Skip to content

Commit

Permalink
Merge pull request #256 from JaGeo/fix_cli_poscar.lobster
Browse files Browse the repository at this point in the history 
Fix cli bug, cleanup and enhancement
  • Loading branch information
@JaGeo
JaGeo committed Mar 12, 2024
2 parents 0d6cb7e + 275168d commit 522ee59
Show file tree
Hide file tree
Showing 6 changed files with 145 additions and 198 deletions.
216 changes: 91 additions & 125 deletions lobsterpy/cli.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import argparse
import json
import os
from math import log, sqrt
from pathlib import Path

Expand All @@ -16,6 +17,7 @@

from lobsterpy.cohp.analyze import Analysis
from lobsterpy.cohp.describe import Description
from lobsterpy.featurize.utils import get_file_paths
from lobsterpy.plotting import (
IcohpDistancePlotter,
PlainCohpPlotter,
Expand Down Expand Up @@ -427,6 +429,15 @@ def get_parser() -> argparse.ArgumentParser:
"with orbital-resolved automatic analysis (--orbitalresolved).",
)

auto_group.add_argument(
"-sspins",
"--summedspins",
"--summed-spins",
action="store_true",
default=False,
help="Sum COHP `Spin.up` and `Spin.down` populations for automatic analysis",
)

# Argument that will help to switch automatic analysis
analysis_switch = argparse.ArgumentParser(add_help=False)
analysis_group = analysis_switch.add_argument_group(
Expand Down Expand Up @@ -738,61 +749,28 @@ def run(args):
"plot-automatic",
"plot-automatic-ia",
]:
# Check for .gz files exist for default values and update accordingly
default_files = {
"structure": "POSCAR",
"charge": "CHARGE.lobster",
"icohplist": "ICOHPLIST.lobster",
"cohpcar": "COHPCAR.lobster",
}

for arg_name in default_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(
"Files necessary for automatic analysis of LOBSTER outputs "
"not found in the current directory"
)
req_files = get_file_paths(
path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure", "charge", "icohplist", "cohpcar"]
)

if args.coops:
default_files_coops = {
"icohplist": "ICOOPLIST.lobster",
"cohpcar": "COOPCAR.lobster",
}
for arg_name, file_name in default_files_coops.items():
setattr(args, arg_name, Path(file_name))
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(
"Files required for automatic analysis of COOPs (ICOOPLIST.lobster and"
" COOPCAR.lobster) not found in the directory"
)
req_files_coops = get_file_paths(
path_to_lobster_calc=Path(os.getcwd()), requested_files=["icooplist", "coopcar"]
)

req_files["icohplist"] = req_files_coops["icooplist"]
req_files["cohpcar"] = req_files_coops["coopcar"]

if args.cobis:
default_files_cobis = {
"icohplist": "ICOBILIST.lobster",
"cohpcar": "COBICAR.lobster",
}
for arg_name, file_name in default_files_cobis.items():
setattr(args, arg_name, Path(file_name))
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(
"Files required for automatic analysis of COBIs (ICOBILIST.lobster and"
" COBICAR.lobster) not found in the directory"
)
req_files_cobis = get_file_paths(
path_to_lobster_calc=Path(os.getcwd()), requested_files=["icobilist", "cobicar"]
)

req_files["icohplist"] = req_files_cobis["icobilist"]
req_files["cohpcar"] = req_files_cobis["cobicar"]

for arg_name in req_files:
setattr(args, arg_name, req_files[arg_name])

if args.action in ["description", "plot-automatic", "plot-automatic-ia"]:
which_bonds = "all" if args.allbonds else "cation-anion"
Expand All @@ -809,6 +787,7 @@ def run(args):
cutoff_icohp=args.cutofficohp,
orbital_cutoff=args.orbitalcutoff,
orbital_resolved=args.orbitalresolved,
summed_spins=args.summedspins,
)

describe = Description(analysis_object=analyse)
Expand Down Expand Up @@ -871,24 +850,24 @@ def run(args):

if args.action == "plot":
if args.cobis:
filename = args.cohpcar.parent / "COBICAR.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["cobicar"]).get(
"cobicar"
)
options = {"are_cobis": True, "are_coops": False}
elif args.coops:
filename = args.cohpcar.parent / "COOPCAR.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["coopcar"]).get(
"coopcar"
)
options = {"are_cobis": False, "are_coops": True}
else:
filename = args.cohpcar.parent / "COHPCAR.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["cohpcar"]).get(
"cohpcar"
)
options = {"are_cobis": False, "are_coops": False}

struture_filename = args.structure.parent / "POSCAR"
if not struture_filename.exists():
struture_filename = struture_filename.with_name(zpath(struture_filename.name))
struture_filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure"]).get(
"structure"
)

completecohp = CompleteCohp.from_file(
fmt="LOBSTER",
Expand Down Expand Up @@ -1051,29 +1030,18 @@ def run(args):

if args.action in ["description-quality"]:
# Check for .gz files exist for default values and update accordingly
mandatory_files = {
"structure": "POSCAR",
"lobsterin": "lobsterin",
"lobsterout": "lobsterout",
}

for arg_name in mandatory_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(
"Mandatory files necessary for LOBSTER calc quality not found in the current directory."
)
req_files = get_file_paths(
path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure", "lobsterin", "lobsterout"]
)
for arg_name in req_files:
setattr(args, arg_name, req_files[arg_name])

optional_file = {
optional_files = {
"bandoverlaps": "bandOverlaps.lobster",
"potcar": "POTCAR",
}

for arg_name in optional_file:
for arg_name in optional_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
Expand All @@ -1083,34 +1051,26 @@ def run(args):
bva_comp = args.bvacomp

if bva_comp:
bva_files = {
"charge": "CHARGE.lobster",
}
bva_files = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["charge"])
for arg_name in bva_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError("BVA charge requested but CHARGE.lobster file not found.")
setattr(args, arg_name, bva_files[arg_name])

dos_comparison = args.doscomp

if dos_comparison:
dos_files = {
"doscar": "DOSCAR.lobster",
"vasprun": "vasprun.xml",
}

dos_files = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["doscar", "vasprun"])
for arg_name in dos_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError("DOS comparisons requested but DOSCAR.lobster, vasprun.xml file not found.")
if arg_name == "doscar":
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(f"{file_path} or {gz_file_path} not found in current directory")
else:
setattr(args, arg_name, dos_files[arg_name])

potcar_file_path = args.potcar

quality_dict = Analysis.get_lobster_calc_quality_summary(
Expand All @@ -1137,19 +1097,19 @@ def run(args):
json.dump(quality_dict, fd)

if args.action in ["plot-dos", "plotdos"]:
mandatory_files = {
"doscar": "DOSCAR.lobster",
"structure": "POSCAR",
}
req_files = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure", "doscar"])

for arg_name in mandatory_files:
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(f"{file_path.name} necessary for plotting DOS not found in the current directory.")
for arg_name in req_files:
if arg_name == "doscar":
file_path = getattr(args, arg_name)
if not file_path.exists():
gz_file_path = file_path.with_name(zpath(file_path.name))
if gz_file_path.exists():
setattr(args, arg_name, gz_file_path)
else:
raise ValueError(f"{file_path} or {gz_file_path} not found in current directory")
else:
setattr(args, arg_name, req_files[arg_name])

from pymatgen.io.lobster import Doscar

Expand Down Expand Up @@ -1218,22 +1178,28 @@ def run(args):

if args.action in ["plot-icohp-distance", "ploticohpdistance"]:
if args.cobis:
filename = args.icohplist.parent / "ICOBILIST.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["icobilist"]).get(
"icobilist"
)
args.icohplist = filename
# filename = args.icohplist.parent / "ICOBILIST.lobster"
# if not filename.exists():
# filename = filename.with_name(zpath(filename.name))
options = {"are_cobis": True, "are_coops": False}
elif args.coops:
filename = args.icohplist.parent / "ICOOPLIST.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["icooplist"]).get(
"icooplist"
)
args.icohplist = filename
options = {"are_cobis": False, "are_coops": True}
else:
filename = args.icohplist.parent / "ICOHPLIST.lobster"
if not filename.exists():
filename = filename.with_name(zpath(filename.name))
filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["icohplist"]).get(
"icohplist"
)
args.icohplist = filename
options = {"are_cobis": False, "are_coops": False}

icohpcollection = Icohplist(filename=filename, **options).icohpcollection
icohpcollection = Icohplist(filename=args.icohplist, **options).icohpcollection
icohp_plotter = IcohpDistancePlotter(**options)

icohp_plotter.add_icohps(icohpcollection=icohpcollection, label="")
Expand Down
Loading

0 comments on commit 522ee59

Please sign in to comment.