Update generateDFTD3.py

Probe-Particle · Oct 23, 2023 · c64eaf4 · c64eaf4
1 parent d732b8e
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -30,20 +30,20 @@ repos:
           - id: black
             args: [--line-length, '180']
             language_version: python3
-    # - repo: https://github.com/PyCQA/flake8
-    #   rev: 6.0.0
-    #   hooks:
-    #       - id: flake8
-    #         args: [--count, --show-source, --statistics]
-    #         additional_dependencies:
-    #             - flake8-bugbear
-    #             - flake8-builtins
-    #             - flake8-comprehensions
-    #             - flake8-debugger
-    #             - flake8-logging-format
-    #             - pep8-naming
-    #             - pyflakes
-    #             - tryceratops
+    - repo: https://github.com/PyCQA/flake8
+      rev: 6.0.0
+      hooks:
+          - id: flake8
+            args: [--count, --show-source, --statistics]
+            additional_dependencies:
+                - flake8-bugbear
+                - flake8-builtins
+                - flake8-comprehensions
+                - flake8-debugger
+                - flake8-logging-format
+                - pep8-naming
+                - pyflakes
+                - tryceratops
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v0.961
       hooks:

diff --git a/ppafm/cli/generateDFTD3.py b/ppafm/cli/generateDFTD3.py
@@ -2,51 +2,57 @@
 
 import sys
 
-import numpy as np
-
-import ppafm as PPU
-import ppafm.fieldFFT as fFFT
-import ppafm.HighLevel as PPH
-from ppafm import elements
 from ppafm.defaults import d3
 
+from .. import common
+from ..HighLevel import computeDFTD3
 
-def main():
 
-    parser = PPU.CLIParser(
-        description='Generate Grimme DFT-D3 vdW force field using the Becke-Johnson damping function. '
-            'The generated force field is saved to FFvdW_{x,y,z}.[ext].'
+def main():
+    parser = common.CLIParser(
+        description="Generate Grimme DFT-D3 vdW force field using the Becke-Johnson damping function. " "The generated force field is saved to FFvdW_{x,y,z}.[ext]."
     )
 
-    parser.add_arguments(['input', 'input_format', 'output_format', 'noPBC', 'energy'])
-    parser.add_argument('--df_name', action='store', default='PBE',
-        help='Which density functional-specific scaling parameters (s6, s8, a1, a2) to use. Give the name of the functional. '
-            'The following functionals are available: PBE, B1B95, B2GPPLYP, B3PW91, BHLYP, BMK, BOP, BPBE, CAMB3LYP, LCwPBE, '
-            'MPW1B95, MPWB1K, mPWLYP, OLYP, OPBE, oTPSS, PBE38, PBEsol, PTPSS, PWB6K, revSSB, SSB, TPSSh, HCTH120, B2PLYP, '
-            'B3LYP, B97D, BLYP, BP86, DSDBLYP, PBE0, PBE, PW6B95, PWPB95, revPBE0, revPBE38, revPBE, rPW86PBE, TPSS0, TPSS.')
-    parser.add_argument('--df_params', action='store', default=None, nargs=4, type=float, metavar=('s6', 's8', 'a1', 'a2'),
-        help='Manually specify scaling parameters s6, s8, a1, a2. Overwrites --df_name.')
+    parser.add_arguments(["input", "input_format", "output_format", "noPBC", "energy"])
+    parser.add_argument(
+        "--df_name",
+        action="store",
+        default="PBE",
+        help="Which density functional-specific scaling parameters (s6, s8, a1, a2) to use. Give the name of the functional. "
+        "The following functionals are available: PBE, B1B95, B2GPPLYP, B3PW91, BHLYP, BMK, BOP, BPBE, CAMB3LYP, LCwPBE, "
+        "MPW1B95, MPWB1K, mPWLYP, OLYP, OPBE, oTPSS, PBE38, PBEsol, PTPSS, PWB6K, revSSB, SSB, TPSSh, HCTH120, B2PLYP, "
+        "B3LYP, B97D, BLYP, BP86, DSDBLYP, PBE0, PBE, PW6B95, PWPB95, revPBE0, revPBE38, revPBE, rPW86PBE, TPSS0, TPSS.",
+    )
+    parser.add_argument(
+        "--df_params",
+        action="store",
+        default=None,
+        nargs=4,
+        type=float,
+        metavar=("s6", "s8", "a1", "a2"),
+        help="Manually specify scaling parameters s6, s8, a1, a2. Overwrites --df_name.",
+    )
     args = parser.parse_args()
 
     try:
-        # Try overwriting global parameters with params.ini file
-        PPU.loadParams('params.ini')
-    except:
+        # Try overwriting global parameters with params.ini file.
+        common.loadParams("params.ini")
+    except Exception:
         print("No params.ini provided => using default parameters.")
 
-    # Overwrite global parameters with command line arguments
-    PPU.apply_options(vars(args))
+    # Overwrite global parameters with command line arguments.
+    common.apply_options(vars(args))
 
     if args.df_params is not None:
         p = args.df_params
-        df_params = {'s6': p[0], 's8': p[1], 'a1': p[2], 'a2': p[3]}
+        df_params = {"s6": p[0], "s8": p[1], "a1": p[2], "a2": p[3]}
     else:
         if args.df_name not in d3.DF_DEFAULT_PARAMS:
-            print(f'Unknown functional name `{args.df_name}`!')
+            print(f"Unknown functional name `{args.df_name}`!")
             sys.exit(1)
         df_params = args.df_name
 
-    PPH.computeDFTD3(args.input, df_params=df_params, geometry_format=args.input_format, save_format=args.output_format, compute_energy=args.energy)
+    computeDFTD3(args.input, df_params=df_params, geometry_format=args.input_format, save_format=args.output_format, compute_energy=args.energy)
 
 
 if __name__ == "__main__":