pymdkit 1.2.0__tar.gz → 1.2.1__tar.gz

{pymdkit-1.2.0/src/pymdkit.egg-info → pymdkit-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.0
+Version: 1.2.1
 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 +14,9 @@ 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: pyxtal
-Requires-Dist: gemmi
-Requires-Dist: tqdm
 Requires-Dist: dpdata
 Dynamic: license-file
 
@@ -45,8 +41,7 @@ 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, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.1}/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, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.0"
+version = "1.2.1"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -25,13 +25,9 @@ classifiers = [
 # individual commands, so the dispatcher and `pymdkit -help` stay fast.
 dependencies = [
     "numpy",
-    "scipy",
     "ase",
     "pymatgen",
-    "mp_api",
-    "pyxtal",
-    "gemmi",
-    "tqdm",
+    "pyxtal",
     "dpdata",
 ]
 

{pymdkit-1.2.0 → pymdkit-1.2.1}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.0"
+__version__ = "1.2.1"

{pymdkit-1.2.0 → pymdkit-1.2.1}/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-1.2.0 → pymdkit-1.2.1}/src/pymdkit/commands/stable_entry.py

@@ -11,7 +11,28 @@ HELP = "Download stable Materials Project structures for a chemical system."
 
 
 def safe_formula(formula):
-    return re.sub(r"[^A-Za-z0-9_.-]+", "", formula)
+    return re.sub(r"[^A-Za-z0-9_.-]+", "", str(formula))
+
+
+def entry_id_text(entry):
+    entry_id = getattr(entry, "entry_id", "")
+    if isinstance(entry_id, dict):
+        for key in ("material_id", "task_id", "entry_id", "id"):
+            if entry_id.get(key):
+                return str(entry_id[key])
+        return "-".join(f"{k}-{v}" for k, v in sorted(entry_id.items()))
+    if entry_id:
+        return str(entry_id)
+    data = getattr(entry, "data", {}) or {}
+    for key in ("material_id", "task_id", "entry_id", "id"):
+        if data.get(key):
+            return str(data[key])
+    return "unknown"
+
+
+def entry_sort_key(entry):
+    formula = str(entry.composition.reduced_formula)
+    return (len(entry.composition.elements), formula, entry_id_text(entry))
 
 
 def add_arguments(parser: argparse.ArgumentParser) -> None:
@@ -36,10 +57,10 @@ def run(args) -> int:
             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))
+    entries = sorted(entries, key=entry_sort_key)
     written = 0
     for entry in entries:
-        mpid = str(entry.entry_id).split(" ")[0]
+        mpid = safe_formula(entry_id_text(entry).split(" ")[0])
         formula = safe_formula(entry.composition.reduced_formula)
         path = out_dir / f"{mpid}-{formula}.cif"
         CifWriter(entry.structure).write_file(str(path))

{pymdkit-1.2.0 → pymdkit-1.2.1/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.0
+Version: 1.2.1
 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 +14,9 @@ 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: pyxtal
-Requires-Dist: gemmi
-Requires-Dist: tqdm
 Requires-Dist: dpdata
 Dynamic: license-file
 
@@ -45,8 +41,7 @@ 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, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.0 → pymdkit-1.2.1}/src/pymdkit.egg-info/requires.txt

@@ -1,9 +1,5 @@
 numpy
-scipy
 ase
 pymatgen
-mp_api
 pyxtal
-gemmi
-tqdm
 dpdata