yu-mcal 0.1.6__py3-none-any.whl → 0.2.1__py3-none-any.whl

mcal/mcal.py

@@ -6,6 +6,9 @@ from pathlib import Path
 from time import time
 from typing import Dict, List, Literal, Optional, Tuple, Union
 
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
 import numpy as np
 from numpy.typing import NDArray
 from tcal import Tcal
@@ -33,40 +36,41 @@ def main():
     --------
     Basic usage:
         - Calculate p-type mobility for xxx crystal\n
-        $ python hop_mcal.py xxx.cif p
+        $ mcal xxx.cif p
 
         - Calculate n-type mobility for xxx crystal\n
-        $ python hop_mcal.py xxx.cif n
+        $ mcal xxx.cif n
 
     With resource options:
         - Use 8 CPUs and 16GB memory\n
-        $ python hop_mcal.py xxx.cif p -c 8 -m 16
+        $ mcal xxx.cif p -c 8 -m 16
 
         - Use different calculation method (default is B3LYP/6-31G(d,p))\n
-        $ python hop_mcal.py xxx.cif p -M "B3LYP/6-311G(d,p)"
+        $ mcal xxx.cif p -M "B3LYP/6-311G(d,p)"
 
     High-precision calculation:
         - Calculate all transfer integrals without speedup using moment of inertia and distance between centers of weight\n
-        $ python hop_mcal.py xxx.cif p --fullcal
-
-        - Expand calculation range to 3x3x3 supercell\n
-        $ python hop_mcal.py xxx.cif p --cellsize 1
+        $ mcal xxx.cif p --fullcal
 
         - Expand calculation range to 5x5x5 supercell to widen transfer integral calculation range\n
-        $ python hop_mcal.py xxx.cif p --cellsize 2
+        $ mcal xxx.cif p --cellsize 2
 
     Resume and save results:
         - Resume from existing calculations\n
-        $ python hop_mcal.py xxx.cif p --resume
+        $ mcal xxx.cif p --resume
 
         - Save results to pickle file\n
-        $ python hop_mcal.py xxx.cif p --pickle
+        $ mcal xxx.cif p --pickle
 
         - Read results from existing pickle file\n
-        $ python hop_mcal.py xxx_result.pkl p -rp
+        $ mcal xxx_result.pkl p -rp
 
         - Read results from existing log files without running Gaussian\n
-        $ python hop_mcal.py xxx.cif p -r
+        $ mcal xxx.cif p -r
+
+    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
@@ -119,6 +123,13 @@ def main():
         help='use Ordinary Differential Equation method to calculate diffusion coefficient',
         action='store_true',
     )
+    parser.add_argument(
+        '--plot-plane',
+        help='plot mobility tensor in 2D plane (Examples: ab, ac, ba, bc, ca, cb (default is ab))',
+        type=str,
+        default=None,
+        choices=['ab', 'ac', 'ba', 'bc', 'ca', 'cb'],
+    )
     parser.add_argument(
         '--resume',
         help='resume calculation',
@@ -140,11 +151,11 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
 
     print('----------------------------------------')
-    print(' mcal 0.1.6 (2026/01/29) by Matsui Lab. ')
+    print(' mcal 0.2.1 (2026/01/29) by Matsui Lab. ')
     print('----------------------------------------')
 
     if args.read_pickle:
-        read_pickle(args.file)
+        read_pickle(args.file, args.plot_plane)
         exit()
 
     print(f'\nCalculate as {args.osc_type}-type organic semiconductor.')
@@ -352,6 +363,14 @@ def main():
                 'mobility_vector': vector
             }, f)
 
+    if args.plot_plane:
+        plot_mobility_2d(
+            Path(f'{cif_path_without_ext}_result.pkl'),
+            mu,
+            cif_reader.lattice,
+            args.plot_plane
+        )
+
     Tcal.print_timestamp()
     end_time = time()
     elapsed_time = end_time - start_time
@@ -720,6 +739,82 @@ def create_ti_gjf(
     gjf_maker.export_gjf(file_name=gjf_basename, save_dir=save_dir)
 
 
+def plot_mobility_2d(
+    save_path: Path,
+    mobility_tensor: NDArray[np.float64],
+    lattice: NDArray[np.float64],
+    plane: Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb'] = 'ab'
+) -> None:
+    """Plot mobility tensor in 2D plane.
+
+    Parameters
+    ----------
+    save_path : Path
+        Path to save the plot
+    mobility_tensor : NDArray[np.float64]
+        Mobility tensor
+    lattice : NDArray[np.float64]
+        Lattice vectors [Å]
+    plane : Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb']
+        Plane to plot, by default 'ab'
+    """
+    print(f"Plot mobility in {plane} plane.")
+    angle_list = np.arange(0, 360, 1)
+    mobility_values = []
+
+    a_vec = lattice[0]
+    b_vec = lattice[1]
+    c_vec = lattice[2]
+    if plane == 'ab':
+        v1, v2, = a_vec, b_vec
+    elif plane == 'ba':
+        v1, v2, = b_vec, a_vec
+    elif plane == 'bc':
+        v1, v2, = b_vec, c_vec
+    elif plane == 'cb':
+        v1, v2, = c_vec, b_vec
+    elif plane == 'ac':
+        v1, v2, = a_vec, c_vec
+    elif plane == 'ca':
+        v1, v2 = c_vec, a_vec
+
+    # Angle between the two specified crystal axes
+    second_axis_angle = np.rad2deg(np.arccos(np.dot(v1, v2) / (np.linalg.norm(v1) * np.linalg.norm(v2))))
+    print('Crystal axis directions in the plotted plane:')
+    print(f'{plane[0]}-axis: 0.0 deg')
+    print(f'{plane[1]}-axis: {second_axis_angle:.1f} deg')
+    print()
+
+    # Gram–Schmidt orthonormalization
+    e1 = v1 / np.linalg.norm(v1)
+    e2 = v2 - np.dot(v2, e1) * e1
+    e2 = e2 / np.linalg.norm(e2)
+
+    for angle in angle_list:
+        phi = np.deg2rad(angle)
+        direction = np.cos(phi) * e1 + np.sin(phi) * e2
+        mobility_value = direction @ mobility_tensor @ direction
+        mobility_values.append(mobility_value)
+
+    plt.rcParams['font.size'] = 12
+    width_cm, height_cm = 20, 8
+    width_inch, height_inch = width_cm / 2.54, height_cm / 2.54
+
+    fig, ax = plt.subplots(subplot_kw={'projection': 'polar'}, tight_layout=True, figsize=(width_inch, height_inch))
+    ax.set_theta_zero_location('E')
+    ax.grid(True, linestyle='--', linewidth=0.5)
+    ax.plot(np.deg2rad(angle_list), mobility_values, linewidth=2)
+
+    ax.set_rlim(bottom=0)
+    ax.set_xticks(np.arange(0, 2*np.pi, np.pi/6))
+    ax.tick_params(axis="x", pad=5)
+    ax.set_ylabel(R'Mobility [$\mathrm{cm}^2 \mathrm{V}^{-1} \mathrm{s}^{-1}$]')
+    ax.yaxis.set_label_coords(-0.2, 0.5)
+    ax.set_rlabel_position(90)
+    plt.savefig(save_path.parent / f"{save_path.stem}_{plane}.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+
 def print_mobility(value: NDArray[np.float64], vector: NDArray[np.float64], sim_type: Literal['MC', 'ODE'] = ''):
     """Print mobility and mobility vector
 
@@ -811,14 +906,24 @@ def print_transfer_integral(osc_type: Literal['p', 'n'], transfer: float):
     print(f'{mol_orb[osc_type]}: {transfer:12.6g} eV\n')
 
 
-def read_pickle(file_name: str):
+def read_pickle(
+    file_name: str,
+    plot_plane: Optional[Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb']] = None
+) -> None:
+    """Read pickle file and plot mobility tensor in 2D plane.
+
+    Parameters
+    ----------
+    file_name : str
+        Path to the pickle file
+    plot_plane : Optional[Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb']]
+        Plane to plot, by default None
+    """
     print(f'\nInput File Name: {file_name}')
 
     with open(file_name, 'rb') as f:
         results = pickle.load(f)
 
-    # print(results)
-
     print(f'\nCalculate as {results["osc_type"]}-type organic semiconductor.')
 
     print_reorg_energy(results['osc_type'], results['reorganization'])
@@ -834,6 +939,14 @@ def read_pickle(file_name: str):
 
     print_mobility(results['mobility_value'], results['mobility_vector'])
 
+    if plot_plane:
+        plot_mobility_2d(
+            Path(file_name).with_suffix(''),
+            results['mobility_tensor'],
+            results['lattice'],
+            plot_plane,
+        )
+
 
 class OSCTypeError(Exception):
     """Exception for semiconductor type"""

{yu_mcal-0.1.6.dist-info → yu_mcal-0.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.6
+Version: 0.2.1
 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>
@@ -40,6 +40,7 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
+Requires-Dist: matplotlib>=3.9.4
 Requires-Dist: numpy>=2.0.2
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: yu-tcal==3.1.0
@@ -57,6 +58,7 @@ Description-Content-Type: text/markdown
 * Python 3.9 or newer
 * NumPy
 * Pandas
+* Matplotlib
 * yu-tcal==3.1.0
 * Gaussian 09 or 16
 
@@ -157,6 +159,14 @@ Specify the number of unit cells to expand in each direction around the central
 Save calculation results to a pickle file.
 - **Example**: `mcal xxx.cif p -p`
 
+#### `--plot-plane <plane>`
+Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
+- **Available planes**: `ab`, `ac`, `ba`, `bc`, `ca`, `cb`
+- **Default**: None (no plot generated)
+- **Examples**: 
+  - `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`

{yu_mcal-0.1.6.dist-info → yu_mcal-0.2.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 mcal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-mcal/mcal.py,sha256=LRKAcLKG8Uv0yI16zZW0GmOEiRkbUHuVWVYOrHZR014,29280
+mcal/mcal.py,sha256=1XkovOZTkSlBlyOuWjZ85BTU2VvU30gU5Zf0hgfZk_o,32816
 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
@@ -8,8 +8,8 @@ mcal/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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-0.1.6.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,,
+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,,