rsspolymlp 0.3.4__tar.gz → 0.4.1__tar.gz

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2025 Hayato Wakai
+Copyright (c) 2026 Hayato Wakai
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{rsspolymlp-0.3.4/src/rsspolymlp.egg-info → rsspolymlp-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rsspolymlp
-Version: 0.3.4
+Version: 0.4.1
 Summary: A framework for random structure search using polynomial MLPs
 Author-email: Hayato Wakai <wakai@cms.mtl.kyoto-u.ac.jp>
 Maintainer-email: Hayato Wakai <wakai@cms.mtl.kyoto-u.ac.jp>
@@ -29,23 +29,27 @@ Requires-Dist: matplotlib; extra == "tools"
 Requires-Dist: seaborn; extra == "tools"
 Dynamic: license-file
 
-# A framework for random structure search (RSS) using polynomial MLPs
+# Framework for random structure search using polynomial machine learning potentials
 
 ## Citation of rsspolymlp
 
 If you use `rsspolymlp` in your study, please cite the following articles.
 
-“Efficient global crystal structure prediction using polynomial machine learning potential in the binary Al–Cu alloy system”, [J. Ceram. Soc. Jpn. 131, 762 (2023)](https://www.jstage.jst.go.jp/article/jcersj2/131/10/131_23053/_article/-char/ja/)
+“Systematic global structure search of bismuth-based binary systems under pressure using machine learning potentials”, [Phys. Rev. Materials 10, 093801 (2026)](https://doi.org/10.1103/k9sg-v7hl)
 ```
-@article{HayatoWakai202323053,
-  title="{Efficient global crystal structure prediction using polynomial machine learning potential in the binary Al–Cu alloy system}",
-  author={Hayato Wakai and Atsuto Seko and Isao Tanaka},
-  journal={J. Ceram. Soc. Jpn.},
-  volume={131},
-  number={10},
-  pages={762-766},
-  year={2023},
-  doi={10.2109/jcersj2.23053}
+@article{Phys.Rev.Mater.10.093801,
+  title = {Systematic global structure search of bismuth-based binary systems under pressure using machine learning potentials},
+  author = {Wakai, Hayato and Ishiwata, Shintaro and Seko, Atsuto},
+  journal = {Phys. Rev. Mater.},
+  volume = {10},
+  issue = {9},
+  pages = {093801},
+  numpages = {28},
+  year = {2026},
+  month = {Sep},
+  publisher = {American Physical Society},
+  doi = {10.1103/k9sg-v7hl},
+  url = {https://link.aps.org/doi/10.1103/k9sg-v7hl}
 }
 ```
 
@@ -61,8 +65,8 @@ If you use `rsspolymlp` in your study, please cite the following articles.
 - symfc
 
 [Optional]
-- matplotlib (if plotting RSS results)
-- seaborn (if plotting RSS results)
+- matplotlib, seaborn
+- pymatgen
 
 ### How to install
 - Install from conda-forge
@@ -91,9 +95,8 @@ pip install rsspolymlp
    - Initial structure generation
    - Global RSS with polynomial MLPs
    - Unique structure identification and RSS result summarization
-   - Ghost minimum structure elimination
    - Phase stability analysis
- - [Development kit for polynomial MLPs](docs/rsspolymlp_devkit.md)
+ - [Development kit for polynomial MLPs](docs/rsspolymlp_dev.md)
    - MLP dataset generation
    - DFT dataset division
    - Polynomial MLP development

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/README.md

@@ -1,20 +1,24 @@
-# A framework for random structure search (RSS) using polynomial MLPs
+# Framework for random structure search using polynomial machine learning potentials
 
 ## Citation of rsspolymlp
 
 If you use `rsspolymlp` in your study, please cite the following articles.
 
-“Efficient global crystal structure prediction using polynomial machine learning potential in the binary Al–Cu alloy system”, [J. Ceram. Soc. Jpn. 131, 762 (2023)](https://www.jstage.jst.go.jp/article/jcersj2/131/10/131_23053/_article/-char/ja/)
+“Systematic global structure search of bismuth-based binary systems under pressure using machine learning potentials”, [Phys. Rev. Materials 10, 093801 (2026)](https://doi.org/10.1103/k9sg-v7hl)
 ```
-@article{HayatoWakai202323053,
-  title="{Efficient global crystal structure prediction using polynomial machine learning potential in the binary Al–Cu alloy system}",
-  author={Hayato Wakai and Atsuto Seko and Isao Tanaka},
-  journal={J. Ceram. Soc. Jpn.},
-  volume={131},
-  number={10},
-  pages={762-766},
-  year={2023},
-  doi={10.2109/jcersj2.23053}
+@article{Phys.Rev.Mater.10.093801,
+  title = {Systematic global structure search of bismuth-based binary systems under pressure using machine learning potentials},
+  author = {Wakai, Hayato and Ishiwata, Shintaro and Seko, Atsuto},
+  journal = {Phys. Rev. Mater.},
+  volume = {10},
+  issue = {9},
+  pages = {093801},
+  numpages = {28},
+  year = {2026},
+  month = {Sep},
+  publisher = {American Physical Society},
+  doi = {10.1103/k9sg-v7hl},
+  url = {https://link.aps.org/doi/10.1103/k9sg-v7hl}
 }
 ```
 
@@ -30,8 +34,8 @@ If you use `rsspolymlp` in your study, please cite the following articles.
 - symfc
 
 [Optional]
-- matplotlib (if plotting RSS results)
-- seaborn (if plotting RSS results)
+- matplotlib, seaborn
+- pymatgen
 
 ### How to install
 - Install from conda-forge
@@ -60,9 +64,8 @@ pip install rsspolymlp
    - Initial structure generation
    - Global RSS with polynomial MLPs
    - Unique structure identification and RSS result summarization
-   - Ghost minimum structure elimination
    - Phase stability analysis
- - [Development kit for polynomial MLPs](docs/rsspolymlp_devkit.md)
+ - [Development kit for polynomial MLPs](docs/rsspolymlp_dev.md)
    - MLP dataset generation
    - DFT dataset division
    - Polynomial MLP development

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "rsspolymlp"
-version = "0.3.4"
+version = "0.4.1"
 description = "A framework for random structure search using polynomial MLPs"
 license = "MIT"
 authors = [

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/src/rsspolymlp/analysis/eos.py

@@ -90,7 +90,7 @@ class EOSFit:
         else:
             self.parameters = result[0]
 
-        print(f"RMSE of EOS fit (energy): {self.rmse*1000:.6f} meV")
+        print(f"RMSE of EOS fit (energy): {self.rmse * 1000:.6f} meV")
 
     @property
     def rmse(self) -> float:

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/src/rsspolymlp/analysis/ghost_minima.py

@@ -8,9 +8,8 @@ import shutil
 import numpy as np
 from sklearn.cluster import KMeans
 
-from pypolymlp.core.interface_vasp import Vasprun
 from pypolymlp.core.units import EVtoGPa
-from rsspolymlp.common.atomic_energy import atomic_energy
+from rsspolymlp.common.interface_vasp import parse_properties_from_vasprun
 
 
 def detect_ghost_minima(energies: np.array, distances: np.array):
@@ -118,7 +117,7 @@ def get_ghost_minima_dists(dir_path):
 
 def ghost_minima_candidates(result_paths):
     # Prepare output directory: remove existing files if already exists
-    out_dir = "ghost_minima/ghost_minima_candidates"
+    out_dir = "ghost_minima/ghost_minima_cands"
     os.makedirs(out_dir, exist_ok=True)
     for filename in os.listdir(out_dir):
         if "POSCAR" in filename:
@@ -136,14 +135,14 @@ def ghost_minima_candidates(result_paths):
         logname = os.path.basename(res_path).split(".json")[0]
         for res in rss_results:
             if res.get("is_ghost_minima"):
-                dest = f"ghost_minima/ghost_minima_candidates/POSCAR_{logname}_No{res['struct_no']}"
+                dest = f"ghost_minima/ghost_minima_cands/POSCAR_{logname}_No{res['struct_tag']}"
                 shutil.copy(res["struct_path"], dest)
                 _res = res
                 _res.pop("structure", None)
-                _res["ghost_minima_poscar"] = f"POSCAR_{logname}_No{res['struct_no']}"
+                _res["ghost_minima_poscar"] = f"POSCAR_{logname}_No{res['struct_tag']}"
                 ghost_minima_all.append(_res)
 
-    with open("ghost_minima/ghost_minima_candidates.dat", "w") as f:
+    with open("ghost_minima/ghost_minima_cands.dat", "w") as f:
         for res in ghost_minima_all:
             print(res, file=f)
     print(f"Detected {len(ghost_minima_all)} potential ghost_minima")
@@ -152,7 +151,7 @@ def ghost_minima_candidates(result_paths):
 def detect_actual_ghost_minima(dft_path):
     # Load ghost_minima candidates
     ghost_minima_all = []
-    with open("ghost_minima/ghost_minima_candidates.dat") as f:
+    with open("ghost_minima/ghost_minima_cands.dat") as f:
         for line in f:
             ghost_minima_all.append(ast.literal_eval(line.strip()))
 
@@ -165,7 +164,9 @@ def detect_actual_ghost_minima(dft_path):
         vasprun_get = False
         for vasprun in vasprun_paths:
             try:
-                vaspobj = Vasprun(vasprun)
+                structure, (energy_dft, _, stress_dft) = parse_properties_from_vasprun(
+                    vasprun, units="GPa"
+                )
                 vasprun_get = True
             except Exception:
                 continue
@@ -182,22 +183,17 @@ def detect_actual_ghost_minima(dft_path):
             )
             continue
 
-        energy_dft = vaspobj.energy
-        structure = vaspobj.structure
-        for element in structure.elements:
-            energy_dft -= atomic_energy(element)
-        energy_dft /= len(structure.elements)
         vol_per_atom = structure.volume / len(structure.elements)
 
-        # Subtract pressure term from MLP enthalpy
         mlp_energy = res["energy"]
         mlp_energy -= pressure * vol_per_atom / EVtoGPa
+        energy_dft /= len(structure.elements)
+        e_diff = mlp_energy - energy_dft
 
-        stress_dft = [(vaspobj.stress / 10).tolist()[i][i] for i in range(3)]
+        stress_dft = [stress_dft[i][i] for i in range(3)]
         press_diff = [pressure - stress_dft[i] for i in range(3)]
         stress_diff = np.max(np.abs(press_diff)) * vol_per_atom / EVtoGPa
 
-        e_diff = mlp_energy - energy_dft
         diff_all.append(
             {
                 "energy_diff": e_diff,
@@ -221,8 +217,8 @@ def detect_actual_ghost_minima(dft_path):
 
             print(f"  - structure: {poscar}", file=f)
             if not delta_e == "null":
-                print(f"    energy_diff_meV_per_atom: {delta_e*1000:.3f}", file=f)
-                print(f"    stress_diff_meV_per_atom: {delta_s*1000:.3f}", file=f)
+                print(f"    energy_diff_meV_per_atom: {delta_e * 1000:.3f}", file=f)
+                print(f"    stress_diff_meV_per_atom: {delta_s * 1000:.3f}", file=f)
                 e_threshold = -0.1  # unit: eV/atom
                 s_threshold = 0.5
                 if delta_e < e_threshold or delta_s > s_threshold:

{rsspolymlp-0.3.4 → rsspolymlp-0.4.1}/src/rsspolymlp/analysis/phase_analysis.py

@@ -7,9 +7,8 @@ import numpy as np
 import yaml
 from scipy.spatial import ConvexHull
 
-from pypolymlp.core.interface_vasp import Vasprun
-from rsspolymlp.common.atomic_energy import atomic_energy
 from rsspolymlp.common.composition import compute_composition
+from rsspolymlp.common.interface_vasp import parse_properties_from_vasprun
 
 
 class ConvexHullAnalyzer:
@@ -247,9 +246,9 @@ class ConvexHullAnalyzer:
     def parse_results(self, input_paths, ghost_minima_file=None, parse_vasp=False):
         """
         Populate composition_data by parsing RSS JSON or VASP vasprun.xml outputs.
-        :param input_paths: List of RSS JSON files or VASP directories.
-        :param ghost_minima_file: YAML file listing ghost minima to exclude (RSS only).
-        :param parse_vasp: If True, parse VASP outputs; otherwise parse RSS JSON.
+        input_paths: List of RSS JSON files or VASP directories.
+        ghost_minima_file: YAML file listing ghost minima to exclude (RSS only).
+        parse_vasp: If True, parse VASP outputs; otherwise parse RSS JSON.
         """
         if parse_vasp:
             self._parse_vasp_results(input_paths)
@@ -294,7 +293,7 @@ class ConvexHullAnalyzer:
                     [r["is_ghost_minima"] for r in rss_results]
                 ),
                 "struct_tag": np.array(
-                    [f"POSCAR_{logname}_No{r['struct_no']}" for r in rss_results]
+                    [f"POSCAR_{logname}_No{r['struct_tag']}" for r in rss_results]
                 ),
             }
 
@@ -319,15 +318,13 @@ class ConvexHullAnalyzer:
         for dft_path in input_paths:
             vasprun_path = f"{dft_path}/vasprun.xml"
             try:
-                vaspobj = Vasprun(vasprun_path)
+                structure, (energy_dft, _, _) = parse_properties_from_vasprun(
+                    vasprun_path
+                )
             except Exception:
                 print(vasprun_path, "failed")
                 continue
 
-            energy_dft = vaspobj.energy
-            structure = vaspobj.structure
-            for element in structure.elements:
-                energy_dft -= atomic_energy(element)
             energy_dft /= len(structure.elements)
             if energy_dft < -15:
                 print(vasprun_path, "exhibits very low energy:", energy_dft, "eV/atom")