yu-mcal 0.2.1__py3-none-any.whl → 0.3.1__py3-none-any.whl

mcal/calculations/hopping_mobility_model.py

@@ -1,4 +1,4 @@
-"""hopping_mobility_model.py (2025/10/06)"""
+"""hopping_mobility_model.py (2026/01/29)"""
 import math
 import random
 from typing import List, Tuple
@@ -22,11 +22,11 @@ def demo():
     for d in D:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (ODE):")
-    D_ode = diffusion_coefficient_tensor_ODE(lattice, hop)
+    D_ode = _diffusion_coefficient_tensor_ODE(lattice, hop)
     for d in D_ode:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (MC):")
-    D_mc = diffusion_coefficient_tensor_MC(lattice, hop)
+    D_mc = _diffusion_coefficient_tensor_MC(lattice, hop)
     for d in D_mc:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
 
@@ -43,11 +43,11 @@ def demo():
     for d in D:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (ODE):")
-    D_ode = diffusion_coefficient_tensor_ODE(lattice, hop)
+    D_ode = _diffusion_coefficient_tensor_ODE(lattice, hop)
     for d in D_ode:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (MC):")
-    D_mc = diffusion_coefficient_tensor_MC(lattice, hop)
+    D_mc = _diffusion_coefficient_tensor_MC(lattice, hop)
     for d in D_mc:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
 
@@ -70,11 +70,11 @@ def demo():
     for d in D:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (ODE):")
-    D_ode = diffusion_coefficient_tensor_ODE(lattice, hop)
+    D_ode = _diffusion_coefficient_tensor_ODE(lattice, hop)
     for d in D_ode:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
     print("Diffusion coefficient tensor (MC):")
-    D_mc = diffusion_coefficient_tensor_MC(lattice, hop)
+    D_mc = _diffusion_coefficient_tensor_MC(lattice, hop)
     for d in D_mc:
         print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
 
@@ -220,10 +220,10 @@ def diffusion_coefficient_tensor(
     return D
 
 
-def diffusion_coefficient_tensor_ODE(
+def _diffusion_coefficient_tensor_ODE(
     lattice: NDArray[np.float64],
     hop: List[Tuple[int, int, int, int, int, float]],
-    max_steps: int = 200,
+    max_steps: int = 10000,
     size: int = 40,
     max_rate: float = 0.05
 ) -> NDArray[np.float64]:
@@ -280,10 +280,10 @@ def diffusion_coefficient_tensor_ODE(
     return D
 
 
-def diffusion_coefficient_tensor_MC(
+def _diffusion_coefficient_tensor_MC(
     lattice: NDArray[np.float64],
     hop: List[Tuple[int, int, int, int, int, float]],
-    steps: int = 100,
+    steps: int = 10000,
     particles: int = 10000
 ) -> NDArray[np.float64]:
     """Calculate diffusion coefficient tensor from Monte Carlo simulation using Gillespie algorithm.

mcal/mcal.py

@@ -18,8 +18,8 @@ from mcal.utils.gaus_log_reader import check_normal_termination
 from mcal.utils.gjf_maker import GjfMaker
 from mcal.calculations.hopping_mobility_model import (
     diffusion_coefficient_tensor,
-    diffusion_coefficient_tensor_MC,
-    diffusion_coefficient_tensor_ODE,
+    _diffusion_coefficient_tensor_MC,
+    _diffusion_coefficient_tensor_ODE,
     marcus_rate,
     mobility_tensor
 )
@@ -71,10 +71,6 @@ def main():
     Plot mobility tensor in 2D plane:
         - Plot mobility tensor in 2D plane (Examples: ab, ac, ba, bc, ca, cb (default is ab))\n
         $ python hop_mcal.py xxx.cif p --plot-plane ab
-
-    Compare calculation methods:
-        - Compare results using kinetic Monte Carlo and ODE methods\n
-        $ python hop_mcal.py xxx.cif p --mc --ode
     """
     # Error range for skipping calculation of transfer integrals using moment of inertia and distance between centers of weight.
     CENTER_OF_WEIGHT_ERROR = 1.0e-7
@@ -117,10 +113,10 @@ def main():
         help='do not process for speeding up using moment of inertia and distance between centers of weight',
         action='store_true',
     )
-    parser.add_argument('--mc', help='use Monte Carlo method to calculate diffusion coefficient', action='store_true')
+    parser.add_argument('--mc', help=argparse.SUPPRESS, action='store_true')
     parser.add_argument(
         '--ode',
-        help='use Ordinary Differential Equation method to calculate diffusion coefficient',
+        help=argparse.SUPPRESS,
         action='store_true',
     )
     parser.add_argument(
@@ -151,7 +147,7 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
 
     print('----------------------------------------')
-    print(' mcal 0.2.1 (2026/01/29) by Matsui Lab. ')
+    print(' mcal 0.3.1 (2026/02/05) by Matsui Lab. ')
     print('----------------------------------------')
 
     if args.read_pickle:
@@ -331,7 +327,7 @@ def main():
 
     ##### Simulate mobility tensor calculation using Monte Carlo method #####
     if args.mc:
-        D_MC = diffusion_coefficient_tensor_MC(cif_reader.lattice * 1e-8, hop)
+        D_MC = _diffusion_coefficient_tensor_MC(cif_reader.lattice * 1e-8, hop)
         print_tensor(D_MC, msg="Diffusion coefficient tensor (cm^2/s) (MC)")
         mu_MC = mobility_tensor(D_MC)
         print_tensor(mu_MC, msg="Mobility tensor (cm^2/Vs) (MC)")
@@ -340,7 +336,7 @@ def main():
 
     ##### Simulate mobility tensor calculation using Ordinary Differential Equation method #####
     if args.ode:
-        D_ODE = diffusion_coefficient_tensor_ODE(cif_reader.lattice * 1e-8, hop)
+        D_ODE = _diffusion_coefficient_tensor_ODE(cif_reader.lattice * 1e-8, hop)
         print_tensor(D_ODE, msg="Diffusion coefficient tensor (cm^2/s) (ODE)")
         mu_ODE = mobility_tensor(D_ODE)
         print_tensor(mu_ODE, msg="Mobility tensor (cm^2/Vs) (ODE)")

mcal/utils/cif_reader.py

@@ -1,4 +1,4 @@
-"""CifReader beta (2026/01/29)"""
+"""CifReader beta (2026/02/05)"""
 import os
 import re
 import warnings
@@ -220,9 +220,9 @@ class CifReader:
         for atom_idx in self.bonded_atoms:
             for i, c in enumerate(self.calc_cen_of_weight(self.sym_coords[atom_idx])):
                 if 1 <= c:
-                    change = -int(c)
+                    change = -np.floor(c)
                 elif c < 0:
-                    change = abs(int(c)) + 1
+                    change = np.ceil(np.abs(c))
                 else:
                     change = 0
                 self.sym_coords[atom_idx, i] += change

{yu_mcal-0.2.1.dist-info → yu_mcal-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.2.1
+Version: 0.3.1
 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>
@@ -167,16 +167,6 @@ Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
   - `mcal xxx.cif p --plot-plane ab` (plot on ab-plane)
   - `mcal xxx.cif p --plot-plane bc` (plot on bc-plane)
 
-### Diffusion Coefficient Calculation Methods
-
-#### `--mc`
-Calculate diffusion coefficient tensor using kinetic Monte Carlo method.
-- **Example**: `mcal xxx.cif p --mc`
-
-#### `--ode`
-Calculate diffusion coefficient tensor using Ordinary Differential Equation method.
-- **Example**: `mcal xxx.cif p --ode`
-
 ## Practical Usage Examples
 
 ### Basic Calculations
@@ -215,12 +205,6 @@ mcal xxx.cif p --resume
 mcal xxx.cif p -p
 ```
 
-### Comparing Diffusion Coefficients
-```bash
-# Compare with normal calculation + kinetic Monte Carlo + ODE methods
-mcal xxx.cif p --mc --ode
-```
-
 ## Output
 
 ### Standard Output

{yu_mcal-0.2.1.dist-info → yu_mcal-0.3.1.dist-info}/RECORD

@@ -1,15 +1,15 @@
 mcal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-mcal/mcal.py,sha256=1XkovOZTkSlBlyOuWjZ85BTU2VvU30gU5Zf0hgfZk_o,32816
+mcal/mcal.py,sha256=L2t1TSgCWIUQS6MMWCF4LCbxwkqcOvQtyUvJx8biaMI,32563
 mcal/calculations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mcal/calculations/hopping_mobility_model.py,sha256=eD9doesa1yVDQxzBYW0N41OyjikZb77S69I_mIMbL2g,13180
+mcal/calculations/hopping_mobility_model.py,sha256=OdeMwWKcl3Xt_86cl_jPi3D-ecIXNicAqPcLZYu3gAs,13192
 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=QAV6xXMd3nfKLpJqBncA6fbGJ5kgYKDeKIx-sK_4P_M,24532
+mcal/utils/cif_reader.py,sha256=v9Y7RRqvHrJ11vFs_cwEC9c9zddI3gpK929wDje2Q4E,24540
 mcal/utils/gaus_log_reader.py,sha256=nNIgBae9hRUgpmNF7eIC5LOENSo6NQmuckMM4A3HAa8,3159
 mcal/utils/gjf_maker.py,sha256=Kkh_gNcifFfhTikZar6SzoNJ7AyEBiCBXJTQkHxHX-0,8193
-yu_mcal-0.2.1.dist-info/METADATA,sha256=OtLCHoL8h1mqApWdTlB9-34BWqey1Spgcp8N-0m6YPA,8270
-yu_mcal-0.2.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-yu_mcal-0.2.1.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
-yu_mcal-0.2.1.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
-yu_mcal-0.2.1.dist-info/RECORD,,
+yu_mcal-0.3.1.dist-info/METADATA,sha256=XJZ_joNdQ-aAuqZJeqb6DeexGe09kBahZ_FqO7UwKzE,7818
+yu_mcal-0.3.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+yu_mcal-0.3.1.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
+yu_mcal-0.3.1.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
+yu_mcal-0.3.1.dist-info/RECORD,,