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MDEval.jl

Package to evaluate molecular dynamics (MD) simulations.

1. Installation

To register the module locally, type

Pkg> add https://github.com/se-schmitt/MDEval.jl

in package mode (type ] in REPL to enter Pkg mode).

Then, the module can be loaded by

using MDEval

2. Manual

2.1 Function mdeval

mdeval(mode::Symbol, folder::String, keywords::NamedTuple)

Input arguments:

  • mode: defines the mode of the simulations/evaluation. Possible values: :single_run, :tdm, :vle, :nemd_shear, or :nemd_heat (see Section 2.1)
  • folder: path to main folder containing all simulation data (see Section 2.3)
  • keywords: options to define the evaluation parameters (see Section 2.2)

Examples are provided in the examples folder.

2.1 Evaluation Modes

Different simulation types can be evaluated:

  • Evaluation of single run simulations for thermodynamic properties (including transport properties) (:single_run)
  • Time decomposition method (TDM) for transport properties (:tdm)
  • Evaluation of vapou-liquid equilibrium (VLE) simulations (direct two phase simualtions) (:vle)
  • Evaluation of non-equilibrium molecular dynamics (NEMD) shear simulations to determine viscosity (:nemd_shear)
  • Evaluation of NEMD heat transfer simulation to determine thermal conductivity (:nemd_heat)

2.2 Keywords

Name Possible values [default value] Modes Description
ensemble NVT, NVE, NpT :single_run, :tdm, :nemd_shear ensemble to evaluate
timesteps_equ interger ≥ 0 [0] :single_run, :tdm, :vle number of timesteps to ignore at the start of each simulation
do_single true, false [true] :tdm, :nemd_shear evaluate single folders
do_state true, false [true] :tdm, :nemd_shear evaluate complete thermodynamic state (main folder)
n_boot integer ≥ 0 [0] :tdm number of bootstrapping repetitions
cutcrit float ≥ 0 [0.4] :tdm cut criteria for :tdm method
do_transport true, false :single_run evaluation of transport properties
corr_length integer ≥ 0 :single_run length (timesteps) of correlation function
span_corr_fun integer ≥ 0 :single_run timesteps between single correlation functions
n_blocks integer ≥ 0 :single_run number of blocks for static properties
n_every integer ≥ 1 :single_run skip n_every timesteps when calculating acf (useful for slowly converging states, e.g. ideal gas)
debug_mode true, false :single_run if debug mode is enables, errors are thrown directly
acf_calc_mode autocov, fft [autocov/fft] :single_run, :tdm mode for acf calculation (autocov: full acf by Julia autocov command (can be slowly for long signals), fft: acf calculation by FFT (fast, but inaccurate for long times))
do_structure true, false [false] all structure evaluation
n_bin integer ≥ 0 [100] all number of bins for radial pair distribution (RDF) calculation
r_cut float [10.0] all cut-off radius for RDF (unit: Å) calculation
units metal, reduced [real] all units of simulation (real: LAMMPS SI units, reduced: reduced by LJ parameters)
k_L_thermo float [0.1] :nemd_heat reduced length of thermostats (as fraction of total box length)

2.3 Folder structure

  • Single run/ NEMD shear/ NEMD heat simulations
├── SIM_1* [contains all output files of a EMD simulation of one state point]
:
  • TDM
├── STATE_1 [contains all replica simulations of one state point]
│   ├── Sim_001
│   ├── Sim_002
:   :
  • VLE simulations
├── FOLDER_1 [contains all simulations for one substance]
│   ├── Sim_T1 [VLE simulation at temperature T1]
│   ├── Sim_T2 [VLE simulation at temperature T2]
:   :
  • NEMD shear simulations
├── STATE_1 [contains all simulations of one state point]
│   ├── Sim_S1 [VLE simulation with shear rate S1]
│   ├── Sim_S2 [VLE simulation with shear rate S2]
:   :

2.4 Units

Either reduced or real units can be used. The given unit defines the input as well as the output units. reduced units refer to the Lennard-Jones units system. The input units for real units are the LAMMPS metal units. The units of the output are defined in the following table.

Property Symbol Unit
mass m g/mol
time t ps
temperature T K
pressure p MPa
energy E eV
viscosity η Pa*s
self-diffusion coefficient D m²/s
thermal conductivity λ W/(m*K)