pymdkit 1.2.3__tar.gz → 1.2.5__tar.gz

{pymdkit-1.2.3/src/pymdkit.egg-info → pymdkit-1.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.3
+Version: 1.2.5
 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-1.2.3 → pymdkit-1.2.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.3"
+version = "1.2.5"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.2.3 → pymdkit-1.2.5}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.3"
+__version__ = "1.2.5"

pymdkit-1.2.5/src/pymdkit/commands/stable_entry.py

@@ -0,0 +1,119 @@
+"""Download stable Materials Project structures 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_.-]+", "", str(formula))
+
+
+def mpid_text(value):
+    if value is None:
+        return ""
+    if isinstance(value, dict):
+        for key in ("material_id", "task_id", "entry_id", "id", "identifier"):
+            if value.get(key):
+                return mpid_text(value[key])
+        return "-".join(f"{k}-{v}" for k, v in sorted(value.items()))
+    for attr in ("string", "identifier"):
+        text = getattr(value, attr, None)
+        if text:
+            return str(text)
+    text = str(value)
+    match = re.search(r"mp-\d+", text)
+    if match:
+        return match.group(0)
+    match = re.search(r"identifier=['\"]?(mp-[A-Za-z0-9]+)", text)
+    if match:
+        return match.group(1)
+    return text
+
+
+def entry_id_text(entry):
+    entry_id = getattr(entry, "entry_id", None)
+    text = mpid_text(entry_id)
+    if text:
+        return text
+    data = getattr(entry, "data", {}) or {}
+    for key in ("material_id", "task_id", "entry_id", "id"):
+        text = mpid_text(data.get(key))
+        if text:
+            return text
+    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:
+    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_entries(elements, api_key=None):
+    """Fetch entries and keep only entries stable on the full MP phase diagram."""
+    from pymatgen.analysis.phase_diagram import PhaseDiagram
+    from pymatgen.ext.matproj import MPRester
+
+    with MPRester(api_key) as mpr:
+        entries = mpr.get_entries_in_chemsys(
+            elements,
+            inc_structure=True,
+            additional_criteria={"thermo_types": ["GGA_GGA+U"]},
+        )
+    phase_diagram = PhaseDiagram(entries)
+    stable_entries = list(phase_diagram.stable_entries)
+    print(f"Fetched {len(entries)} MP thermo entries; {len(stable_entries)} are stable on the full phase diagram.")
+    by_mpid = {}
+    for entry in stable_entries:
+        by_mpid[entry_id_text(entry)] = entry
+    return list(by_mpid.values())
+
+
+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_entries(elements, args.mp_api_key)
+    except ModuleNotFoundError as exc:
+        if exc.name == "emmet":
+            raise SystemExit(
+                "Error: stable-entry requires emmet models from mp-api. "
+                "Reinstall pymdkit 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_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))
+        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()))

{pymdkit-1.2.3 → pymdkit-1.2.5/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.3
+Version: 1.2.5
 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-1.2.3/src/pymdkit/commands/stable_entry.py

@@ -1,116 +0,0 @@
-"""Download stable Materials Project structures for a chemical system."""
-
-from __future__ import annotations
-
-import argparse
-import re
-from itertools import combinations
-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 subsystem_labels(elements):
-    """Return all subsystem labels needed to build the full chemsys hull."""
-    labels = []
-    for size in range(1, len(elements) + 1):
-        for subset in combinations(elements, size):
-            labels.append("-".join(subset))
-    return labels
-
-
-def fetch_stable_structures(elements, api_key=None):
-    from mp_api.client import MPRester
-
-    fields = ["material_id", "formula_pretty", "structure"]
-    by_mpid = {}
-    with MPRester(api_key) as mpr:
-        for chemsys in subsystem_labels(elements):
-            docs = mpr.materials.summary.search(
-                chemsys=chemsys,
-                is_stable=True,
-                fields=fields,
-            )
-            for doc in docs:
-                entry = normalize_doc(doc)
-                by_mpid[entry.material_id] = entry
-    return list(by_mpid.values())
-
-
-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 1.2.3+ "
-                "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()))