yu-mcal 0.1.4__py3-none-any.whl → 0.1.6__py3-none-any.whl

mcal/mcal.py

@@ -140,7 +140,7 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
 
     print('----------------------------------------')
-    print(' mcal 0.1.4 (2026/01/20) by Matsui Lab. ')
+    print(' mcal 0.1.6 (2026/01/29) by Matsui Lab. ')
     print('----------------------------------------')
 
     if args.read_pickle:
@@ -471,8 +471,8 @@ def cal_eigenvalue_decomposition(mobility_tensor: NDArray[np.float64]) -> Tuple[
     Tuple[NDArray[np.float64], NDArray[np.float64]]
         Eigenvalue(mobility value) and eigenvector(mobility vector)
     """
-    value, vector = np.linalg.eig(mobility_tensor)
-    return value, vector
+    value, vector = np.linalg.eigh(mobility_tensor)
+    return value[::-1], vector[:, ::-1]
 
 
 def cal_min_distance(

mcal/utils/cif_reader.py

@@ -1,10 +1,11 @@
-"""CifReader beta (2025/10/30)"""
+"""CifReader beta (2026/01/29)"""
 import os
 import re
+import warnings
+from collections import deque
 from itertools import product
 from pathlib import Path
 from typing import Dict, List, Literal, Tuple
-import warnings
 
 import numpy as np
 import pandas as pd
@@ -67,13 +68,26 @@ class CifReader:
         self._make_adjacency_mat()
         self._split_mols()
         self._put_unit_cell()
+        self._unwrap_molecules()
+        self._put_unit_cell()
+        # Remove duplicates again as they may occur when moving atoms into the unit cell
         self.sym_symbols, self.sym_coords = self.remove_duplicates(self.sym_symbols, self.sym_coords)
         self._make_adjacency_mat()
         self._split_mols()
         self._calc_z_value()
 
         if self._ref_z_value != 0 and self.z_value != self._ref_z_value:
-            raise ZValueIsNotMatchError('Z value is not match.')
+            raise ZValueIsNotMatchError(
+                f'Z value is not match. Z value in cif file is {self._ref_z_value}, but calculated Z value is {self.z_value}.'
+            )
+
+    def _apply_minimum_image(self):
+        """Apply minimum image convention."""
+        frac_diff = self.sym_coords[:, np.newaxis, :] - self.sym_coords[np.newaxis, :, :]
+        frac_diff = frac_diff - np.round(frac_diff)
+        cart_diff = np.dot(frac_diff, self.lattice)
+        distance = np.linalg.norm(cart_diff, axis=-1)
+        return distance
 
     def _calc_lattice(self):
         """Calculate lattice."""
@@ -128,7 +142,7 @@ class CifReader:
         num_atoms = len(self.sym_symbols)
         self.adjacency_mat = np.zeros((num_atoms, num_atoms), dtype=bool)
 
-        self.cart_coords = np.dot(self.sym_coords, self.lattice)
+        distance = self._apply_minimum_image()
 
         try:
             covalent_distance = np.array([self.COVALENT_RADII[symbol] for symbol in self.sym_symbols]) \
@@ -136,7 +150,6 @@ class CifReader:
         except KeyError:
             raise ElementPropertiesIsNotDefinedError('Element properties is not defined.')
 
-        distance = np.linalg.norm(self.cart_coords[:, np.newaxis, :] - self.cart_coords[np.newaxis, :, :], axis=-1)
         self.adjacency_mat[(distance <= covalent_distance * 1.3) & (distance != 0)] = 1
 
     def _operate_sym(self) -> None:
@@ -293,10 +306,11 @@ class CifReader:
                         if '?' not in tmp_atom_data[atom_data_index['_atom_site_label']]:
                             if atom_data_index['_atom_site_type_symbol'] is None:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
-                                symbol = symbol_label
-                                for s in ['A', 'B', 'C']:
-                                    symbol = symbol.replace(s, '')
-                                symbol = re.sub(r'\d+', '', symbol)
+                                symbol = re.match(r'[A-Z][a-z]?', symbol_label)
+                                if symbol:
+                                    symbol = symbol.group(0)
+                                else:
+                                    raise ValueError(f'Symbol label {symbol_label} is not valid.')
                             else:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
                                 symbol = tmp_atom_data[atom_data_index['_atom_site_type_symbol']]
@@ -310,11 +324,10 @@ class CifReader:
                     # get symmetry operation information
                     elif is_read_sym:
                         if "'" in line:
-                            line = list(map(lambda x: x.strip().replace(' ', ''), line.split("'")))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                            line = list(map(lambda x: x.strip().replace(' ', '').replace("'", ""), line.split()))
                         else:
                             line = list(map(lambda x: x.strip().replace(' ', ''), line.split()))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                        self.symmetry_pos.append(line[symmetry_data_index].lower())
 
             self.symbols = np.array(self.symbols)
             self.coordinates = np.array(self.coordinates)
@@ -359,6 +372,35 @@ class CifReader:
             sub_matrix = self.adjacency_mat[np.ix_(index_group, index_group)]
             self.sub_matrices.append(sub_matrix)
 
+    def _unwrap_molecules(self):
+        """Unwrap molecules using the adjacency matrix based on the minimum image convention."""
+        for atom_group in self.bonded_atoms:
+            if len(atom_group) <= 1:
+                continue
+
+            criterion_idx = atom_group[0]
+
+            # Depth-first search
+            visited = {criterion_idx}
+            stack = deque([criterion_idx])
+
+            while stack:
+                current_idx = stack.popleft()
+                current_coord = self.sym_coords[current_idx]
+
+                for neighbor_idx in atom_group:
+                    if neighbor_idx in visited:
+                        continue
+
+                    if self.adjacency_mat[current_idx, neighbor_idx]:
+                        # Minimum image convention
+                        frac_diff = self.sym_coords[neighbor_idx] - current_coord
+                        frac_diff = frac_diff - np.round(frac_diff)
+                        self.sym_coords[neighbor_idx] = current_coord + frac_diff
+
+                        visited.add(neighbor_idx)
+                        stack.append(neighbor_idx)
+
     def calc_cen_of_weight(self, coordinates: NDArray[np.float64]) -> NDArray[np.float64]:
         """Calculate center of weight.
 

{yu_mcal-0.1.4.dist-info → yu_mcal-0.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.4
+Version: 0.1.6
 Summary: Program for the calculation of mobility tensor for organic semiconductor crystals
 Author: Koki Ozawa
 Author-email: Hiroyuki Matsui <h-matsui@yz.yamagata-u.ac.jp>

{yu_mcal-0.1.4.dist-info → yu_mcal-0.1.6.dist-info}/RECORD

@@ -1,15 +1,15 @@
 mcal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-mcal/mcal.py,sha256=dUw4CrbtrSDrez47MwwnpX-OFv3OcnArVOuaHlLixrk,29264
+mcal/mcal.py,sha256=LRKAcLKG8Uv0yI16zZW0GmOEiRkbUHuVWVYOrHZR014,29280
 mcal/calculations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mcal/calculations/hopping_mobility_model.py,sha256=eD9doesa1yVDQxzBYW0N41OyjikZb77S69I_mIMbL2g,13180
 mcal/calculations/rcal.py,sha256=CH3iV18KTM8xU7M7zKR3e1m67GbJLH8zi0j50TsUXLE,13500
 mcal/constants/element_properties.csv,sha256=_Yanl713VZQaAqPYoLNn-hXDdg01ZfkYsCLQ1SQSX8w,4073
 mcal/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mcal/utils/cif_reader.py,sha256=nhvk7y8ix4yKhyKjDaw2Luotw6YFMGbGCaeBVP6Qd5E,22901
+mcal/utils/cif_reader.py,sha256=QAV6xXMd3nfKLpJqBncA6fbGJ5kgYKDeKIx-sK_4P_M,24532
 mcal/utils/gaus_log_reader.py,sha256=nNIgBae9hRUgpmNF7eIC5LOENSo6NQmuckMM4A3HAa8,3159
 mcal/utils/gjf_maker.py,sha256=Kkh_gNcifFfhTikZar6SzoNJ7AyEBiCBXJTQkHxHX-0,8193
-yu_mcal-0.1.4.dist-info/METADATA,sha256=y_vQTgF-UcwXOuyV3BpWh9WfCAvtn5Z3bv1KmmL91k4,7890
-yu_mcal-0.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-yu_mcal-0.1.4.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
-yu_mcal-0.1.4.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
-yu_mcal-0.1.4.dist-info/RECORD,,
+yu_mcal-0.1.6.dist-info/METADATA,sha256=6qhMLEDBBrwAKLXWz7hlohj-2JI26xxrX2kuf0AF8gE,7890
+yu_mcal-0.1.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+yu_mcal-0.1.6.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
+yu_mcal-0.1.6.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
+yu_mcal-0.1.6.dist-info/RECORD,,