yu-mcal 0.1.0__py3-none-any.whl → 0.1.1__py3-none-any.whl

mcal/mcal.py

@@ -139,9 +139,9 @@ def main():
     filename = cif_file.stem
     cif_path_without_ext = f'{directory}/{filename}'
 
-    print('---------------------------------------')
-    print(' mcal 0.1.0 (2025/12/30) by Matsui Lab. ')
-    print('---------------------------------------')
+    print('----------------------------------------')
+    print(' mcal 0.1.1 (2026/01/08) by Matsui Lab. ')
+    print('----------------------------------------')
 
     if args.read_pickle:
         read_pickle(args.file)
@@ -312,27 +312,27 @@ def main():
         hop.append((s, t, i, j, k, marcus_rate(ti, reorg_energy)))
 
     diffusion_coef_tensor = diffusion_coefficient_tensor(cif_reader.lattice * 1e-8, hop)
-    print_tensor(diffusion_coef_tensor, msg="Diffusion coefficient tensor")
+    print_tensor(diffusion_coef_tensor, msg="Diffusion coefficient tensor (cm^2/s)")
     mu = mobility_tensor(diffusion_coef_tensor)
-    print_tensor(mu)
+    print_tensor(mu, msg="Mobility tensor (cm^2/Vs)")
     value, vector = cal_eigenvalue_decomposition(mu)
     print_mobility(value, vector)
 
     ##### Simulate mobility tensor calculation using Monte Carlo method #####
     if args.mc:
         D_MC = diffusion_coefficient_tensor_MC(cif_reader.lattice * 1e-8, hop)
-        print_tensor(D_MC, msg="Diffusion coefficient tensor (MC)")
+        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 (MC)")
+        print_tensor(mu_MC, msg="Mobility tensor (cm^2/Vs) (MC)")
         value_MC, vector_MC = cal_eigenvalue_decomposition(mu_MC)
         print_mobility(value_MC, vector_MC, sim_type='MC')
 
     ##### Simulate mobility tensor calculation using Ordinary Differential Equation method #####
     if args.ode:
         D_ODE = diffusion_coefficient_tensor_ODE(cif_reader.lattice * 1e-8, hop)
-        print_tensor(D_ODE, msg="Diffusion coefficient tensor (ODE)")
+        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 (ODE)")
+        print_tensor(mu_ODE, msg="Mobility tensor (cm^2/Vs) (ODE)")
         value_ODE, vector_ODE = cal_eigenvalue_decomposition(mu_ODE)
         print_mobility(value_ODE, vector_ODE, sim_type='ODE')
 
@@ -355,14 +355,18 @@ def main():
     Tcal.print_timestamp()
     end_time = time()
     elapsed_time = end_time - start_time
+    elapsed_time_h = int(elapsed_time // 3600)
+    elapsed_time_min = int((elapsed_time - elapsed_time_h * 3600) // 60)
+    elapsed_time_sec = int(elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60)
+    elapsed_time_ms = (elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60 - elapsed_time_sec) * 1000
     if elapsed_time < 1:
-        print(f'Elapsed Time: {elapsed_time*1000:.0f} ms')
+        print(f'Elapsed Time: {elapsed_time_ms:.0f} ms')
     elif elapsed_time < 60:
-        print(f'Elapsed Time: {elapsed_time:.0f} s')
+        print(f'Elapsed Time: {elapsed_time_sec} sec')
     elif elapsed_time < 3600:
-        print(f'Elapsed Time: {elapsed_time/60:.0f} min')
+        print(f'Elapsed Time: {elapsed_time_min} min {elapsed_time_sec} sec')
     else:
-        print(f'Elapsed Time: {elapsed_time/3600:.0f} h')
+        print(f'Elapsed Time: {elapsed_time_h} h {elapsed_time_min} min {elapsed_time_sec} sec')
 
 
 def atom_weight(symbol: str) -> float:
@@ -728,8 +732,9 @@ def print_mobility(value: NDArray[np.float64], vector: NDArray[np.float64], sim_
     sim_type : str
         Simulation type (MC or ODE)
     """
-    msg_value = 'Mobility value'
-    msg_vector = 'Mobility vector'
+    msg_value = 'Mobility eigenvalues (cm^2/Vs)'
+    msg_vector = 'Mobility eigenvectors'
+    direction = ['x', 'y', 'z']
 
     if sim_type:
         msg_value += f' ({sim_type})'
@@ -746,8 +751,9 @@ def print_mobility(value: NDArray[np.float64], vector: NDArray[np.float64], sim_
     print('-' * (len(msg_vector)+2))
     print(f' {msg_vector} ')
     print('-' * (len(msg_vector)+2))
-    for v in vector:
-        print(f"{v[0]:12.6g} {v[1]:12.6g} {v[2]:12.6g}")
+    print('       vector1      vector2      vector3')
+    for v, d in zip(vector, direction):
+        print(f'{d} {v[0]:12.6g} {v[1]:12.6g} {v[2]:12.6g}')
     print()
 
 
@@ -822,9 +828,9 @@ def read_pickle(file_name: str):
         print(f'{s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell')
         print_transfer_integral(results['osc_type'], ti)
 
-    print_tensor(results['diffusion_coefficient_tensor'], msg="Diffusion coefficient tensor")
+    print_tensor(results['diffusion_coefficient_tensor'], msg="Diffusion coefficient tensor (cm^2/s)")
 
-    print_tensor(results['mobility_tensor'])
+    print_tensor(results['mobility_tensor'], msg="Mobility tensor (cm^2/Vs)")
 
     print_mobility(results['mobility_value'], results['mobility_vector'])
 

{yu_mcal-0.1.0.dist-info → yu_mcal-0.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.0
+Version: 0.1.1
 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>
@@ -47,6 +47,7 @@ Description-Content-Type: text/markdown
 # mcal: Program for the calculation of mobility tensor for organic semiconductor crystals
 [![Python](https://img.shields.io/badge/python-3.9%20or%20newer-blue)](https://www.python.org)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![docs](https://img.shields.io/badge/docs-here-11419572)](https://matsui-lab-yamagata.github.io/mcal/)
 
 # Overview
 `mcal.py` is a tool for calculating mobility tensors of organic semiconductors. It calculates transfer integrals and reorganization energy from crystal structures, and determines mobility tensors considering anisotropy and path continuity.

{yu_mcal-0.1.0.dist-info → yu_mcal-0.1.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 mcal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-mcal/mcal.py,sha256=eL57d_vm8Rf0kAZwVgRphRvIpEB9_u1NaBSPUs_wvlI,28648
+mcal/mcal.py,sha256=Wxsl5J88VdsLK7MgppG_P3Uw38caPy6GTmXGuckxV7c,29282
 mcal/calculations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mcal/calculations/hopping_mobility_model.py,sha256=kjE_07nC4hbhWV5B37G0rtsgPqjBuHP0wsJ53rXoPOQ,13180
 mcal/calculations/rcal.py,sha256=CH3iV18KTM8xU7M7zKR3e1m67GbJLH8zi0j50TsUXLE,13500
@@ -9,8 +9,8 @@ mcal/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mcal/utils/cif_reader.py,sha256=nhvk7y8ix4yKhyKjDaw2Luotw6YFMGbGCaeBVP6Qd5E,22901
 mcal/utils/gaus_log_reader.py,sha256=nNIgBae9hRUgpmNF7eIC5LOENSo6NQmuckMM4A3HAa8,3159
 mcal/utils/gjf_maker.py,sha256=Kkh_gNcifFfhTikZar6SzoNJ7AyEBiCBXJTQkHxHX-0,8193
-yu_mcal-0.1.0.dist-info/METADATA,sha256=oBAS8ZHFduaZrGTw-O9-reJlUGEn-VJNPxbl4iQvS7E,7630
-yu_mcal-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-yu_mcal-0.1.0.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
-yu_mcal-0.1.0.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
-yu_mcal-0.1.0.dist-info/RECORD,,
+yu_mcal-0.1.1.dist-info/METADATA,sha256=7j9QEcJfmDr-ctUKn9APFdrR5HQH2fTD7sWM6zYH7Ao,7734
+yu_mcal-0.1.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+yu_mcal-0.1.1.dist-info/entry_points.txt,sha256=_0xZR3t9qvFSd9L6Iot03NixVLxXioEY19L6w3Fs1Ew,40
+yu_mcal-0.1.1.dist-info/licenses/LICENSE,sha256=JP8vm7gYE73jLgnMFTOLNo_RnH88RrB4Goyh7H_muto,1072
+yu_mcal-0.1.1.dist-info/RECORD,,