pymdkit 1.2.0__tar.gz → 1.2.2__tar.gz

{pymdkit-1.2.0/src/pymdkit.egg-info → pymdkit-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.0
+Version: 1.2.2
 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
@@ -14,13 +14,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: scipy
 Requires-Dist: ase
 Requires-Dist: pymatgen
-Requires-Dist: mp_api
+Requires-Dist: mp-api
 Requires-Dist: pyxtal
-Requires-Dist: gemmi
-Requires-Dist: tqdm
 Requires-Dist: dpdata
 Dynamic: license-file
 
@@ -45,8 +42,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its dependencies (numpy, scipy, ase, pymatgen, pyxtal, mp_api, gemmi,
-tqdm).
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.2}/README.md

@@ -19,8 +19,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its dependencies (numpy, scipy, ase, pymatgen, pyxtal, mp_api, gemmi,
-tqdm).
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.0"
+version = "1.2.2"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -25,13 +25,10 @@ classifiers = [
 # individual commands, so the dispatcher and `pymdkit -help` stay fast.
 dependencies = [
     "numpy",
-    "scipy",
     "ase",
-    "pymatgen",
-    "mp_api",
-    "pyxtal",
-    "gemmi",
-    "tqdm",
+    "pymatgen",
+    "mp-api",
+    "pyxtal",
     "dpdata",
 ]
 

{pymdkit-1.2.0 → pymdkit-1.2.2}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.0"
+__version__ = "1.2.2"

{pymdkit-1.2.0 → pymdkit-1.2.2}/src/pymdkit/commands/compute_msd_all_groups.py

@@ -25,7 +25,6 @@ from pathlib import Path
 from typing import Dict, Tuple
 
 import numpy as np
-import scipy.constants as consts
 
 try:
     from . import _fileio
@@ -37,6 +36,8 @@ HELP = "Diffusivity & conductivity from GPUMD MSD jobs (auto-scans <structure>/<
 
 JOB_FILES = ("msd.out", "thermo.out", "model.xyz", "run.in")
 SUMMARY_FILE = "msd_summary.txt"
+ELEMENTARY_CHARGE_C = 1.602176634e-19
+BOLTZMANN_J_PER_K = 1.380649e-23
 
 
 class MDAnalyzer:
@@ -176,8 +177,8 @@ class MDAnalyzer:
     def calculate_conductivity(self, diffusivities, num_ions, charge) -> np.ndarray:
         """Nernst-Einstein conductivity in mS/cm."""
         vol_cm3 = self.volume * 1e-24
-        factor = (num_ions * charge ** 2 * consts.e ** 2
-                  / (vol_cm3 * consts.k * self.temperature))
+        factor = (num_ions * charge ** 2 * ELEMENTARY_CHARGE_C ** 2
+                  / (vol_cm3 * BOLTZMANN_J_PER_K * self.temperature))
         return diffusivities * factor * 1000  # S/cm -> mS/cm
 
     def _format_summary(self, element, group_id, num_ions, temp, D, sigma=None) -> str:

pymdkit-1.2.2/src/pymdkit/commands/stable_entry.py

@@ -0,0 +1,102 @@
+"""Download stable Materials Project structures for a chemical system."""
+
+from __future__ import annotations
+
+import argparse
+import re
+from dataclasses import dataclass
+from pathlib import Path
+
+COMMAND = "stable-entry"
+HELP = "Download stable Materials Project structures for a chemical system."
+
+
+@dataclass
+class StableStructure:
+    material_id: str
+    formula: str
+    structure: object
+
+
+def safe_formula(formula):
+    return re.sub(r"[^A-Za-z0-9_.-]+", "", str(formula))
+
+
+def doc_get(doc, name, default=None):
+    if isinstance(doc, dict):
+        return doc.get(name, default)
+    return getattr(doc, name, default)
+
+
+def normalize_doc(doc):
+    material_id = str(doc_get(doc, "material_id", "unknown"))
+    formula = doc_get(doc, "formula_pretty") or doc_get(doc, "formula")
+    structure = doc_get(doc, "structure")
+    if formula is None and structure is not None:
+        formula = structure.composition.reduced_formula
+    if structure is None:
+        raise ValueError(f"MP document {material_id} has no structure field")
+    return StableStructure(material_id=material_id, formula=str(formula), structure=structure)
+
+
+def entry_sort_key(entry):
+    return (len(entry.structure.composition.elements), entry.formula, entry.material_id)
+
+
+def add_arguments(parser: argparse.ArgumentParser) -> None:
+    parser.add_argument("-s", nargs="+", required=True,
+                        help="Chemical system elements, e.g. -s Li La Ta Cl.")
+    parser.add_argument("-mp-api-key", default=None,
+                        help="Materials Project API key.")
+
+
+def fetch_stable_structures(elements, api_key=None):
+    from mp_api.client import MPRester
+
+    chemsys = "-".join(elements)
+    fields = ["material_id", "formula_pretty", "structure"]
+    with MPRester(api_key) as mpr:
+        docs = mpr.materials.summary.search(
+            chemsys=chemsys,
+            is_stable=True,
+            fields=fields,
+        )
+    return [normalize_doc(doc) for doc in docs]
+
+
+def run(args) -> int:
+    from pymatgen.io.cif import CifWriter
+
+    elements = list(dict.fromkeys(args.s))
+    label = "-".join(elements)
+    out_dir = Path(f"{label}-stable-entries")
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    try:
+        entries = fetch_stable_structures(elements, args.mp_api_key)
+    except ModuleNotFoundError as exc:
+        if exc.name == "mp_api":
+            raise SystemExit(
+                "Error: stable-entry requires mp-api. Reinstall pymdkit 1.2.2+ "
+                "or run `pip install mp-api`."
+            ) from exc
+        raise
+
+    entries = sorted(entries, key=entry_sort_key)
+    written = 0
+    for entry in entries:
+        mpid = safe_formula(entry.material_id)
+        formula = safe_formula(entry.formula)
+        path = out_dir / f"{mpid}-{formula}.cif"
+        CifWriter(entry.structure).write_file(str(path))
+        print(f"{mpid}\t{entry.formula}\t-> {path}")
+        written += 1
+
+    print(f"Wrote {written} stable entr{'y' if written == 1 else 'ies'} to {out_dir}")
+    return 0 if written else 1
+
+
+if __name__ == "__main__":
+    _parser = argparse.ArgumentParser(description=__doc__)
+    add_arguments(_parser)
+    raise SystemExit(run(_parser.parse_args()))

{pymdkit-1.2.0 → pymdkit-1.2.2/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.0
+Version: 1.2.2
 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
@@ -14,13 +14,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: scipy
 Requires-Dist: ase
 Requires-Dist: pymatgen
-Requires-Dist: mp_api
+Requires-Dist: mp-api
 Requires-Dist: pyxtal
-Requires-Dist: gemmi
-Requires-Dist: tqdm
 Requires-Dist: dpdata
 Dynamic: license-file
 
@@ -45,8 +42,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its dependencies (numpy, scipy, ase, pymatgen, pyxtal, mp_api, gemmi,
-tqdm).
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.2}/src/pymdkit.egg-info/requires.txt

@@ -1,9 +1,6 @@
 numpy
-scipy
 ase
 pymatgen
-mp_api
+mp-api
 pyxtal
-gemmi
-tqdm
 dpdata

pymdkit-1.2.0/src/pymdkit/commands/stable_entry.py

@@ -1,56 +0,0 @@
-"""Download stable Materials Project entries for a chemical system."""
-
-from __future__ import annotations
-
-import argparse
-import re
-from pathlib import Path
-
-COMMAND = "stable-entry"
-HELP = "Download stable Materials Project structures for a chemical system."
-
-
-def safe_formula(formula):
-    return re.sub(r"[^A-Za-z0-9_.-]+", "", formula)
-
-
-def add_arguments(parser: argparse.ArgumentParser) -> None:
-    parser.add_argument("-s", nargs="+", required=True,
-                        help="Chemical system elements, e.g. -s Li La Ta Cl.")
-    parser.add_argument("-mp-api-key", default=None,
-                        help="Materials Project API key.")
-
-
-def run(args) -> int:
-    from pymatgen.ext.matproj import MPRester
-    from pymatgen.io.cif import CifWriter
-
-    elements = list(dict.fromkeys(args.s))
-    label = "-".join(elements)
-    out_dir = Path(f"{label}-stable-entries")
-    out_dir.mkdir(parents=True, exist_ok=True)
-
-    with MPRester(args.mp_api_key) as mpr:
-        entries = mpr.get_entries_in_chemsys(
-            elements, inc_structure=True,
-            additional_criteria={"thermo_types": ["GGA_GGA+U"], "is_stable": True},
-        )
-
-    entries = sorted(entries, key=lambda e: (len(e.composition.elements), e.composition.reduced_formula, e.entry_id))
-    written = 0
-    for entry in entries:
-        mpid = str(entry.entry_id).split(" ")[0]
-        formula = safe_formula(entry.composition.reduced_formula)
-        path = out_dir / f"{mpid}-{formula}.cif"
-        CifWriter(entry.structure).write_file(str(path))
-        print(f"{mpid}\t{entry.composition.reduced_formula}\t-> {path}")
-        written += 1
-
-    print(f"Wrote {written} stable entr{'y' if written == 1 else 'ies'} to {out_dir}")
-    return 0 if written else 1
-
-
-if __name__ == "__main__":
-    _parser = argparse.ArgumentParser(description=__doc__)
-    add_arguments(_parser)
-    raise SystemExit(run(_parser.parse_args()))