rsspolymlp 0.3.4__tar.gz → 0.4.0__tar.gz

{rsspolymlp-0.3.4/src/rsspolymlp.egg-info → rsspolymlp-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rsspolymlp
-Version: 0.3.4
+Version: 0.4.0
 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>
@@ -35,17 +35,21 @@ Dynamic: license-file
 
 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}
 }
 ```
 
@@ -93,7 +97,7 @@ pip install rsspolymlp
    - 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-0.4.0}/README.md

@@ -4,17 +4,21 @@
 
 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}
 }
 ```
 
@@ -62,7 +66,7 @@ pip install rsspolymlp
    - 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-0.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "rsspolymlp"
-version = "0.3.4"
+version = "0.4.0"
 description = "A framework for random structure search using polynomial MLPs"
 license = "MIT"
 authors = [

{rsspolymlp-0.3.4 → rsspolymlp-0.4.0}/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-0.4.0}/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):
@@ -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-0.4.0}/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)
@@ -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")

{rsspolymlp-0.3.4 → rsspolymlp-0.4.0}/src/rsspolymlp/analysis/rss_summarize.py

@@ -9,7 +9,6 @@ from time import time
 
 import numpy as np
 
-from pypolymlp.core.interface_vasp import Vasprun
 from pypolymlp.utils.vasp_utils import write_poscar_file
 from rsspolymlp.analysis.ghost_minima import detect_ghost_minima
 from rsspolymlp.analysis.unique_struct import (
@@ -18,9 +17,9 @@ from rsspolymlp.analysis.unique_struct import (
     log_all_unique_structures,
     log_unique_structures,
 )
-from rsspolymlp.common.atomic_energy import atomic_energy
 from rsspolymlp.common.composition import compute_composition
 from rsspolymlp.common.convert_dict import polymlp_struct_from_dict
+from rsspolymlp.common.interface_vasp import Vasprun, parse_properties_from_vasprun
 from rsspolymlp.common.property import PropUtil
 
 
@@ -132,19 +131,22 @@ class RSSResultSummarizer:
             for ustr in unique_structs:
                 num_opt_str += len(list(ustr.dupstr_paths))
 
-            with open(composition_tag + ".yaml", "w") as f:
-                print("general_information:", file=f)
-                print(f"  sorting_time_sec:      {round(time_finish, 2)}", file=f)
-                print(f"  pressure_GPa:          {self.pressure}", file=f)
-                print(f"  num_optimized_structs: {num_opt_str}", file=f)
-                print(f"  num_unique_structs:    {len(unique_structs)}", file=f)
-                print("", file=f)
-
             energies = np.array([s.energy for s in unique_structs])
             distances = np.array([s.least_distance for s in unique_structs])
 
             sort_idx = np.argsort(energies)
             unique_str_sorted = [unique_structs[i] for i in sort_idx]
+            if self.thresholds is not None:
+                e_min = None
+                for idx, u in enumerate(unique_str_sorted):
+                    if e_min is None:
+                        e_min = u.energy
+                    if u.energy - e_min > self.thresholds[0] * 0.001:
+                        unique_str_sorted = unique_str_sorted[:idx]
+                        break
+                output_file = f"{composition_tag}_{self.thresholds[0]}"
+            else:
+                output_file = composition_tag
 
             if not self.parse_vasp:
                 os.makedirs("ghost_minima", exist_ok=True)
@@ -160,19 +162,27 @@ class RSSResultSummarizer:
             else:
                 is_ghost_minima = None
 
+            with open(output_file + ".yaml", "w") as f:
+                print("general_information:", file=f)
+                print(f"  sorting_time_sec:      {round(time_finish, 2)}", file=f)
+                print(f"  pressure_GPa:          {self.pressure}", file=f)
+                print(f"  num_optimized_structs: {num_opt_str}", file=f)
+                print(f"  num_unique_structs:    {len(unique_structs)}", file=f)
+                print("", file=f)
+
             rss_result_all = log_unique_structures(
-                composition_tag + ".yaml",
+                output_file + ".yaml",
                 unique_str_sorted,
                 is_ghost_minima,
                 pressure=self.pressure,
             )
 
-            with open(f"json/{composition_tag}.json", "w") as f:
+            with open(f"json/{output_file}.json", "w") as f:
                 json.dump(rss_result_all, f)
 
             if self.thresholds is not None or self.output_poscar is not False:
                 self.generate_poscars(
-                    f"json/{composition_tag}.json",
+                    f"json/{output_file}.json",
                     thresholds=self.thresholds,
                     output_poscar=self.output_poscar,
                 )
@@ -188,6 +198,13 @@ class RSSResultSummarizer:
             print(f"Composition {composition_tag}: summarizing...")
             self.analyzer = UniqueStructureAnalyzer()
 
+            if not self.parse_vasp:
+                axis_tol = 0.03
+                pos_tol = 0.03
+            else:
+                axis_tol = 0.1
+                pos_tol = 0.1
+
             time_start = time()
             for res_path in res_paths:
                 print(f" - Processing result file (parent): {res_path}")
@@ -195,8 +212,8 @@ class RSSResultSummarizer:
                     results_same_comp[composition_tag][res_path],
                     standardize_axis=True,
                     keep_unique=True,
-                    axis_tol=0.03,
-                    pos_tol=0.03,
+                    axis_tol=axis_tol,
+                    pos_tol=pos_tol,
                 )
             time_finish = time() - time_start
 
@@ -333,7 +350,7 @@ class RSSResultSummarizer:
 
             for res in rss_results:
                 if threshold is not None:
-                    diff = abs(e_min - res["energy"])
+                    diff = res["energy"] - e_min
                     if diff * 1000 > threshold:
                         continue
 
@@ -348,11 +365,10 @@ class RSSResultSummarizer:
                             shutil.copy(poscar_path, dest)
                         else:
                             try:
-                                vaspobj = Vasprun(res["struct_path"])
+                                polymlp_st = Vasprun(res["struct_path"]).structure
                             except Exception:
                                 print(res["struct_path"], "failed")
                                 continue
-                            polymlp_st = vaspobj.structure
                             write_poscar_file(polymlp_st, filename=dest)
                         shutil.copy(res["struct_path"], dest_vasp)
                     else:
@@ -368,12 +384,16 @@ class RSSResultSummarizer:
 
         def resolve_path(base: Path, p):
             cwd = Path.cwd()
+            target = Path(p)
             if p is None:
                 return None
-            p = Path(p)
-            target = (
-                base / p if "opt_struct" in p.parts else base / "opt_struct" / p.name
-            )
+            if not self.parse_vasp:
+                p = Path(p)
+                target = (
+                    base / p
+                    if "opt_struct" in p.parts
+                    else base / "opt_struct" / p.name
+                )
             return os.path.relpath(target, start=cwd)
 
         paths_same_comp = defaultdict(list)
@@ -418,24 +438,21 @@ class RSSResultSummarizer:
                 "dupstr_paths": None,
             }
             try:
-                vaspobj = Vasprun(path_name + "/vasprun.xml")
+                polymlp_st, (energy_dft, _, _) = parse_properties_from_vasprun(
+                    path_name + "/vasprun.xml",
+                )
             except Exception:
                 print("ParseError:", path_name + "/vasprun.xml")
                 continue
 
-            polymlp_st = vaspobj.structure
-            objprop = PropUtil(polymlp_st.axis.T, polymlp_st.positions.T)
-            spg_list = objprop.analyze_space_group(polymlp_st.elements)
-
-            energy_dft = vaspobj.energy
-            for element in polymlp_st.elements:
-                energy_dft -= atomic_energy(element)
             energy_dft /= len(polymlp_st.elements)
-
             if energy_dft < -10:
                 print(path_name, "exhibits an unphysically low energy. Skipping.")
                 continue
 
+            objprop = PropUtil(polymlp_st.axis.T, polymlp_st.positions.T)
+            spg_list = objprop.analyze_space_group(polymlp_st.elements)
+
             res_dict["struct_path"] = os.path.relpath(
                 path_name + "/vasprun.xml", os.getcwd()
             )

{rsspolymlp-0.3.4 → rsspolymlp-0.4.0}/src/rsspolymlp/analysis/struct_matcher/struct_match.py

@@ -1,15 +1,17 @@
+import math
 import re
 from collections import Counter
+from contextlib import redirect_stdout
 from dataclasses import dataclass
 from typing import Optional
 
 import numpy as np
 
 from pypolymlp.core.data_format import PolymlpStructure
-from pypolymlp.core.interface_vasp import Poscar
 from pypolymlp.utils.vasp_utils import write_poscar_file
 from rsspolymlp.analysis.struct_matcher.reduced_position import StructRepReducer
 from rsspolymlp.common.composition import compute_composition
+from rsspolymlp.common.interface_vasp import Poscar
 from rsspolymlp.utils.spglib_utils import SymCell
 
 
@@ -30,6 +32,7 @@ def struct_match(
     pos_tol: float = 0.01,
     spg_match: bool = True,
     verbose: bool = False,
+    output_file: str = "struct_matcher.yaml",
 ) -> bool:
     """
     Determine whether two sets of ReducedStructRep objects are structurally
@@ -111,40 +114,64 @@ def struct_match(
 
     if verbose:
 
-        def log_axis_positions(symprec, axis, positions):
+        def log_axis_positions(symprec, axis, positions, round_axis=4, round_pos=3):
             print("    - symprec:", np.round(symprec, 5).tolist())
-            print("      metric_tensor:", np.round(axis, 4).tolist())
+            print("      metric_tensor:", np.round(axis, round_axis).tolist())
             print("      positions:")
-            for axis_tag, p in zip(
-                ["a", "b", "c"], np.round(positions.reshape(3, -1), 3).tolist()
-            ):
-                formatted = ",".join(f"{val:6.3f}" for val in p)
+            for p in positions.reshape(3, -1).tolist():
+                formatted = ",".join(f"{val:{round_pos + 3}.{round_pos}f}" for val in p)
                 print(f"      - [{formatted}]")
 
-        print("--- results of rsspolymlp.analysis.struct_matcher ---")
-        print("tolerance:")
-        print("  axis_tol:", axis_tol)
-        print("  pos_tol:", pos_tol)
-        print("structures:")
-        for i, st_set in enumerate([st_1_set, st_2_set]):
-            print(f"  - struct_No: {i+1}")
-            for st in st_set:
-                print("    spg_number:", st.spg_number)
-                print("    representations:")
-                for h, pos in enumerate(st.positions):
-                    log_axis_positions(st.symprec_set[h], st.axis[h], pos)
-        print("min_axis_l2_norm:", np.round(min_axis_l2_norm, 3))
-        if axis_d_min is not None:
-            print("difference_log:")
-            print("  - axis_l2_norm:", np.round(axis_d_min[0], 3))
-            print("    pos_max_abs:", np.round(pos_d_min[0], 3))
-            print("    structure_1:")
-            log_axis_positions(pos_d_min[1][0], axis_d_min[1][0], pos_d_min[1][1])
-            print("    structure_2:")
-            log_axis_positions(pos_d_min[1][2], axis_d_min[1][1], pos_d_min[1][3])
-            print("    diffs:")
-            log_axis_positions([], axis_d_min[1][2], pos_d_min[1][4])
-        print("Match:", struct_match)
+        with open(output_file, "w") as f, redirect_stdout(f):
+            print("tolerance:")
+            print("  axis_tol:", axis_tol)
+            print("  pos_tol:", pos_tol)
+            print("structures:")
+            for i, st_set in enumerate([st_1_set, st_2_set]):
+                print(f"  - struct_No: {i + 1}")
+                for st in st_set:
+                    print("    spg_number:", st.spg_number)
+                    print("    representations:")
+                    for h, pos in enumerate(st.positions):
+                        log_axis_positions(st.symprec_set[h], st.axis[h], pos)
+            print("min_axis_l2_norm:", np.round(min_axis_l2_norm, 3))
+            if axis_d_min is not None:
+                x_axis = abs(float(axis_d_min[0]))
+                if x_axis <= 1e-12:
+                    round_axis = 6
+                else:
+                    round_axis = min(-math.floor(math.log10(x_axis)) + 1, 6)
+                x_pos = abs(float(pos_d_min[0]))
+                if x_pos <= 1e-12:
+                    round_pos = 6
+                else:
+                    round_pos = min(-math.floor(math.log10(x_pos)) + 1, 6)
+
+                print("difference_log:")
+                print("  - axis_l2_norm:", np.round(axis_d_min[0], round_axis))
+                print("    pos_max_abs:", np.round(pos_d_min[0], round_pos))
+                print("    structure_1:")
+                log_axis_positions(
+                    pos_d_min[1][0],
+                    axis_d_min[1][0],
+                    pos_d_min[1][1],
+                    round_axis,
+                    round_pos,
+                )
+                print("    structure_2:")
+                log_axis_positions(
+                    pos_d_min[1][2],
+                    axis_d_min[1][1],
+                    pos_d_min[1][3],
+                    round_axis,
+                    round_pos,
+                )
+                print("    diffs:")
+                log_axis_positions(
+                    [], axis_d_min[1][2], pos_d_min[1][4], round_axis, round_pos
+                )
+            print("Match:", struct_match)
+        print(f"{output_file} is generated.")
 
     return struct_match
 
@@ -153,6 +180,7 @@ def generate_primitive_cells(
     poscar_name: Optional[str] = None,
     polymlp_st: Optional[PolymlpStructure] = None,
     symprec_set: list[float] = [1e-5, 1e-4, 1e-3, 1e-2],
+    refine_cell: bool = False,
 ) -> tuple[list[PolymlpStructure], list[int]]:
     """
     Generate primitive cells of a given structure under different symmetry tolerances.
@@ -189,7 +217,10 @@ def generate_primitive_cells(
             continue
         else:
             try:
-                primitive_st = symutil.primitive_cell()
+                if not refine_cell:
+                    primitive_st = symutil.primitive_cell()
+                else:
+                    primitive_st = symutil.refine_cell()
             except TypeError:
                 continue
             primitive_st_set.append(primitive_st)

{rsspolymlp-0.3.4 → rsspolymlp-0.4.0}/src/rsspolymlp/analysis/unique_struct.py

@@ -6,7 +6,7 @@ import joblib
 import numpy as np
 
 from pypolymlp.core.data_format import PolymlpStructure
-from pypolymlp.core.interface_vasp import Poscar
+from rsspolymlp.common.interface_vasp import Poscar
 from rsspolymlp.analysis.struct_matcher.struct_match import (
     ReducedStructRep,
     generate_primitive_cells,
@@ -430,11 +430,11 @@ def log_all_unique_structures(
     with open(file_name, "a") as f:
         print("unique_structures:", file=f)
         for idx1, _str in enumerate(unique_structs):
-            print(f"  - struct_No: {idx1+1}", file=f)
+            print(f"  - struct_No: {idx1 + 1}", file=f)
             print("    structures:", file=f)
             for idx2, _str in enumerate(unique_structs[idx1]):
-                print(f"    - sub_struct_No: '{idx1+1}_{idx2+1}'", file=f)
-                print(f"      poscar_name: {_str.struct_path}", file=f)
+                print(f"    - sub_struct_No: '{idx1 + 1}_{idx2 + 1}'", file=f)
+                print(f"      struct_path: {_str.struct_path}", file=f)
                 print(f"      pressure: {_str.pressure}", file=f)
                 print(f"      enthalpy: {_str.energy}", file=f)
                 print(f"      axis: {_str.axis_abc}", file=f)
@@ -460,7 +460,7 @@ def log_all_unique_structures(
                 _res["energy"] = _str.energy
                 _res["pressure"] = None
                 _res["spg_list"] = _str.spg_list
-                _res["struct_no"] = f"{idx1 + 1}_{idx2+1}"
+                _res["struct_no"] = f"{idx1 + 1}_{idx2 + 1}"
                 _res["is_ghost_minima"] = False
                 rss_results.append(_res)
             if unique_structs_prop is not None:

{rsspolymlp-0.3.4 → rsspolymlp-0.4.0}/src/rsspolymlp/api/cli_rsspolymlp.py

@@ -4,9 +4,9 @@ from rsspolymlp.api.rsspolymlp import (
     rss_ghost_minima_cands,
     rss_ghost_minima_validate,
     rss_init_struct,
+    rss_opt,
     rss_phase_analysis,
     rss_polymlp,
-    rss_run_parallel,
     rss_summarize,
     rss_uniq_struct,
 )
@@ -21,9 +21,9 @@ def run():
         help="Mode: Initial random structure generation",
     )
     parser.add_argument(
-        "--rss_parallel",
+        "--rss_opt",
         action="store_true",
-        help="Mode: RSS using the polynomial MLP in parallel",
+        help="Mode: RSS using the polynomial MLP",
     )
     parser.add_argument(
         "--rss_single",
@@ -100,7 +100,7 @@ def run():
         help="Minimum interatomic distance in initial structure (angstrom)",
     )
 
-    # --rss_parallel mode
+    # --rss_opt mode
     parser.add_argument(
         "--pot",
         nargs="*",
@@ -108,6 +108,12 @@ def run():
         default=["polymlp.yaml"],
         help="Potential file for polynomial MLP",
     )
+    parser.add_argument(
+        "--init_poscars_dir",
+        type=str,
+        default="initial_struct",
+        help="Directory containing POSCARs describing initial structures",
+    )
     parser.add_argument(
         "--n_opt_str",
         type=int,
@@ -131,6 +137,7 @@ def run():
     parser.add_argument(
         "--solver_method", type=str, default="CG", help="Type of solver"
     )
+    parser.add_argument("--gtol", type=float, default=1e-6, help="")
     parser.add_argument(
         "--c_maxiter",
         type=int,
@@ -260,12 +267,14 @@ def run():
             max_volume=args.max_volume,
         )
 
-    if args.rss_parallel:
-        rss_run_parallel(
+    if args.rss_opt:
+        rss_opt(
             pot=args.pot,
+            init_poscars_dir=args.init_poscars_dir,
             pressure=args.pressure,
             with_symmetry=args.symmetry,
             solver_method=args.solver_method,
+            gtol=args.gtol,
             c_maxiter=args.c_maxiter,
             n_opt_str=args.n_opt_str,
             not_stop_rss=args.not_stop_rss,
@@ -292,6 +301,7 @@ def run():
             max_volume=args.max_volume,
             least_distance=args.least_distance,
             solver_method=args.solver_method,
+            gtol=args.gtol,
             not_stop_rss=args.not_stop_rss,
             num_process=args.num_process,
             backend=args.backend,