main_project.py | 1 + .../src/engines/lammps-UD/project.py | 1 + .../src/engines/lammps-VU/project.py | 1 + .../src/engines/mcccs/analysis.py | 1 + .../src/engines/mcccs/example-project.py | 1 + .../src/engines/mcccs/project.py | 1 + .../engines/mcccs_lammps_foyer/analysis.py | 1 + .../mcccs_lammps_foyer/example-project.py | 1 + .../src/engines/mcccs_lammps_foyer/project.py | 1 + .../src/system_snapshots/create_snapshots.py | 1 + .../spe_subproject/subproject-init.py | 43 +++++++++++-------- .../spe_subproject/summarize.py | 1 + .../spe_subproject/templates/ndcrc.py | 1 + .../templates/ndcrc_scheduler.py | 1 + .../generate_comparison_plots.py | 9 ++-- .../Comparison_Figures/generate_densities.py | 1 + .../analysis/Comparison_Figures/plotting.py | 1 + .../src/analysis/__init__.py | 1 + .../src/analysis/equilibration.py | 1 + reproducibility_project/src/dashboard.py | 1 + .../engine_input/mcccs/fort77maker_onebox.py | 7 +-- .../engine_input/mcccs/fort77maker_twobox.py | 7 +-- .../src/engines/cassandra/project.py | 1 + .../src/engines/gomc/project.py | 19 ++++---- .../src/engines/hoomd/project.py | 1 + .../src/engines/hoomd/project_rahman.py | 1 + .../src/engines/lammps-UD/project.py | 1 + .../src/engines/lammps-VU/project.py | 1 + .../src/engines/mcccs/analysis.py | 1 + .../src/engines/mcccs/conv_traj.py | 1 + .../src/engines/mcccs/plot_water.py | 1 + .../src/engines/mcccs/project.py | 1 + .../src/molecules/ethanol_aa.py | 1 + .../src/molecules/system_builder.py | 1 + .../src/utils/convert_spce_params.py | 1 + .../src/utils/forcefields.py | 1 + reproducibility_project/src/utils/plotting.py | 1 + .../src/utils/trajectory_conversion.py | 1 + reproducibility_project/templates/ndcrc.py | 1 + .../templates/ndcrc_scheduler.py | 1 + .../tests/test_utils_forcefields.py | 1 + .../aggregate_summary/aggregate_init.py | 43 +++++++++++-------- .../aggregate_summary/analyze_data.py | 1 + .../src/engines/lammps-VU/project.py | 1 + .../subproject-analysis.py | 1 + .../subproject-init.py | 43 +++++++++++-------- .../templates/ndcrc.py | 1 + .../templates/ndcrc_scheduler.py | 1 + .../restart_file/fort77maker_onebox.py | 7 +-- .../007-1728/restart_file/makerestart77.py | 1 + .../007-1728/restart_file/system_builder.py | 1 + .../wca/mcccs/n1728-nvt/clear_folder.py | 1 + .../wca/mcccs/n1728-nvt/find_job.py | 1 + .../engine_input/mcccs/fort77maker_onebox.py | 7 +-- .../engine_input/mcccs/fort77maker_twobox.py | 7 +-- .../src/engines/lammps-VU/Tconfig_overall.py | 1 + .../src/engines/lammps-VU/Tconfig_perjob.py | 1 + .../src/engines/lammps-VU/analysis.py | 1 + .../engines/lammps-VU/pressure_analysis.py | 1 + .../src/engines/lammps-VU/project.py | 1 + .../engines/lammps-VU/temperature_analysis.py | 1 + .../n1728-nvt/src/engines/mcccs/analysis.py | 1 + .../src/engines/mcccs/pressure_analysis.py | 1 + .../n1728-nvt/src/engines/mcccs/project.py | 1 + .../src/engines/mcccs/rdf_analysis_overall.py | 1 + .../src/engines/mcccs/rdf_analysis_perjob.py | 1 + .../wca/mcccs/n1728-nvt/subproject-init.py | 43 +++++++++++-------- .../wca/mcccs/n1728-nvt/templates/ndcrc.py | 1 + .../n1728-nvt/templates/ndcrc_scheduler.py | 1 + .../wca/mcccs/n1728/clear_folder.py | 1 + .../wca/mcccs/n1728/find_job.py | 1 + .../engine_input/mcccs/fort77maker_onebox.py | 7 +-- .../engine_input/mcccs/fort77maker_twobox.py | 7 +-- .../src/engines/lammps-VU/Tconfig_overall.py | 1 + .../src/engines/lammps-VU/Tconfig_perjob.py | 1 + .../n1728/src/engines/lammps-VU/analysis.py | 1 + .../engines/lammps-VU/pressure_analysis.py | 1 + .../n1728/src/engines/lammps-VU/project.py | 1 + .../engines/lammps-VU/temperature_analysis.py | 1 + .../mcccs/n1728/src/engines/mcccs/analysis.py | 1 + .../src/engines/mcccs/pressure_analysis.py | 1 + .../mcccs/n1728/src/engines/mcccs/project.py | 1 + .../src/engines/mcccs/rdf_analysis_overall.py | 1 + .../src/engines/mcccs/rdf_analysis_perjob.py | 1 + .../wca/mcccs/n1728/subproject-init.py | 43 +++++++++++-------- .../wca/mcccs/n1728/templates/ndcrc.py | 1 + .../mcccs/n1728/templates/ndcrc_scheduler.py | 1 + setup.py | 1 + 682 files changed, 1926 insertions(+), 995 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 05cd6ba0..85b79101 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,12 +16,12 @@ repos: - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 23.9.1 + rev: 24.2.0 hooks: - id: black args: [--line-length=80, --target-version=py38] - repo: https://github.com/pycqa/isort - rev: 5.12.0 + rev: 5.13.2 hooks: - id: isort name: isort (python) diff --git a/reproducibility_project/aggregate_summary/aggregate_init.py b/reproducibility_project/aggregate_summary/aggregate_init.py index ba0782c1..d189c421 100644 --- a/reproducibility_project/aggregate_summary/aggregate_init.py +++ b/reproducibility_project/aggregate_summary/aggregate_init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -183,28 +184,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), # "mass": np.round( # mass.to_value("amu"), # decimals=3, diff --git a/reproducibility_project/aggregate_summary/analyze_data.py b/reproducibility_project/aggregate_summary/analyze_data.py index e509be95..4e104637 100644 --- a/reproducibility_project/aggregate_summary/analyze_data.py +++ b/reproducibility_project/aggregate_summary/analyze_data.py @@ -1,4 +1,5 @@ """Create summary data based on the aggregate values.""" + import pathlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/aggregate_summary/plotting.py b/reproducibility_project/aggregate_summary/plotting.py index 64310475..79ce6c0b 100644 --- a/reproducibility_project/aggregate_summary/plotting.py +++ b/reproducibility_project/aggregate_summary/plotting.py @@ -1,4 +1,5 @@ """Plotting code for main project.""" + import textwrap import matplotlib.pyplot as plt diff --git a/reproducibility_project/clean_dicts.py b/reproducibility_project/clean_dicts.py index 28185ce2..bbb71627 100644 --- a/reproducibility_project/clean_dicts.py +++ b/reproducibility_project/clean_dicts.py @@ -1,4 +1,5 @@ """Remove job doc entries related to the analysis of the simulation data.""" + import signac diff --git a/reproducibility_project/clean_workspace.py b/reproducibility_project/clean_workspace.py index 730ead17..80aba5e8 100644 --- a/reproducibility_project/clean_workspace.py +++ b/reproducibility_project/clean_workspace.py @@ -1,4 +1,5 @@ """Move and remove obsolete jobs from workspace. Use with care.""" + import json import os import os.path diff --git a/reproducibility_project/clear_folder.py b/reproducibility_project/clear_folder.py index 10d976c9..32f08c72 100644 --- a/reproducibility_project/clear_folder.py +++ b/reproducibility_project/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/delete_empty_folders.py b/reproducibility_project/delete_empty_folders.py index e8e0395c..e44f458c 100644 --- a/reproducibility_project/delete_empty_folders.py +++ b/reproducibility_project/delete_empty_folders.py @@ -1,4 +1,5 @@ """Delete folders in ws which are empty.""" + import os from glob import glob diff --git a/reproducibility_project/find_job.py b/reproducibility_project/find_job.py index 7cb120e9..57cf1e06 100644 --- a/reproducibility_project/find_job.py +++ b/reproducibility_project/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py b/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py index 44688b8c..5e033209 100644 --- a/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py +++ b/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py @@ -1,4 +1,5 @@ """Analysis routines and helper methods.""" + from reproducibility_project.src.analysis.equilibration import * from reproducibility_project.src.analysis.rdf import gsd_rdf from reproducibility_project.src.analysis.sampler import sample_job diff --git a/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py b/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py index b11ade10..7fc7459c 100644 --- a/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py +++ b/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py @@ -1,4 +1,5 @@ """Timeseries and pyMBAR related methods.""" + import pathlib from typing import List diff --git a/reproducibility_project/hoomd4_subproject/src/dashboard.py b/reproducibility_project/hoomd4_subproject/src/dashboard.py index 2260cdd4..1bcdef7e 100644 --- a/reproducibility_project/hoomd4_subproject/src/dashboard.py +++ b/reproducibility_project/hoomd4_subproject/src/dashboard.py @@ -1,4 +1,5 @@ """Dashboard for viewing data associated with jobs in a signac project.""" + from signac_dashboard import Dashboard from signac_dashboard.modules import ( ImageViewer, diff --git a/reproducibility_project/hoomd4_subproject/src/engines/hoomd4/project.py b/reproducibility_project/hoomd4_subproject/src/engines/hoomd4/project.py index 98c834a6..db0868c7 100644 --- a/reproducibility_project/hoomd4_subproject/src/engines/hoomd4/project.py +++ b/reproducibility_project/hoomd4_subproject/src/engines/hoomd4/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import datetime import os import pathlib diff --git a/reproducibility_project/init.py b/reproducibility_project/init.py index 1a98411b..743c2d6b 100644 --- a/reproducibility_project/init.py +++ b/reproducibility_project/init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -187,28 +188,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py b/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py index d1a39e85..38c6b453 100644 --- a/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py +++ b/reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -128,28 +129,34 @@ "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/lrc_shift_subproject/aggregate_summary/analyze_data.py b/reproducibility_project/lrc_shift_subproject/aggregate_summary/analyze_data.py index e509be95..4e104637 100644 --- a/reproducibility_project/lrc_shift_subproject/aggregate_summary/analyze_data.py +++ b/reproducibility_project/lrc_shift_subproject/aggregate_summary/analyze_data.py @@ -1,4 +1,5 @@ """Create summary data based on the aggregate values.""" + import pathlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/lrc_shift_subproject/clean_dicts.py b/reproducibility_project/lrc_shift_subproject/clean_dicts.py index 28185ce2..bbb71627 100644 --- a/reproducibility_project/lrc_shift_subproject/clean_dicts.py +++ b/reproducibility_project/lrc_shift_subproject/clean_dicts.py @@ -1,4 +1,5 @@ """Remove job doc entries related to the analysis of the simulation data.""" + import signac diff --git a/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_onebox.py index b98ba8f4..1e53784d 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/cassandra/project.py b/reproducibility_project/lrc_shift_subproject/src/engines/cassandra/project.py index eaa58154..3d294882 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/cassandra/project.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/cassandra/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + # import foyer import os from pathlib import Path diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/gromacs/project.py b/reproducibility_project/lrc_shift_subproject/src/engines/gromacs/project.py index ec208e4d..a47cb1f1 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/gromacs/project.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/gromacs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/hoomd/project_rahman.py b/reproducibility_project/lrc_shift_subproject/src/engines/hoomd/project_rahman.py index 2db8cc0d..4240a2bf 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/hoomd/project_rahman.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/hoomd/project_rahman.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import datetime import os import pathlib diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/lammps-VU/project.py b/reproducibility_project/lrc_shift_subproject/src/engines/lammps-VU/project.py index 14bf04d9..b6cba0f7 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/lammps-VU/project.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/analysis.py b/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/analysis.py index 58366297..d88d22a0 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/analysis.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/project.py b/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/project.py index 23383575..282127aa 100644 --- a/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/project.py +++ b/reproducibility_project/lrc_shift_subproject/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/lrc_shift_subproject/subproject-analysis.py b/reproducibility_project/lrc_shift_subproject/subproject-analysis.py index 23eb2b08..e245b0de 100644 --- a/reproducibility_project/lrc_shift_subproject/subproject-analysis.py +++ b/reproducibility_project/lrc_shift_subproject/subproject-analysis.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import pathlib from copy import copy from typing import List diff --git a/reproducibility_project/lrc_shift_subproject/subproject-init.py b/reproducibility_project/lrc_shift_subproject/subproject-init.py index 806acbec..91ba86f0 100644 --- a/reproducibility_project/lrc_shift_subproject/subproject-init.py +++ b/reproducibility_project/lrc_shift_subproject/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -132,28 +133,34 @@ "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/lrc_shift_subproject/templates/ndcrc.py b/reproducibility_project/lrc_shift_subproject/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/lrc_shift_subproject/templates/ndcrc.py +++ b/reproducibility_project/lrc_shift_subproject/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/lrc_shift_subproject/templates/ndcrc_scheduler.py b/reproducibility_project/lrc_shift_subproject/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/lrc_shift_subproject/templates/ndcrc_scheduler.py +++ b/reproducibility_project/lrc_shift_subproject/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/aggregate_init.py b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/aggregate_init.py index e02230d4..5847a9a2 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/aggregate_init.py +++ b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/aggregate_init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -121,28 +122,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/analyze_data.py b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/analyze_data.py index e509be95..4e104637 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/analyze_data.py +++ b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/analyze_data.py @@ -1,4 +1,5 @@ """Create summary data based on the aggregate values.""" + import pathlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/plotting.py b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/plotting.py index d42fff6c..06339ffd 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/plotting.py +++ b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/plotting.py @@ -1,4 +1,5 @@ """Plotting code for ethanol subproject.""" + import glob import itertools import textwrap diff --git a/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py b/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py index 7db55fd1..461e8d95 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py +++ b/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/Density_Analysis.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/Density_Analysis.py index 138f1ce4..2adad6b7 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/Density_Analysis.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/Density_Analysis.py @@ -1,4 +1,5 @@ """Quick Analysis to output average densities locally for LAMMPS-VU.""" + import math import sys diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/analysis.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/analysis.py index 5189aa46..0e053f08 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall.py index 6b249f1a..25137f7f 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall_old.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall_old.py index 129b3bc8..7c056e4a 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall_old.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bl_analysis_overall_old.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bond_length_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bond_length_analysis_perjob.py index 940eaf96..aa698d1c 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bond_length_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/bond_length_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running LAMMPS-VU simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_overall.py index 279e7774..605ad3db 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_perjob.py index 0cb99282..44df6ba6 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running LAMMPS-VU simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_elliptical.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_elliptical.py index cdd44352..8622aa78 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_elliptical.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_elliptical.py @@ -1,4 +1,5 @@ """Base code to find hbonding in trajectory files.""" + import math import os @@ -81,9 +82,7 @@ def ellipticalFun(dist, degangle): Boolean Returns True if the point lies in the elliptical region. Otherwise False. """ - if ( - ((dist - 0.275) / 0.05) ** 2 + (1 / 50**2) * (degangle - 180) ** 2 - ) < 1: + if (((dist - 0.275) / 0.05) ** 2 + (1 / 50**2) * (degangle - 180) ** 2) < 1: return True else: diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/project.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/project.py index adbeb633..9e752ddc 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/project.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_overall.py index 174b84e7..f766198b 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_perjob.py index 7fd04f1f..7e3793a7 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running LAMMPS-VU simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/analysis.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/analysis.py index 0a1ac6c3..ca800c13 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/analysis.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bl_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bl_analysis_overall.py index 6b249f1a..25137f7f 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bl_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bl_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bond_length_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bond_length_analysis_perjob.py index eda6ba34..72d93a16 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bond_length_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/bond_length_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/comp_hist.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/comp_hist.py index b361489a..7406ee76 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/comp_hist.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/comp_hist.py @@ -1,4 +1,5 @@ """Compare O-H bond-length distribution between LAMMPS, MCCCS-MN-flex, and MCCCS-MN.""" + import matplotlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_overall.py index e0f7dd68..c7acf7be 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_perjob.py index 438b3a1b..f275e684 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_elliptical.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_elliptical.py index a169b0ea..7246c8d8 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_elliptical.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_elliptical.py @@ -1,4 +1,5 @@ """Base code to find hbonding in trajectory files.""" + import math import os @@ -81,9 +82,7 @@ def ellipticalFun(dist, degangle): Boolean Returns True if the point lies in the elliptical region. Otherwise False. """ - if ( - ((dist - 0.275) / 0.05) ** 2 + (1 / 50**2) * (degangle - 180) ** 2 - ) < 1: + if (((dist - 0.275) / 0.05) ** 2 + (1 / 50**2) * (degangle - 180) ** 2) < 1: return True else: diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py index 02dafa1b..8eec0f70 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_overall.py index e458d93f..999aafc8 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_perjob.py index e371a954..8ed6defc 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_comparison.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_comparison.py index 38d1b2c6..2af1285f 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_comparison.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/rdf_comparison.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/mdmc_ethanol_subproject/subproject-analysis.py b/reproducibility_project/mdmc_ethanol_subproject/subproject-analysis.py index 23eb2b08..e245b0de 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/subproject-analysis.py +++ b/reproducibility_project/mdmc_ethanol_subproject/subproject-analysis.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import pathlib from copy import copy from typing import List diff --git a/reproducibility_project/mdmc_ethanol_subproject/subproject-init.py b/reproducibility_project/mdmc_ethanol_subproject/subproject-init.py index 1b61d555..4653b310 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/subproject-init.py +++ b/reproducibility_project/mdmc_ethanol_subproject/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -125,28 +126,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc.py b/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc.py +++ b/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc_scheduler.py b/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc_scheduler.py +++ b/reproducibility_project/mdmc_ethanol_subproject/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/final_data_rcut/plot_methanercut.py b/reproducibility_project/methane_systemsize/final_data_rcut/plot_methanercut.py index 7e063789..6adfc7e5 100644 --- a/reproducibility_project/methane_systemsize/final_data_rcut/plot_methanercut.py +++ b/reproducibility_project/methane_systemsize/final_data_rcut/plot_methanercut.py @@ -1,4 +1,5 @@ """Plot methane systemsize density.""" + import matplotlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize.py b/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize.py index 94858677..4ffec460 100644 --- a/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize.py +++ b/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize.py @@ -1,4 +1,5 @@ """Plot methane systemsize density.""" + import matplotlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize_N3.py b/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize_N3.py index fe977b1a..ae347987 100644 --- a/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize_N3.py +++ b/reproducibility_project/methane_systemsize/final_data_systemsize/plot_methanesystemsize_N3.py @@ -1,4 +1,5 @@ """Plot methane systemsize density.""" + import matplotlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/clear_folder.py b/reproducibility_project/methane_systemsize/lammps_small_dt/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/clear_folder.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/find_job.py b/reproducibility_project/methane_systemsize/lammps_small_dt/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/find_job.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/analysis.py index cc5a1708..4cfe27d3 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/project.py index 5f0c81b7..f011c114 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/subproject-init.py b/reproducibility_project/methane_systemsize/lammps_small_dt/subproject-init.py index 003ea66d..78507d75 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/subproject-init.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -131,28 +132,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc.py b/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/lammps_small_dt/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/aggregate_init.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/aggregate_init.py index ef5a3a98..5030f909 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/aggregate_init.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/aggregate_init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -122,28 +123,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), # "mass": np.round( # mass.to_value("amu"), # decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/analyze_data.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/analyze_data.py index e509be95..4e104637 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/analyze_data.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/analyze_data.py @@ -1,4 +1,5 @@ """Create summary data based on the aggregate values.""" + import pathlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/plotting.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/plotting.py index bc3ac125..80712b31 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/plotting.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/aggregate_summary/plotting.py @@ -1,4 +1,5 @@ """Plotting code for methane system size subproject.""" + import textwrap import matplotlib.pyplot as plt diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/clear_folder.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/clear_folder.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/find_job.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/find_job.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-analysis.py index 0c25fd5b..e990a370 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-analysis.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import pathlib from copy import copy from typing import List diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-init.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-init.py index 22979e2d..4af6fec0 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -132,28 +133,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MN/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/clear_folder.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/clear_folder.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/find_job.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/find_job.py index 8e2635d2..26e888d7 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/find_job.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/project.py index 542c4a0d..bce30791 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/pressure_analysis.py index 392f9f0e..8274ad03 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/project.py index 5602c024..2e15a776 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/subproject-init.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/subproject-init.py index 22979e2d..4af6fec0 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -132,28 +133,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_systemsize_subproject_MCCCS-MNmod/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/subproject-init.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/subproject-init.py index b38e164f..206b1f8e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/subproject-init.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/subproject-init.py index 1a896a0d..8af80e96 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N3600/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/subproject-init.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/subproject-init.py index 600f03bc..d694f839 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N450/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/subproject-init.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/subproject-init.py index 2f46b85c..98434138 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N600/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/subproject-init.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/subproject-init.py index d7e3bb68..21c6b3e9 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/subproject-init.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/methane_updatedT/N900/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/subproject-init.py index 1aa031fe..b44c2a9f 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/10/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/subproject-init.py index 3cad1f8b..358f365c 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/14/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/subproject-init.py index 00dda687..3024573c 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_notailc/18/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/subproject-init.py index 2aca5ce7..4842694d 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10.7_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/subproject-init.py index 6aee29f1..09fd5040 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/subproject-init.py index 6aee29f1..09fd5040 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/10_900/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/subproject-init.py index 8c83c873..22967bf2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/11.4_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/subproject-init.py index 4efdc74a..97be25b6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/12.5_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/subproject-init.py index 84bf5350..28a2fb05 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/13.2_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/subproject-init.py index 68cb4ea5..2b40c628 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14.3_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/subproject-init.py index fff25604..b77ddf93 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/subproject-init.py index fff25604..b77ddf93 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/14_900/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/subproject-init.py index 2acfb7cb..7779f1cc 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/15.1_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/subproject-init.py index da7d3688..9fe4f897 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.0_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/subproject-init.py index 781c6516..5efcb66f 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/16.9_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/subproject-init.py index 3ab1e574..9830ac37 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.0_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_perjob.py index 9c2d4538..91977175 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/subproject-init.py index 781c6516..5efcb66f 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/17.9_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/subproject-init.py index 0741bf16..2e8de108 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_overall.py index d04d8d50..cbd862ff 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_perjob.py index ef9502ab..abf4274b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/subproject-init.py index 8e82dbfc..3279eb47 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/subproject-init.py index 0741bf16..2e8de108 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/18_900/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/subproject-init.py index 5fcc61e8..ad14715c 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/clear_folder.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/clear_folder.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/find_job.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/find_job.py index 408bd130..a3d204a1 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/find_job.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_overall.py index b729c140..5cb8f00b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_perjob.py index 1d04a83b..de414f5b 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/analysis.py index 952c61c6..89231734 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/project.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/project.py index 0849fba3..ea6d217a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/project.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_overall.py index daec3581..053407af 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_perjob.py index e4aef4ad..48cf2c86 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/subproject-init.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/subproject-init.py index 5fcc61e8..ad14715c 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/subproject-init.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -127,28 +128,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc_scheduler.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc_scheduler.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/24_1800/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/methane_systemsize/rcut_test_tailc/lj_percentage.py b/reproducibility_project/methane_systemsize/rcut_test_tailc/lj_percentage.py index a380525e..bed1b8c9 100644 --- a/reproducibility_project/methane_systemsize/rcut_test_tailc/lj_percentage.py +++ b/reproducibility_project/methane_systemsize/rcut_test_tailc/lj_percentage.py @@ -1,4 +1,5 @@ """Script to calculate LJ potential/epsilon at various rcuts.""" + import matplotlib.pyplot as plt import numpy as np diff --git a/reproducibility_project/project-analysis.py b/reproducibility_project/project-analysis.py index 23eb2b08..e245b0de 100644 --- a/reproducibility_project/project-analysis.py +++ b/reproducibility_project/project-analysis.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import pathlib from copy import copy from typing import List diff --git a/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_onebox.py index b98ba8f4..1e53784d 100644 --- a/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/spe_subproject/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_onebox.py b/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_onebox.py index b98ba8f4..1e53784d 100644 --- a/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_onebox.py +++ b/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_twobox.py b/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_twobox.py +++ b/reproducibility_project/spe_subproject/src/engine_input/mcccs_lammps_foyer/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/spe_subproject/src/engines/cassandra/example-project.py b/reproducibility_project/spe_subproject/src/engines/cassandra/example-project.py index 5427069b..8e205ee8 100644 --- a/reproducibility_project/spe_subproject/src/engines/cassandra/example-project.py +++ b/reproducibility_project/spe_subproject/src/engines/cassandra/example-project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/cassandra/project.py b/reproducibility_project/spe_subproject/src/engines/cassandra/project.py index 05d84e51..6d4e93d7 100644 --- a/reproducibility_project/spe_subproject/src/engines/cassandra/project.py +++ b/reproducibility_project/spe_subproject/src/engines/cassandra/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/gomc/project.py b/reproducibility_project/spe_subproject/src/engines/gomc/project.py index e97cb216..c61a55b7 100644 --- a/reproducibility_project/spe_subproject/src/engines/gomc/project.py +++ b/reproducibility_project/spe_subproject/src/engines/gomc/project.py @@ -1,4 +1,5 @@ """GOMC's single point energy analysis setup for signac, signac-flow, signac-dashboard for this study.""" + # project.py import os diff --git a/reproducibility_project/spe_subproject/src/engines/gromacs/project.py b/reproducibility_project/spe_subproject/src/engines/gromacs/project.py index d12887a3..abdd89db 100644 --- a/reproducibility_project/spe_subproject/src/engines/gromacs/project.py +++ b/reproducibility_project/spe_subproject/src/engines/gromacs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/spe_subproject/src/engines/hoomd/project.py b/reproducibility_project/spe_subproject/src/engines/hoomd/project.py index 3aaed70c..19ebf9be 100644 --- a/reproducibility_project/spe_subproject/src/engines/hoomd/project.py +++ b/reproducibility_project/spe_subproject/src/engines/hoomd/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/spe_subproject/src/engines/hoomd/project_rahman.py b/reproducibility_project/spe_subproject/src/engines/hoomd/project_rahman.py index f4b06266..e0211b34 100644 --- a/reproducibility_project/spe_subproject/src/engines/hoomd/project_rahman.py +++ b/reproducibility_project/spe_subproject/src/engines/hoomd/project_rahman.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py b/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py index 5427069b..8e205ee8 100644 --- a/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py +++ b/reproducibility_project/spe_subproject/src/engines/lammps-UD/example-project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-UD/main_project.py b/reproducibility_project/spe_subproject/src/engines/lammps-UD/main_project.py index 10e734b8..2dfa6ce5 100644 --- a/reproducibility_project/spe_subproject/src/engines/lammps-UD/main_project.py +++ b/reproducibility_project/spe_subproject/src/engines/lammps-UD/main_project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-UD/project.py b/reproducibility_project/spe_subproject/src/engines/lammps-UD/project.py index 7696c066..d14d1bb5 100644 --- a/reproducibility_project/spe_subproject/src/engines/lammps-UD/project.py +++ b/reproducibility_project/spe_subproject/src/engines/lammps-UD/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/lammps-VU/project.py b/reproducibility_project/spe_subproject/src/engines/lammps-VU/project.py index 94d1218e..1126a8c2 100644 --- a/reproducibility_project/spe_subproject/src/engines/lammps-VU/project.py +++ b/reproducibility_project/spe_subproject/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs/analysis.py b/reproducibility_project/spe_subproject/src/engines/mcccs/analysis.py index 8b6a0f2c..65f1a2a1 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs/analysis.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs/example-project.py b/reproducibility_project/spe_subproject/src/engines/mcccs/example-project.py index 5427069b..8e205ee8 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs/example-project.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs/example-project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs/project.py b/reproducibility_project/spe_subproject/src/engines/mcccs/project.py index a14f1d92..e016a39f 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs/project.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/analysis.py b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/analysis.py index 155cbdc0..9e40c66e 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/analysis.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/example-project.py b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/example-project.py index 5427069b..8e205ee8 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/example-project.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/example-project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib diff --git a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/project.py b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/project.py index d6bbb3f3..6bc91580 100644 --- a/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/project.py +++ b/reproducibility_project/spe_subproject/src/engines/mcccs_lammps_foyer/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/spe_subproject/src/system_snapshots/create_snapshots.py b/reproducibility_project/spe_subproject/src/system_snapshots/create_snapshots.py index 5e123f9c..30751c5c 100644 --- a/reproducibility_project/spe_subproject/src/system_snapshots/create_snapshots.py +++ b/reproducibility_project/spe_subproject/src/system_snapshots/create_snapshots.py @@ -2,6 +2,7 @@ Create and return only liquid boxes for all systems """ + import numpy as np import unyt as u diff --git a/reproducibility_project/spe_subproject/subproject-init.py b/reproducibility_project/spe_subproject/subproject-init.py index 5be69d56..2c0386ee 100644 --- a/reproducibility_project/spe_subproject/subproject-init.py +++ b/reproducibility_project/spe_subproject/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -171,28 +172,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/spe_subproject/summarize.py b/reproducibility_project/spe_subproject/summarize.py index 7507ede5..10ff319a 100644 --- a/reproducibility_project/spe_subproject/summarize.py +++ b/reproducibility_project/spe_subproject/summarize.py @@ -1,4 +1,5 @@ """Summarize spe data and save as csv files.""" + import os import numpy as np diff --git a/reproducibility_project/spe_subproject/templates/ndcrc.py b/reproducibility_project/spe_subproject/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/spe_subproject/templates/ndcrc.py +++ b/reproducibility_project/spe_subproject/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/spe_subproject/templates/ndcrc_scheduler.py b/reproducibility_project/spe_subproject/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/spe_subproject/templates/ndcrc_scheduler.py +++ b/reproducibility_project/spe_subproject/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/src/analysis/Comparison_Figures/generate_comparison_plots.py b/reproducibility_project/src/analysis/Comparison_Figures/generate_comparison_plots.py index c5384065..dde69788 100644 --- a/reproducibility_project/src/analysis/Comparison_Figures/generate_comparison_plots.py +++ b/reproducibility_project/src/analysis/Comparison_Figures/generate_comparison_plots.py @@ -1,4 +1,5 @@ """Functionality to generate figure plots to compare MoSDeF to RR relative errors.""" + import warnings warnings.filterwarnings("ignore") @@ -168,9 +169,11 @@ def _transform_ff_names(df): ) df["ff-mol"] = df[["molecule", "forcefield"]].agg("-".join, axis=1) df["ff-mol"] = df["ff-mol"].transform( - lambda x: re.sub("([a-zA-Z])", lambda y: y.groups()[0].upper(), x, 1) - if "Butane" not in x - else x + lambda x: ( + re.sub("([a-zA-Z])", lambda y: y.groups()[0].upper(), x, 1) + if "Butane" not in x + else x + ) ) diff --git a/reproducibility_project/src/analysis/Comparison_Figures/generate_densities.py b/reproducibility_project/src/analysis/Comparison_Figures/generate_densities.py index 5d0ce339..31e63dc9 100644 --- a/reproducibility_project/src/analysis/Comparison_Figures/generate_densities.py +++ b/reproducibility_project/src/analysis/Comparison_Figures/generate_densities.py @@ -1,4 +1,5 @@ """Generate CSV from job docs for job densities.""" + import os import camelot diff --git a/reproducibility_project/src/analysis/Comparison_Figures/plotting.py b/reproducibility_project/src/analysis/Comparison_Figures/plotting.py index aebe5061..406ce43c 100644 --- a/reproducibility_project/src/analysis/Comparison_Figures/plotting.py +++ b/reproducibility_project/src/analysis/Comparison_Figures/plotting.py @@ -1,4 +1,5 @@ """Utility methods for plotting data.""" + import pathlib import textwrap diff --git a/reproducibility_project/src/analysis/__init__.py b/reproducibility_project/src/analysis/__init__.py index 44688b8c..5e033209 100644 --- a/reproducibility_project/src/analysis/__init__.py +++ b/reproducibility_project/src/analysis/__init__.py @@ -1,4 +1,5 @@ """Analysis routines and helper methods.""" + from reproducibility_project.src.analysis.equilibration import * from reproducibility_project.src.analysis.rdf import gsd_rdf from reproducibility_project.src.analysis.sampler import sample_job diff --git a/reproducibility_project/src/analysis/equilibration.py b/reproducibility_project/src/analysis/equilibration.py index 5be3241b..cb993795 100644 --- a/reproducibility_project/src/analysis/equilibration.py +++ b/reproducibility_project/src/analysis/equilibration.py @@ -1,4 +1,5 @@ """Timeseries and pyMBAR related methods.""" + import pathlib from typing import List diff --git a/reproducibility_project/src/dashboard.py b/reproducibility_project/src/dashboard.py index 2260cdd4..1bcdef7e 100644 --- a/reproducibility_project/src/dashboard.py +++ b/reproducibility_project/src/dashboard.py @@ -1,4 +1,5 @@ """Dashboard for viewing data associated with jobs in a signac project.""" + from signac_dashboard import Dashboard from signac_dashboard.modules import ( ImageViewer, diff --git a/reproducibility_project/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/src/engine_input/mcccs/fort77maker_onebox.py index 8e9f1df5..4f9dcc5f 100644 --- a/reproducibility_project/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/src/engine_input/mcccs/fort77maker_twobox.py index 525bd253..f241b6d5 100644 --- a/reproducibility_project/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/src/engines/cassandra/project.py b/reproducibility_project/src/engines/cassandra/project.py index 1003b3ad..7005f06c 100644 --- a/reproducibility_project/src/engines/cassandra/project.py +++ b/reproducibility_project/src/engines/cassandra/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + # import foyer import os from pathlib import Path diff --git a/reproducibility_project/src/engines/gomc/project.py b/reproducibility_project/src/engines/gomc/project.py index 8ebcff8f..ebe63b10 100644 --- a/reproducibility_project/src/engines/gomc/project.py +++ b/reproducibility_project/src/engines/gomc/project.py @@ -1,4 +1,5 @@ """GOMC's setup for signac, signac-flow, signac-dashboard for this study.""" + # project.py import os @@ -2753,15 +2754,15 @@ def part_5b_avg_std_dev_of_replicates_analysis(*jobs): setMeanZ2[replicateAverageName2[i]] = ( setMeanZ2[replicateAverageName2[i]] + replicateAverageZ2[i] ) - setMeanTemperature2[ - replicateAverageName2[i] - ] = replicateAverageT2[i] - setMeanMolecule2[ - replicateAverageName2[i] - ] = replicateAverageMolecule2[i] - setMeanOptions2[ - replicateAverageName2[i] - ] = replicateAverageOptions2[i] + setMeanTemperature2[replicateAverageName2[i]] = ( + replicateAverageT2[i] + ) + setMeanMolecule2[replicateAverageName2[i]] = ( + replicateAverageMolecule2[i] + ) + setMeanOptions2[replicateAverageName2[i]] = ( + replicateAverageOptions2[i] + ) for i in np.unique(replicateAverageName): setMeanEnergy[i] /= replicaCount diff --git a/reproducibility_project/src/engines/hoomd/project.py b/reproducibility_project/src/engines/hoomd/project.py index aaf9758b..56b860a0 100644 --- a/reproducibility_project/src/engines/hoomd/project.py +++ b/reproducibility_project/src/engines/hoomd/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import datetime import os import pathlib diff --git a/reproducibility_project/src/engines/hoomd/project_rahman.py b/reproducibility_project/src/engines/hoomd/project_rahman.py index 8cf84108..5c029cf4 100644 --- a/reproducibility_project/src/engines/hoomd/project_rahman.py +++ b/reproducibility_project/src/engines/hoomd/project_rahman.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import datetime import os import pathlib diff --git a/reproducibility_project/src/engines/lammps-UD/project.py b/reproducibility_project/src/engines/lammps-UD/project.py index 1df4a3d4..b34aca43 100644 --- a/reproducibility_project/src/engines/lammps-UD/project.py +++ b/reproducibility_project/src/engines/lammps-UD/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + # import foyer import os import pathlib diff --git a/reproducibility_project/src/engines/lammps-VU/project.py b/reproducibility_project/src/engines/lammps-VU/project.py index aaf2f8ce..f59a32e0 100644 --- a/reproducibility_project/src/engines/lammps-VU/project.py +++ b/reproducibility_project/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/src/engines/mcccs/analysis.py b/reproducibility_project/src/engines/mcccs/analysis.py index d858c220..a8e6b519 100644 --- a/reproducibility_project/src/engines/mcccs/analysis.py +++ b/reproducibility_project/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/src/engines/mcccs/conv_traj.py b/reproducibility_project/src/engines/mcccs/conv_traj.py index cbf821c3..c28d5167 100644 --- a/reproducibility_project/src/engines/mcccs/conv_traj.py +++ b/reproducibility_project/src/engines/mcccs/conv_traj.py @@ -1,4 +1,5 @@ """Reads the .xyz files for different seeds in NPT MC simulations, and combines and saves them in the gsd format.""" + import os import shutil from glob import glob diff --git a/reproducibility_project/src/engines/mcccs/plot_water.py b/reproducibility_project/src/engines/mcccs/plot_water.py index 731926b6..a4655003 100644 --- a/reproducibility_project/src/engines/mcccs/plot_water.py +++ b/reproducibility_project/src/engines/mcccs/plot_water.py @@ -1,4 +1,5 @@ """Plotting water results to debig why caluclated pressure is different from set pressure.""" + import os import matplotlib.pyplot as plt diff --git a/reproducibility_project/src/engines/mcccs/project.py b/reproducibility_project/src/engines/mcccs/project.py index aed315d1..009cd3fe 100644 --- a/reproducibility_project/src/engines/mcccs/project.py +++ b/reproducibility_project/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/src/molecules/ethanol_aa.py b/reproducibility_project/src/molecules/ethanol_aa.py index 02e89a2c..6f766056 100644 --- a/reproducibility_project/src/molecules/ethanol_aa.py +++ b/reproducibility_project/src/molecules/ethanol_aa.py @@ -1,4 +1,5 @@ """Create atomistic representation of ethanol.""" + import os import mbuild as mb diff --git a/reproducibility_project/src/molecules/system_builder.py b/reproducibility_project/src/molecules/system_builder.py index fc102590..d9df5f56 100644 --- a/reproducibility_project/src/molecules/system_builder.py +++ b/reproducibility_project/src/molecules/system_builder.py @@ -1,4 +1,5 @@ """Methods used to create systems from job statepoint.""" + import mbuild as mb from mbuild.lib.molecules.water import WaterSPC diff --git a/reproducibility_project/src/utils/convert_spce_params.py b/reproducibility_project/src/utils/convert_spce_params.py index 81e16600..fc3ab366 100644 --- a/reproducibility_project/src/utils/convert_spce_params.py +++ b/reproducibility_project/src/utils/convert_spce_params.py @@ -1,4 +1,5 @@ """Convert water-SPC/E parameters from the original paper to epsilon and sigma.""" + # U = -(A/r)^6+(B/r)^12 # that makes # sigma = B^2/A and epsilon = (1/4)*(A/B)^12 diff --git a/reproducibility_project/src/utils/forcefields.py b/reproducibility_project/src/utils/forcefields.py index 77ed4bc4..b0f173b3 100644 --- a/reproducibility_project/src/utils/forcefields.py +++ b/reproducibility_project/src/utils/forcefields.py @@ -1,4 +1,5 @@ """Utilities to load forcefields based on forcefield names.""" + import os import foyer diff --git a/reproducibility_project/src/utils/plotting.py b/reproducibility_project/src/utils/plotting.py index aebe5061..406ce43c 100644 --- a/reproducibility_project/src/utils/plotting.py +++ b/reproducibility_project/src/utils/plotting.py @@ -1,4 +1,5 @@ """Utility methods for plotting data.""" + import pathlib import textwrap diff --git a/reproducibility_project/src/utils/trajectory_conversion.py b/reproducibility_project/src/utils/trajectory_conversion.py index b4044ff1..c4d484fa 100644 --- a/reproducibility_project/src/utils/trajectory_conversion.py +++ b/reproducibility_project/src/utils/trajectory_conversion.py @@ -1,4 +1,5 @@ """Convert trajectory files to gsd format.""" + import io from pathlib import Path diff --git a/reproducibility_project/templates/ndcrc.py b/reproducibility_project/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/templates/ndcrc.py +++ b/reproducibility_project/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/templates/ndcrc_scheduler.py b/reproducibility_project/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/templates/ndcrc_scheduler.py +++ b/reproducibility_project/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/tests/test_utils_forcefields.py b/reproducibility_project/tests/test_utils_forcefields.py index f1ea46b1..867661a0 100644 --- a/reproducibility_project/tests/test_utils_forcefields.py +++ b/reproducibility_project/tests/test_utils_forcefields.py @@ -1,4 +1,5 @@ """Test file to ensure that forcefield loading is behaving as expected.""" + import pytest from foyer import Forcefield diff --git a/reproducibility_project/waterspce_nist_subproject/aggregate_summary/aggregate_init.py b/reproducibility_project/waterspce_nist_subproject/aggregate_summary/aggregate_init.py index c1af52b4..a3957584 100644 --- a/reproducibility_project/waterspce_nist_subproject/aggregate_summary/aggregate_init.py +++ b/reproducibility_project/waterspce_nist_subproject/aggregate_summary/aggregate_init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -129,28 +130,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/waterspce_nist_subproject/aggregate_summary/analyze_data.py b/reproducibility_project/waterspce_nist_subproject/aggregate_summary/analyze_data.py index e509be95..4e104637 100644 --- a/reproducibility_project/waterspce_nist_subproject/aggregate_summary/analyze_data.py +++ b/reproducibility_project/waterspce_nist_subproject/aggregate_summary/analyze_data.py @@ -1,4 +1,5 @@ """Create summary data based on the aggregate values.""" + import pathlib import matplotlib.pyplot as plt diff --git a/reproducibility_project/waterspce_nist_subproject/src/engines/lammps-VU/project.py b/reproducibility_project/waterspce_nist_subproject/src/engines/lammps-VU/project.py index b72a35dd..59f64ac8 100644 --- a/reproducibility_project/waterspce_nist_subproject/src/engines/lammps-VU/project.py +++ b/reproducibility_project/waterspce_nist_subproject/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + # python project.py submit -o lammps_em_nvt -n 72 --bundle 3 import os import pathlib diff --git a/reproducibility_project/waterspce_nist_subproject/subproject-analysis.py b/reproducibility_project/waterspce_nist_subproject/subproject-analysis.py index 5565f22b..d7fa64b2 100644 --- a/reproducibility_project/waterspce_nist_subproject/subproject-analysis.py +++ b/reproducibility_project/waterspce_nist_subproject/subproject-analysis.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import pathlib from copy import copy from typing import List diff --git a/reproducibility_project/waterspce_nist_subproject/subproject-init.py b/reproducibility_project/waterspce_nist_subproject/subproject-init.py index dd64dd57..640b031c 100644 --- a/reproducibility_project/waterspce_nist_subproject/subproject-init.py +++ b/reproducibility_project/waterspce_nist_subproject/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -133,28 +134,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/waterspce_nist_subproject/templates/ndcrc.py b/reproducibility_project/waterspce_nist_subproject/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/waterspce_nist_subproject/templates/ndcrc.py +++ b/reproducibility_project/waterspce_nist_subproject/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/waterspce_nist_subproject/templates/ndcrc_scheduler.py b/reproducibility_project/waterspce_nist_subproject/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/waterspce_nist_subproject/templates/ndcrc_scheduler.py +++ b/reproducibility_project/waterspce_nist_subproject/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/fort77maker_onebox.py b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/fort77maker_onebox.py index 059715b0..ea7770e1 100644 --- a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/fort77maker_onebox.py +++ b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -97,9 +98,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/makerestart77.py b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/makerestart77.py index ab6e4197..18d13b58 100644 --- a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/makerestart77.py +++ b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/makerestart77.py @@ -1,4 +1,5 @@ """Make MCCCS-MN restart file for calculating pressure.""" + import mbuild as mb from fort77maker_onebox import fort77writer from system_builder import get_molecule diff --git a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/system_builder.py b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/system_builder.py index fad61640..cca39f1e 100644 --- a/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/system_builder.py +++ b/reproducibility_project/wca/mcccs/makerest_prescheck/007-1728/restart_file/system_builder.py @@ -1,4 +1,5 @@ """Methods used to create systems from job statepoint.""" + import mbuild as mb from mbuild.lib.molecules.water import WaterSPC diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/clear_folder.py b/reproducibility_project/wca/mcccs/n1728-nvt/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/clear_folder.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/find_job.py b/reproducibility_project/wca/mcccs/n1728-nvt/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/find_job.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/analysis.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/project.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/project.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/analysis.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/analysis.py index 6f574824..7be7ed2c 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/analysis.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/pressure_analysis.py index 0c57e26c..9b19a15a 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/project.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/project.py index 18f98acb..5213f0ae 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/project.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_overall.py index d04d8d50..cbd862ff 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_perjob.py index ef9502ab..abf4274b 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/subproject-init.py b/reproducibility_project/wca/mcccs/n1728-nvt/subproject-init.py index 18cfb1a7..bc14ab3f 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/subproject-init.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=20, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=20, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc.py b/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc_scheduler.py b/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc_scheduler.py +++ b/reproducibility_project/wca/mcccs/n1728-nvt/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/reproducibility_project/wca/mcccs/n1728/clear_folder.py b/reproducibility_project/wca/mcccs/n1728/clear_folder.py index 2dda795d..5eb0563e 100644 --- a/reproducibility_project/wca/mcccs/n1728/clear_folder.py +++ b/reproducibility_project/wca/mcccs/n1728/clear_folder.py @@ -1,4 +1,5 @@ """Script for deleting certain files in a state point folder.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/find_job.py b/reproducibility_project/wca/mcccs/n1728/find_job.py index 20cd2807..90ed41a5 100644 --- a/reproducibility_project/wca/mcccs/n1728/find_job.py +++ b/reproducibility_project/wca/mcccs/n1728/find_job.py @@ -1,4 +1,5 @@ """Script for finding the job ids of specific simulations.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_onebox.py b/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_onebox.py index 5b99548d..fe5fb79e 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_onebox.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_onebox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -94,9 +95,9 @@ def fort77writer( MoleculesBox[1] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NMoleculesBox = {} NMoleculesBox[1] = num_each_moltype # number of molecules diff --git a/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_twobox.py b/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_twobox.py index 0ec93ca2..1e0fca06 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_twobox.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engine_input/mcccs/fort77maker_twobox.py @@ -1,4 +1,5 @@ """Takes an mbuild filled_box and creates a restart file for mcccs simulations.""" + import errno import os import sys @@ -108,9 +109,9 @@ def fort77writer( MoleculesBox[1] = molecule_names MoleculesBox[2] = molecule_names NBeadsBox = {} - NBeadsBox[ - 1 - ] = nbeads_list # list that contains number of beads for each molecule type + NBeadsBox[1] = ( + nbeads_list # list that contains number of beads for each molecule type + ) NBeadsBox[2] = nbeads_list NMoleculesBox = {} diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_overall.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_overall.py index 00458b3a..b1208bfe 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_overall.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_perjob.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_perjob.py index 9088f424..751b3dc6 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_perjob.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/Tconfig_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/analysis.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/analysis.py index c4c3da01..bdce40a2 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/analysis.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/pressure_analysis.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/pressure_analysis.py index b98c4676..7e2530c2 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/pressure_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/project.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/project.py index f89694a6..a7b94de0 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/project.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for this study.""" + import os import pathlib import sys diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/temperature_analysis.py b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/temperature_analysis.py index 4deaa2d4..ab542653 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/temperature_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/lammps-VU/temperature_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/analysis.py b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/analysis.py index ffc8be9f..5b3affec 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/analysis.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/pressure_analysis.py b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/pressure_analysis.py index 0f370dca..42a1c5a2 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/pressure_analysis.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/pressure_analysis.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/project.py b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/project.py index 6e815745..0c735e27 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/project.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/project.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_overall.py b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_overall.py index d04d8d50..cbd862ff 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_overall.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_overall.py @@ -1,4 +1,5 @@ """Script for analysing the results from the 16 different seeds from the 11 systems.""" + # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs.""" import os import shutil diff --git a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_perjob.py b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_perjob.py index ef9502ab..abf4274b 100644 --- a/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_perjob.py +++ b/reproducibility_project/wca/mcccs/n1728/src/engines/mcccs/rdf_analysis_perjob.py @@ -1,4 +1,5 @@ """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study.""" + import fileinput import math import os diff --git a/reproducibility_project/wca/mcccs/n1728/subproject-init.py b/reproducibility_project/wca/mcccs/n1728/subproject-init.py index 77b0f564..335056e1 100644 --- a/reproducibility_project/wca/mcccs/n1728/subproject-init.py +++ b/reproducibility_project/wca/mcccs/n1728/subproject-init.py @@ -1,4 +1,5 @@ """Initialize signac statepoints.""" + import itertools import os @@ -126,28 +127,34 @@ def dict_product(dd): "ensemble": ensemble if ensemble else None, "N_liquid": n_liq, "N_vap": n_vap if n_vap else None, - "box_L_liq": np.round( - liq_box_L.to_value("nm"), - decimals=3, - ).item() - if liq_box_L - else None, - "box_L_vap": np.round( - vap_box_L.to_value("nm"), - decimals=3, - ).item() - if vap_box_L - else None, + "box_L_liq": ( + np.round( + liq_box_L.to_value("nm"), + decimals=3, + ).item() + if liq_box_L + else None + ), + "box_L_vap": ( + np.round( + vap_box_L.to_value("nm"), + decimals=3, + ).item() + if vap_box_L + else None + ), "init_liq_den": np.round( init_liq_den.to_value(g_per_cm3), decimals=3, ).item(), - "init_vap_den": np.round( - init_vap_den.to_value(g_per_cm3), - decimals=3, - ).item() - if init_vap_den - else None, + "init_vap_den": ( + np.round( + init_vap_den.to_value(g_per_cm3), + decimals=3, + ).item() + if init_vap_den + else None + ), "mass": np.round( mass.to_value("amu"), decimals=3, diff --git a/reproducibility_project/wca/mcccs/n1728/templates/ndcrc.py b/reproducibility_project/wca/mcccs/n1728/templates/ndcrc.py index e4bc3a02..3f958bd0 100644 --- a/reproducibility_project/wca/mcccs/n1728/templates/ndcrc.py +++ b/reproducibility_project/wca/mcccs/n1728/templates/ndcrc.py @@ -1,4 +1,5 @@ """Scheduler environment module for NotreDameCRC.""" + import flow from .ndcrc_scheduler import SGEScheduler diff --git a/reproducibility_project/wca/mcccs/n1728/templates/ndcrc_scheduler.py b/reproducibility_project/wca/mcccs/n1728/templates/ndcrc_scheduler.py index f270df79..def5451a 100644 --- a/reproducibility_project/wca/mcccs/n1728/templates/ndcrc_scheduler.py +++ b/reproducibility_project/wca/mcccs/n1728/templates/ndcrc_scheduler.py @@ -2,6 +2,7 @@ This module implements the Scheduler and ClusterJob classes. """ + import errno import getpass import logging diff --git a/setup.py b/setup.py index 8b3d50e9..9285741e 100644 --- a/setup.py +++ b/setup.py @@ -1,4 +1,5 @@ """Shim for pyproject.toml files to have --editable installs.""" + import setuptools if __name__ == "__main__":