Opencode refactor

.gitignore

@@ -16,6 +16,9 @@ build/
 .DS_Store
 Thumbs.db
 
+# Opencode
+.opencode
+
 # Temporary / generated files
 *.log
 temp_*.xyz

Scripts/format_conversion/abacus2xyz_scf.py

@@ -26,6 +26,7 @@
 def main():
     if len(sys.argv) != 3:
         print("Usage: python abacus2xyz_scf.py <dir> <extxyz>")
+        print("   or: gpumdkit.sh -abacus2xyz <dir> <extxyz>")
         sys.exit(1)
 if __name__ == "__main__":
     main()

Scripts/format_conversion/add_groups.py

@@ -24,6 +24,12 @@
 from ase.io import read, write
 import numpy as np
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python add_groups.py <input.xyz> <element1> <element2> ...")
+    print("   or: gpumdkit.sh -addgroup <input.xyz> <element1> <element2> ...")
+    sys.exit(1)
+
 # Read the file name from command line arguments
 file_name = sys.argv[1]
 

Scripts/format_conversion/add_weight.py

@@ -28,7 +28,8 @@
 def main():
     # Check if the correct number of arguments are provided
     if len(sys.argv) != 4:
-        print("Usage: python script.py <input_file> <output_file> <new_weight>")
+        print("Usage: python add_weight.py <input.xyz> <output.xyz> <weight>")
+        print("   or: gpumdkit.sh -addweight <input.xyz> <output.xyz> <weight>")
         sys.exit(1)
 
     # Parse command line arguments

Scripts/format_conversion/cif2exyz.py

@@ -24,7 +24,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print(" Usage: python cif2exyz.py input.cif output.xyz")
+    print("Usage: python cif2exyz.py <input.cif> <output.xyz>")
+    print("   or: gpumdkit.sh -cif2exyz <input.cif> <output.xyz>")
     sys.exit(1)
 
 # Read input and output file paths

Scripts/format_conversion/cif2pos.py

@@ -24,7 +24,8 @@
 
 # Check command line arguments
 if len(sys.argv) != 3:
-    print(" Usage: python cif2poscar.py input.cif output.vasp")
+    print("Usage: python cif2pos.py <input.cif> <output.vasp>")
+    print("   or: gpumdkit.sh -cif2pos <input.cif> <output.vasp>")
     sys.exit(1)
 
 # Read input and output file paths

Scripts/format_conversion/clean_xyz.py

@@ -23,6 +23,12 @@
 from ase.io import read, write
 import sys
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python clean_xyz.py <input.xyz> <output.xyz>")
+    print("   or: gpumdkit.sh -clean_xyz <input.xyz> <output.xyz>")
+    sys.exit(1)
+
 # Read all frames from the input train.xyz file
 frames = read(sys.argv[1], index=':')
 

Scripts/format_conversion/exyz2pos.py

@@ -30,7 +30,13 @@ def print_progress_bar(iteration, total, length=50):
     if iteration == total:
         print()
 
-input_file = sys.argv[1] if len(sys.argv) > 1 else 'train.xyz'
+# Check arguments
+if len(sys.argv) < 2:
+    print("Usage: python exyz2pos.py <input.xyz>")
+    print("   or: gpumdkit.sh -exyz2pos <input.xyz>")
+    sys.exit(1)
+
+input_file = sys.argv[1]
 
 # Read all frames
 frames = read(input_file, index=':')

Scripts/format_conversion/get_frame.py

@@ -22,6 +22,12 @@
 import sys
 from ase.io import read, write
 
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python get_frame.py <input.xyz> <frame_number>")
+    print("   or: gpumdkit.sh -get_frame <input.xyz> <frame_number>")
+    sys.exit(1)
+
 def get_frame():
     input_file = sys.argv[1]
     frame_number = int(sys.argv[2])

Scripts/format_conversion/lmp2exyz.py

@@ -48,7 +48,8 @@ def lmp2exyz(dump_file, elements):
 
 if __name__ == '__main__':
     if len(sys.argv) < 3:
-        print(" Usage: python lmp2exyz.py <dump_file> <element1> <element2> ...")
+        print("Usage: python lmp2exyz.py <dump_file> <element1> <element2> ...")
+        print("   or: gpumdkit.sh -lmp2exyz <dump_file> <element1> <element2> ...")
         sys.exit(1)
 
     dump_file = sys.argv[1]

Scripts/format_conversion/mtp2xyz.py

@@ -132,6 +132,11 @@ def dump_xyz(frames):
 
 
 if __name__ == "__main__":
+    # Check arguments
+    if len(sys.argv) < 3:
+        print("Usage: python mtp2xyz.py <train.cfg> <Symbol1> <Symbol2> ...")
+        sys.exit(1)
+
     type_to_symbol = {i: s for i, s in enumerate(sys.argv[2:])}
     frames = load_cfg(sys.argv[1], type_to_symbol)
     #dump_nep(frames)

Scripts/format_conversion/out2exyz.py

@@ -23,6 +23,12 @@
 from ase import Atoms, Atom
 from tqdm import tqdm
 
+# Check arguments
+if len(sys.argv) < 2:
+    print("Usage: python out2exyz.py <directory>")
+    print("   or: gpumdkit.sh -out2exyz <directory>")
+    sys.exit(1)
+
 def Convert_atoms(atom):
     xx,yy,zz,yz,xz,xy = -atom.calc.results['stress']*atom.get_volume() 
     atom.info['virial'] = np.array([(xx, xy, xz), (xy, yy, yz), (xz, yz, zz)])

Scripts/format_conversion/pos2exyz.py

@@ -44,9 +44,8 @@ def convert_poscar_to_extxyz(poscar_filenames, extxyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 3:
-        print("Usage: python pos2exyz.py <POSCAR> <extxyz_filename>")
-        print("Example 1: python pos2exyz.py POSCAR model.xyz")
-        # print("Example 2: python pos2exyz.py 'POSCAR*' train.xyz")
+        print("Usage: python pos2exyz.py <POSCAR> <output.xyz>")
+        print("   or: gpumdkit.sh -pos2exyz <POSCAR> <output.xyz>")
         sys.exit(1)
 
     poscar_filename_pattern = sys.argv[1]

Scripts/format_conversion/pos2lmp.py

@@ -30,6 +30,7 @@ def convert_poscar_to_lammps(poscar_path, lammps_data_path):
 if __name__ == "__main__":
     if len(sys.argv) != 3:
         print("Usage: python pos2lmp.py <poscar_file> <lammps_data_file>")
+        print("   or: gpumdkit.sh -pos2lmp <poscar_file> <lammps_data_file>")
         sys.exit(1)
 
     poscar_file = sys.argv[1]

Scripts/format_conversion/replicate.py

@@ -106,8 +106,10 @@ def reorder_atoms_by_input_species_order(atoms, original_atoms):
 
 def main():
     if len(sys.argv) < 4:
-        print(" Usage 1: python replicate.py input.vasp output.vasp a b c")
-        print(" Usage 2: python replicate.py input.vasp output.vasp target_num")
+        print("Usage 1: python replicate.py input.vasp output.vasp a b c")
+        print("Usage 2: python replicate.py input.vasp output.vasp target_num")
+        print("   or: gpumdkit.sh -replicate input.vasp output.vasp a b c")
+        print("   or: gpumdkit.sh -replicate input.vasp output.vasp target_num")
         sys.exit(1)
 
     infile = sys.argv[1]

Scripts/format_conversion/split_single_xyz.py

@@ -45,7 +45,7 @@ def split_xyz_to_individual_models(input_xyz_filename):
 if __name__ == '__main__':
     # Check if the number of arguments is correct
     if len(sys.argv) < 2:
-        print(" Usage: python script_name.py <input_xyz_filename>")
+        print("Usage: python split_single_xyz.py <input.xyz>")
         sys.exit(1)
 
     # Get input XYZ filename from command line argument

Scripts/format_conversion/traj2exyz.py

@@ -47,9 +47,10 @@ def convert_traj_to_extxyz(input_file, output_file):
 if __name__ == "__main__":
     # Check if correct number of arguments are provided
     if len(sys.argv) != 3:
-        print(" Usage: python traj2exyz.py <input.traj> <output.xyz>")
-        sys.stdout.flush()
-    else:
-        input_path = sys.argv[1]
-        output_path = sys.argv[2]
-        convert_traj_to_extxyz(input_path, output_path)
+        print("Usage: python traj2exyz.py <input.traj> <output.xyz>")
+        print("   or: gpumdkit.sh -traj2exyz <input.traj> <output.xyz>")
+        sys.exit(1)
+
+    input_path = sys.argv[1]
+    output_path = sys.argv[2]
+    convert_traj_to_extxyz(input_path, output_path)

Scripts/format_conversion/xdatcar2exyz.py

@@ -19,39 +19,38 @@
 =============================================================================
 """
 
-import argparse
 import sys
 from ase.io import read, write
 
-# 1. Setup Argument Parser for positional arguments
-parser = argparse.ArgumentParser(
-    description=" Convert VASP XDATCAR to extxyz format."
-)
-parser.add_argument("input", help=" Path to the input XDATCAR file")
-parser.add_argument("output", help=" Path to the output .xyz file")
+# Check arguments
+if len(sys.argv) < 3:
+    print("Usage: python xdatcar2exyz.py <XDATCAR> <output.xyz>")
+    print("   or: gpumdkit.sh -xdat2exyz <XDATCAR> <output.xyz>")
+    sys.exit(1)
 
-args = parser.parse_args()
+input_file = sys.argv[1]
+output_file = sys.argv[2]
 
-# 2. Execute conversion logic
+# Execute conversion logic
 try:
-    print(f" Reading XDATCAR: {args.input} ...")
+    print(f" Reading XDATCAR: {input_file} ...")
 
     # Read all frames from the trajectory (index=":")
     # ASE automatically parses scaling, lattice, and species
-    trajectory = read(args.input, index=":", format="vasp-xdatcar")
+    trajectory = read(input_file, index=":", format="vasp-xdatcar")
 
     num_frames = len(trajectory)
     print(f" Detected {num_frames} frames.")
 
-    print(f" Writing to extxyz: {args.output} ...")
+    print(f" Writing to extxyz: {output_file} ...")
 
     # Writing in extxyz format preserves the Lattice matrix in the header
-    write(args.output, trajectory, format="extxyz")
+    write(output_file, trajectory, format="extxyz")
 
     print(" Conversion complete.")
 
 except FileNotFoundError:
-    print(f" Error: Could not find '{args.input}'. Please check the path.")
+    print(f" Error: Could not find '{input_file}'. Please check the path.")
     sys.exit(1)
 except Exception as e:
     print(f" An unexpected error occurred: {e}")

Scripts/utils/completion.sh

@@ -13,7 +13,7 @@ _gpumdkit_completions() {
     prev="${COMP_WORDS[COMP_CWORD-1]}" # Previous word
 
     # List of primary options (extracted from gpumdkit.sh)
-    local opts="-h -update -help -clean -time -plt -calc -cbc -range -out2xyz -xml2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -pos2lmp -lmp2exyz -traj2exyz -cp2k2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -get_frame -clean_xyz -get_volume -analyze_comp -replicate -hbond -pda -pynep -frame_range -chem_species -xdat2exyz"
+    local opts="-h -update -help -clean -time -plt -calc -cbc -range -out2xyz -xml2xyz -pos2exyz -cif2pos -cif2exyz -exyz2pos -pos2lmp -lmp2exyz -traj2exyz -cp2k2xyz -addgroup -addlabel -addweight -min_dist -min_dist_pbc -filter_dist -filter_dist_pbc -filter_box -filter_value -get_frame -clean_xyz -get_volume -analyze_comp -replicate -hbond -pda -pynep -frame_range -chem_species -xdat2exyz -nep_modifier"
 
     # Provide secondary completion based on the previous word
     case "$prev" in