pymdkit 1.2.10__tar.gz → 1.2.12__tar.gz

{pymdkit-1.2.10/src/pymdkit.egg-info → pymdkit-1.2.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.10
+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-1.2.10 → pymdkit-1.2.12}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.10"
+version = "1.2.12"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.2.10 → pymdkit-1.2.12}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.10"
+__version__ = "1.2.12"

{pymdkit-1.2.10 → pymdkit-1.2.12}/src/pymdkit/commands/stable_entry.py

@@ -3,10 +3,7 @@
 from __future__ import annotations
 
 import argparse
-import json
 import re
-from urllib.parse import quote
-from urllib.request import Request, urlopen
 from pathlib import Path
 
 COMMAND = "stable-entry"
@@ -152,69 +149,44 @@ def fetch_stable_entries(elements, api_key=None):
     return list(by_mpid.values())
 
 
-def api_key_value(api_key=None):
-    if api_key:
-        return api_key
-    try:
-        from pymatgen.ext.matproj import MPRester
-        return getattr(MPRester(), "api_key", None)
-    except Exception:
-        return None
+def get_api_structure(material_id, api_key=None):
+    """Return the MP API structure for a public material_id."""
+    from mp_api.client import MPRester as MPApiRester
 
+    with MPApiRester(api_key) as mpr:
+        if hasattr(mpr, "get_structure_by_material_id"):
+            try:
+                return mpr.get_structure_by_material_id(
+                    material_id,
+                    conventional_unit_cell=True,
+                )
+            except TypeError:
+                return mpr.get_structure_by_material_id(material_id)
+
+        docs = mpr.materials.summary.search(
+            material_ids=[material_id],
+            fields=["material_id", "structure"],
+        )
+    if not docs:
+        raise RuntimeError(f"no MP summary structure found for {material_id}")
+    return doc_get(docs[0], "structure")
+
+
+def write_mp_symmetrized_cif(material_id, fallback_structure, path, api_key=None):
+    """Write an MP API structure as a symmetrized CIF."""
+    from pymatgen.io.cif import CifWriter
 
-def extract_cif_text(text):
-    stripped = text.lstrip()
-    if not stripped.startswith(("{", "[")):
-        if "_symmetry_space_group_name_H-M" in text or stripped.startswith(("data_", "#")):
-            return text
     try:
-        payload = json.loads(text)
-    except json.JSONDecodeError:
-        return None
-    candidates = []
-    if isinstance(payload, dict):
-        candidates.extend(payload.get("response", []) or [])
-        candidates.extend(payload.get("data", []) or [])
-        candidates.append(payload)
-    for item in candidates:
-        if isinstance(item, dict):
-            cif = item.get("cif") or item.get("cif_symmetrized") or item.get("symmetrized_cif")
-            if cif:
-                return cif
-    return None
-
-
-def download_mp_symmetrized_cif(material_id, path, api_key=None):
-    """Download the Materials Project CIF (Symmetrized) file for material_id."""
-    key = api_key_value(api_key)
-    headers = {"Accept": "text/plain", "User-Agent": "pymdkit"}
-    if key:
-        headers["X-API-KEY"] = key
-    quoted = quote(material_id, safe="")
-    urls = [
-        f"https://api.materialsproject.org/materials/{quoted}/cif?symmetrized=true",
-        f"https://api.materialsproject.org/materials/{quoted}/cif",
-        f"https://api.materialsproject.org/materials/core/{quoted}/cif?symmetrized=true",
-        f"https://api.materialsproject.org/materials/core/{quoted}/cif",
-        f"https://materialsproject.org/materials/{quoted}/cif?download=true&symmetrized=true",
-        f"https://materialsproject.org/materials/{quoted}/cif?symmetrized=true",
-        f"https://www.materialsproject.org/rest/v2/materials/{quoted}/cif",
-    ]
-    errors = []
-    for url in urls:
-        try:
-            req = Request(url, headers=headers)
-            with urlopen(req, timeout=60) as response:
-                text = response.read().decode("utf-8")
-            cif_text = extract_cif_text(text)
-            if cif_text:
-                Path(path).write_text(cif_text, encoding="utf-8")
-                return
-            errors.append(f"{url}: response did not contain CIF text")
-        except Exception as exc:  # noqa: BLE001 - try alternate MP endpoints
-            errors.append(f"{url}: {type(exc).__name__}: {exc}")
-    raise RuntimeError("Could not download MP CIF (Symmetrized): " + " | ".join(errors))
+        structure = get_api_structure(material_id, api_key)
+    except Exception as exc:  # noqa: BLE001 - keep command useful if MP API changes
+        structure = fallback_structure
+        print(f"  ! {material_id}: MP API structure fetch failed ({type(exc).__name__}); "
+              "using thermo structure fallback.")
 
+    try:
+        CifWriter(structure, symprec=0.1, refine_struct=True).write_file(str(path))
+    except TypeError:
+        CifWriter(structure, symprec=0.1).write_file(str(path))
 
 def run(args) -> int:
 
@@ -239,7 +211,7 @@ def run(args) -> int:
         mpid = safe_formula(entry_id_text(entry).split(" ")[0])
         formula = safe_formula(entry.composition.reduced_formula)
         path = out_dir / f"{mpid}-{formula}.cif"
-        download_mp_symmetrized_cif(mpid, path, args.mp_api_key)
+        write_mp_symmetrized_cif(mpid, entry.structure, path, args.mp_api_key)
         print(f"{mpid}\t{entry.composition.reduced_formula}\t-> {path}")
         written += 1
 

{pymdkit-1.2.10 → 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-1.2.10 → 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-1.2.10 → pymdkit-1.2.12/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.10
+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