pymdkit 1.2.11__tar.gz → 1.2.12__tar.gz

{pymdkit-1.2.11/src/pymdkit.egg-info → pymdkit-1.2.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.11
+Version: 1.2.12
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later

{pymdkit-1.2.11 → pymdkit-1.2.12}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.11"
+version = "1.2.12"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.2.11 → pymdkit-1.2.12}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.11"
+__version__ = "1.2.12"

{pymdkit-1.2.11 → pymdkit-1.2.12}/src/pymdkit/commands/supercell.py

@@ -3,7 +3,8 @@ Build a supercell whose cell lengths stay within a maximum (-max-abc).
 
 For each lattice vector the structure is repeated as many times as possible
 without its length exceeding ``-max-abc`` (in Angstrom):
-``n_i = max(1, floor(max_abc / |a_i|))``.
+`
+_i = max(1, floor(max_abc / |a_i|))``.
 
 Single file:  supercell -i example.vasp -o out.vasp -max-abc 20
 Whole folder: supercell -if vasp-opted -of out -max-abc 20
@@ -15,20 +16,28 @@ GPUMD setup:  supercell -if extxyz-vasp-opted -max-abc 24 -individual \\
                  temperature, each seeded with model.xyz + the shared GPUMD
                  input files (target_t in run.in replaced by the temperature).
                  With -add-groups, model.xyz is tagged with a GPUMD group index
-                 by element order (Li->0, Y->1, Cl->2).
+                 by element order (Li->0, Y->1, Cl->2).
+Single GPUMD: supercell -i example.cif -max-abc 24 -temp 500 600
+              -> ./model.xyz plus ./500/ and ./600/ directly, without
+                 creating a structure-name folder.
 """
 
 import argparse
 import shutil
 from pathlib import Path
 
-from ase.io import read, write
-
 try:
-    from . import _fileio, add_groups as _add_groups
+    from . import _fileio
 except ImportError:  # running as a standalone script
     import _fileio
-    import add_groups as _add_groups
+
+
+def tag_groups(path, elements):
+    try:
+        from . import add_groups as _add_groups
+    except ImportError:  # running as a standalone script
+        import add_groups as _add_groups
+    _add_groups._tag_one(path, path, elements)
 
 COMMAND = "supercell"
 HELP = "Build a supercell with cell lengths capped at -max-abc Angstrom."
@@ -43,6 +52,8 @@ def repetitions_for(atoms, max_abc):
 
 
 def make_supercell(in_path, out_path, max_abc):
+    from ase.io import read, write
+
     atoms = read(str(in_path))
     reps = repetitions_for(atoms, max_abc)
     sc = atoms.repeat(reps)
@@ -111,9 +122,18 @@ def add_arguments(parser):
 
 
 def _run_gpumd(args):
-    """GPUMD setup: ./<name>/model.xyz + per-temperature job folders."""
+    """GPUMD setup: model.xyz + per-temperature job folders."""
+    if args.input:
+        model = Path("model.xyz")
+        make_supercell(args.input, model, args.max_abc)
+        if args.add_groups:
+            tag_groups(model, args.add_groups)
+        setup_temp_folders(Path("."), args.temp, args.md_input_folder)
+        print(f"Done: set up single structure with temperatures {args.temp}.")
+        return 0
+
     if not args.input_folder:
-        raise SystemExit("Error: -temp requires -if/-input-folder.")
+        raise SystemExit("Error: -temp requires -i/-input or -if/-input-folder.")
     count = 0
     for f in _fileio.structure_files(args.input_folder):
         folder = Path(_folder_name(f.stem))

{pymdkit-1.2.11 → pymdkit-1.2.12}/src/pymdkit/commands/vasp2xyz.py

@@ -22,7 +22,8 @@ except ImportError:  # running as a standalone script
     import _vasp_output
 
 COMMAND = "vasp2xyz"
-HELP = "Collect SCF-converged VASP job folders into one extxyz file."
+HELP = "Collect SCF-converged VASP job folders into one extxyz file."
+KBAR_TO_EV_PER_A3 = 0.0006241509125883258
 
 
 def folder_sort_key(name):
@@ -79,6 +80,23 @@ def strip_calculation_results(atoms):
         atoms.arrays.pop(key, None)
 
 
+def vasp_stress_to_ase(stress):
+    """Convert VASP stress in kB to ASE stress in eV/A^3."""
+    if stress is None:
+        return None
+    try:
+        import numpy as np
+        return -np.asarray(stress, dtype=float) * KBAR_TO_EV_PER_A3
+    except ImportError:
+        pass
+
+    def convert(value):
+        if isinstance(value, (list, tuple)):
+            return [convert(x) for x in value]
+        return -float(value) * KBAR_TO_EV_PER_A3
+
+    return convert(stress)
+
 def atoms_from_output(output):
     from ase.calculators.singlepoint import SinglePointCalculator
     from pymatgen.io.ase import AseAtomsAdaptor
@@ -92,9 +110,9 @@ def atoms_from_output(output):
     if "forces" in step:
         results["forces"] = step["forces"]
     if "stress" in step:
-        results["stress"] = step["stress"]
+        results["stress"] = vasp_stress_to_ase(step["stress"])
     elif "stresses" in step:
-        results["stress"] = step["stresses"]
+        results["stress"] = vasp_stress_to_ase(step["stresses"])
     atoms.calc = SinglePointCalculator(atoms, **results)
     return atoms
 

{pymdkit-1.2.11 → pymdkit-1.2.12/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.11
+Version: 1.2.12
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later