yu-mcal 0.1.0__tar.gz → 0.1.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (66) hide show
  1. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/PKG-INFO +2 -1
  2. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/README.md +1 -0
  3. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/README_ja.md +2 -0
  4. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/documentation_options.js +1 -1
  5. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/genindex.html +4 -4
  6. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/index.html +6 -6
  7. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.calculations.html +4 -4
  8. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.html +4 -4
  9. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.utils.html +4 -4
  10. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/modules.html +5 -5
  11. yu_mcal-0.1.1/docs/objects.inv +0 -0
  12. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/py-modindex.html +4 -4
  13. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/search.html +4 -4
  14. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/searchindex.js +1 -1
  15. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/pyproject.toml +1 -1
  16. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/mcal.py +25 -19
  17. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/uv.lock +1 -1
  18. yu_mcal-0.1.0/docs/objects.inv +0 -0
  19. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/.gitignore +0 -0
  20. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/.python-version +0 -0
  21. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/LICENSE +0 -0
  22. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/.nojekyll +0 -0
  23. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_sources/index.rst.txt +0 -0
  24. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_sources/mcal.calculations.rst.txt +0 -0
  25. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_sources/mcal.rst.txt +0 -0
  26. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_sources/mcal.utils.rst.txt +0 -0
  27. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_sources/modules.rst.txt +0 -0
  28. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/autodoc_pydantic.css +0 -0
  29. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/basic.css +0 -0
  30. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/debug.css +0 -0
  31. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/doctools.js +0 -0
  32. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/file.png +0 -0
  33. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/language_data.js +0 -0
  34. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/minus.png +0 -0
  35. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/plus.png +0 -0
  36. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/pygments.css +0 -0
  37. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/scripts/furo-extensions.js +0 -0
  38. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/scripts/furo.js +0 -0
  39. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/scripts/furo.js.LICENSE.txt +0 -0
  40. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/scripts/furo.js.map +0 -0
  41. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/searchtools.js +0 -0
  42. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/skeleton.css +0 -0
  43. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/sphinx_highlight.js +0 -0
  44. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/styles/furo-extensions.css +0 -0
  45. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/styles/furo-extensions.css.map +0 -0
  46. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/styles/furo.css +0 -0
  47. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/styles/furo.css.map +0 -0
  48. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/Makefile +0 -0
  49. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/make.bat +0 -0
  50. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/conf.py +0 -0
  51. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/index.rst +0 -0
  52. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/mcal.calculations.rst +0 -0
  53. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/mcal.rst +0 -0
  54. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/mcal.utils.rst +0 -0
  55. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/modules.rst +0 -0
  56. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/requirements.txt +0 -0
  57. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/__init__.py +0 -0
  58. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/calculations/__init__.py +0 -0
  59. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/calculations/hopping_mobility_model.py +0 -0
  60. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/calculations/rcal.py +0 -0
  61. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/calculations/tcal.py +0 -0
  62. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/constants/element_properties.csv +0 -0
  63. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/utils/__init__.py +0 -0
  64. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/utils/cif_reader.py +0 -0
  65. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/utils/gaus_log_reader.py +0 -0
  66. {yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/utils/gjf_maker.py +0 -0
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: yu-mcal
3
- Version: 0.1.0
3
+ Version: 0.1.1
4
4
  Summary: Program for the calculation of mobility tensor for organic semiconductor crystals
5
5
  Author: Koki Ozawa
6
6
  Author-email: Hiroyuki Matsui <h-matsui@yz.yamagata-u.ac.jp>
@@ -47,6 +47,7 @@ Description-Content-Type: text/markdown
47
47
  # mcal: Program for the calculation of mobility tensor for organic semiconductor crystals
48
48
  [![Python](https://img.shields.io/badge/python-3.9%20or%20newer-blue)](https://www.python.org)
49
49
  [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
50
+ [![docs](https://img.shields.io/badge/docs-here-11419572)](https://matsui-lab-yamagata.github.io/mcal/)
50
51
 
51
52
  # Overview
52
53
  `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 → yu_mcal-0.1.1}/README.md RENAMED
@@ -1,6 +1,7 @@
1
1
  # mcal: Program for the calculation of mobility tensor for organic semiconductor crystals
2
2
  [![Python](https://img.shields.io/badge/python-3.9%20or%20newer-blue)](https://www.python.org)
3
3
  [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
4
+ [![docs](https://img.shields.io/badge/docs-here-11419572)](https://matsui-lab-yamagata.github.io/mcal/)
4
5
 
5
6
  # Overview
6
7
  `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 → yu_mcal-0.1.1}/README_ja.md RENAMED
@@ -1,6 +1,8 @@
1
1
  # mcal: 有機半導体結晶の移動度テンソル計算プログラム
2
2
  [![Python](https://img.shields.io/badge/python-3.9%20or%20newer-blue)](https://www.python.org)
3
3
  [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
4
+ [![docs](https://img.shields.io/badge/docs-here-11419572)](https://matsui-lab-yamagata.github.io/mcal/)
5
+
4
6
 
5
7
  # 概要
6
8
  `mcal.py`は有機半導体の移動度テンソルを計算するツールです。結晶構造から移動積分と再配列エネルギーを計算し、異方性と経路の連続性を考慮して移動度テンソルを算出します。
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/documentation_options.js RENAMED
@@ -1,5 +1,5 @@
1
1
  const DOCUMENTATION_OPTIONS = {
2
- VERSION: '0.1.0',
2
+ VERSION: '0.1.1',
3
3
  LANGUAGE: 'en',
4
4
  COLLAPSE_INDEX: false,
5
5
  BUILDER: 'html',
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/genindex.html RENAMED
@@ -4,7 +4,7 @@
4
4
  <meta name="viewport" content="width=device-width,initial-scale=1">
5
5
  <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#"><link rel="search" title="Search" href="search.html">
6
6
 
7
- <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 --><title>Index - mcal 0.1.0 documentation</title>
7
+ <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 --><title>Index - mcal 0.1.1 documentation</title>
8
8
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
9
9
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
10
10
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -160,7 +160,7 @@
160
160
  </label>
161
161
  </div>
162
162
  <div class="header-center">
163
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
163
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
164
164
  </div>
165
165
  <div class="header-right">
166
166
  <div class="theme-toggle-container theme-toggle-header">
@@ -181,7 +181,7 @@
181
181
 
182
182
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
183
183
 
184
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
184
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
185
185
 
186
186
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
187
187
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -709,7 +709,7 @@
709
709
 
710
710
  </aside>
711
711
  </div>
712
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
712
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
713
713
  <script src="_static/doctools.js?v=9a2dae69"></script>
714
714
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
715
715
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/index.html RENAMED
@@ -6,7 +6,7 @@
6
6
  <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="mcal" href="modules.html">
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
- <title>mcal 0.1.0 documentation</title>
9
+ <title>mcal 0.1.1 documentation</title>
10
10
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="#"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="#"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="#">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -240,7 +240,7 @@
240
240
  </div>
241
241
  <article role="main" id="furo-main-content">
242
242
  <section id="mcal-release-documentation">
243
- <h1>mcal 0.1.0 Documentation<a class="headerlink" href="#mcal-release-documentation" title="Link to this heading">¶</a></h1>
243
+ <h1>mcal 0.1.1 Documentation<a class="headerlink" href="#mcal-release-documentation" title="Link to this heading">¶</a></h1>
244
244
  <a class="reference external image-reference" href="https://www.python.org"><img alt="Python" src="https://img.shields.io/badge/python-3.9%20or%20newer-blue" />
245
245
  </a>
246
246
  <a class="reference external image-reference" href="https://opensource.org/licenses/MIT"><img alt="License: MIT" src="https://img.shields.io/badge/License-MIT-blue.svg" />
@@ -614,7 +614,7 @@ mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </s
614
614
  <div class="toc-tree-container">
615
615
  <div class="toc-tree">
616
616
  <ul>
617
- <li><a class="reference internal" href="#">mcal 0.1.0 Documentation</a><ul>
617
+ <li><a class="reference internal" href="#">mcal 0.1.1 Documentation</a><ul>
618
618
  <li><a class="reference internal" href="#overview">Overview</a><ul>
619
619
  <li><a class="reference internal" href="#features">Features</a></li>
620
620
  </ul>
@@ -692,7 +692,7 @@ mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </s
692
692
 
693
693
  </aside>
694
694
  </div>
695
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
695
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
696
696
  <script src="_static/doctools.js?v=9a2dae69"></script>
697
697
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
698
698
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.calculations.html RENAMED
@@ -6,7 +6,7 @@
6
6
  <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="mcal.utils package" href="mcal.utils.html"><link rel="prev" title="mcal package" href="mcal.html">
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
- <title>mcal.calculations package - mcal 0.1.0 documentation</title>
9
+ <title>mcal.calculations package - mcal 0.1.1 documentation</title>
10
10
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -993,7 +993,7 @@ If it is 3, skip dimer calculation.</p></li>
993
993
 
994
994
  </aside>
995
995
  </div>
996
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
996
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
997
997
  <script src="_static/doctools.js?v=9a2dae69"></script>
998
998
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
999
999
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.html RENAMED
@@ -6,7 +6,7 @@
6
6
  <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="mcal.calculations package" href="mcal.calculations.html"><link rel="prev" title="mcal" href="modules.html">
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
- <title>mcal package - mcal 0.1.0 documentation</title>
9
+ <title>mcal package - mcal 0.1.1 documentation</title>
10
10
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -808,7 +808,7 @@
808
808
 
809
809
  </aside>
810
810
  </div>
811
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
811
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
812
812
  <script src="_static/doctools.js?v=9a2dae69"></script>
813
813
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
814
814
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/mcal.utils.html RENAMED
@@ -6,7 +6,7 @@
6
6
  <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="prev" title="mcal.calculations package" href="mcal.calculations.html">
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
- <title>mcal.utils package - mcal 0.1.0 documentation</title>
9
+ <title>mcal.utils package - mcal 0.1.1 documentation</title>
10
10
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -831,7 +831,7 @@ For example, (0, 0, 0) is the origin unit cell, (1, 0, 0) is one unit cell away
831
831
 
832
832
  </aside>
833
833
  </div>
834
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
834
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
835
835
  <script src="_static/doctools.js?v=9a2dae69"></script>
836
836
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
837
837
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/modules.html RENAMED
@@ -3,10 +3,10 @@
3
3
  <head><meta charset="utf-8">
4
4
  <meta name="viewport" content="width=device-width,initial-scale=1">
5
5
  <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
6
- <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="mcal package" href="mcal.html"><link rel="prev" title="mcal 0.1.0 Documentation" href="index.html">
6
+ <link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="mcal package" href="mcal.html"><link rel="prev" title="mcal 0.1.1 Documentation" href="index.html">
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
- <title>mcal - mcal 0.1.0 documentation</title>
9
+ <title>mcal - mcal 0.1.1 documentation</title>
10
10
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -340,7 +340,7 @@
340
340
 
341
341
  </aside>
342
342
  </div>
343
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
343
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
344
344
  <script src="_static/doctools.js?v=9a2dae69"></script>
345
345
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
346
346
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
yu_mcal-0.1.1/docs/objects.inv ADDED
Binary file
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/py-modindex.html RENAMED
@@ -4,7 +4,7 @@
4
4
  <meta name="viewport" content="width=device-width,initial-scale=1">
5
5
  <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html">
6
6
 
7
- <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 --><title>Python Module Index - mcal 0.1.0 documentation</title>
7
+ <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 --><title>Python Module Index - mcal 0.1.1 documentation</title>
8
8
  <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
9
9
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
10
10
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
@@ -160,7 +160,7 @@
160
160
  </label>
161
161
  </div>
162
162
  <div class="header-center">
163
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
163
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
164
164
  </div>
165
165
  <div class="header-right">
166
166
  <div class="theme-toggle-container theme-toggle-header">
@@ -181,7 +181,7 @@
181
181
 
182
182
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
183
183
 
184
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
184
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
185
185
 
186
186
  </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
187
187
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -337,7 +337,7 @@
337
337
 
338
338
  </aside>
339
339
  </div>
340
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
340
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
341
341
  <script src="_static/doctools.js?v=9a2dae69"></script>
342
342
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
343
343
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/search.html RENAMED
@@ -7,7 +7,7 @@
7
7
 
8
8
  <!-- Generated with Sphinx 7.4.7 and Furo 2025.12.19 -->
9
9
  <meta name="robots" content="noindex" />
10
- <title>Search - mcal 0.1.0 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
10
+ <title>Search - mcal 0.1.1 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d111a655" />
11
11
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=7bdb33bb" />
12
12
  <link rel="stylesheet" type="text/css" href="_static/autodoc_pydantic.css" />
13
13
  <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=8dab3a3b" />
@@ -162,7 +162,7 @@
162
162
  </label>
163
163
  </div>
164
164
  <div class="header-center">
165
- <a href="index.html"><div class="brand">mcal 0.1.0 documentation</div></a>
165
+ <a href="index.html"><div class="brand">mcal 0.1.1 documentation</div></a>
166
166
  </div>
167
167
  <div class="header-right">
168
168
  <div class="theme-toggle-container theme-toggle-header">
@@ -183,7 +183,7 @@
183
183
 
184
184
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
185
185
 
186
- <span class="sidebar-brand-text">mcal 0.1.0 documentation</span>
186
+ <span class="sidebar-brand-text">mcal 0.1.1 documentation</span>
187
187
 
188
188
  </a><form class="sidebar-search-container" method="get" action="#" role="search">
189
189
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -276,7 +276,7 @@
276
276
 
277
277
  </aside>
278
278
  </div>
279
- </div><script src="_static/documentation_options.js?v=01f34227"></script>
279
+ </div><script src="_static/documentation_options.js?v=a58bc63e"></script>
280
280
  <script src="_static/doctools.js?v=9a2dae69"></script>
281
281
  <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
282
282
  <script src="_static/scripts/furo.js?v=46bd48cc"></script>
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/searchindex.js RENAMED
@@ -1 +1 @@
1
- Search.setIndex({"alltitles": {"--cellsize <number>": [[0, "cellsize-number"]], "--fullcal": [[0, "fullcal"]], "--mc": [[0, "mc"]], "--ode": [[0, "ode"]], "--resume": [[0, "resume"]], "-M, --method <method>": [[0, "m-method-method"]], "-c, --cpu <number>": [[0, "c-cpu-number"]], "-g, --g09": [[0, "g-g09"]], "-m, --mem <memory>": [[0, "m-mem-memory"]], "-p, --pickle": [[0, "p-pickle"]], "-r, --read": [[0, "r-read"]], "-rp, --read_pickle": [[0, "rp-read-pickle"]], "API Reference": [[0, "api-reference"], [0, null]], "Authors": [[0, "authors"]], "Basic Calculations": [[0, "basic-calculations"]], "Basic Examples": [[0, "basic-examples"]], "Basic Usage": [[0, "basic-usage"]], "Calculation Control": [[0, "calculation-control"]], "Calculation Settings": [[0, "calculation-settings"]], "Comparing Diffusion Coefficients": [[0, "comparing-diffusion-coefficients"]], "Diffusion Coefficient Calculation Methods": [[0, "diffusion-coefficient-calculation-methods"]], "Features": [[0, "features"]], "High-Precision Calculations": [[0, "high-precision-calculations"]], "If calculation stops midway": [[0, "if-calculation-stops-midway"]], "Indices and Tables": [[0, "indices-and-tables"]], "Installation": [[0, "installation"]], "License": [[0, "license"]], "Memory shortage error": [[0, "memory-shortage-error"]], "Module contents": [[1, "module-mcal"], [2, "module-mcal.calculations"], [3, "module-mcal.utils"]], "Notes": [[0, "notes"]], "Options": [[0, "options"]], "Output": [[0, "output"]], "Output Settings": [[0, "output-settings"]], "Overview": [[0, "overview"]], "Practical Usage Examples": [[0, "practical-usage-examples"]], "Required Arguments": [[0, "required-arguments"]], "Requirements": [[0, "requirements"]], "Reusing Results": [[0, "reusing-results"]], "Standard Output": [[0, "standard-output"]], "Submodules": [[1, "submodules"], [2, "submodules"], [3, "submodules"]], "Subpackages": [[1, "subpackages"]], "To reduce calculation time": [[0, "to-reduce-calculation-time"]], "Troubleshooting": [[0, "troubleshooting"]], "Verify Installation": [[0, "verify-installation"]], "mcal": [[4, null]], "mcal 0.1.0 Documentation": [[0, null]], "mcal Usage Manual": [[0, "mcal-usage-manual"]], "mcal package": [[1, null]], "mcal.calculations package": [[2, null]], "mcal.calculations.hopping_mobility_model module": [[2, "module-mcal.calculations.hopping_mobility_model"]], "mcal.calculations.rcal module": [[2, "module-mcal.calculations.rcal"]], "mcal.calculations.tcal module": [[2, "module-mcal.calculations.tcal"]], "mcal.mcal module": [[1, "module-mcal.mcal"]], "mcal.utils package": [[3, null]], "mcal.utils.cif_reader module": [[3, "module-mcal.utils.cif_reader"]], "mcal.utils.gaus_log_reader module": [[3, "module-mcal.utils.gaus_log_reader"]], "mcal.utils.gjf_maker module": [[3, "module-mcal.utils.gjf_maker"]]}, "docnames": ["index", "mcal", "mcal.calculations", "mcal.utils", "modules"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["index.rst", "mcal.rst", "mcal.calculations.rst", "mcal.utils.rst", "modules.rst"], "indexentries": {"add_adjacency_mat() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_adjacency_mat", false]], "add_coordinates() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_coordinates", false]], "add_link() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.add_link", false]], "add_root() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.add_root", false]], "add_symbols() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_symbols", false]], "atom_weight() (in module mcal.mcal)": [[1, "mcal.mcal.atom_weight", false]], "atomic_pair_transfer_analysis() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.atomic_pair_transfer_analysis", false]], "atomic_weights (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.ATOMIC_WEIGHTS", false]], "cal_cen_of_weight() (in module mcal.mcal)": [[1, "mcal.mcal.cal_cen_of_weight", false]], "cal_distance_between_cen_of_weight() (in module mcal.mcal)": [[1, "mcal.mcal.cal_distance_between_cen_of_weight", false]], "cal_eigenvalue_decomposition() (in module mcal.mcal)": [[1, "mcal.mcal.cal_eigenvalue_decomposition", false]], "cal_min_distance() (in module mcal.mcal)": [[1, "mcal.mcal.cal_min_distance", false]], "cal_moment_of_inertia() (in module mcal.mcal)": [[1, "mcal.mcal.cal_moment_of_inertia", false]], "cal_pinv() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.cal_pinv", false]], "cal_transfer_integrals() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.cal_transfer_integrals", false]], "calc_cen_of_weight() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.calc_cen_of_weight", false]], "calc_reorganization() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.calc_reorganization", false]], "check_error_term() (mcal.calculations.rcal.rcal static method)": [[2, "mcal.calculations.rcal.Rcal.check_error_term", false]], "check_extension_log() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.check_extension_log", false]], "check_extension_log() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.check_extension_log", false]], "check_normal_termination() (in module mcal.utils.gaus_log_reader)": [[3, "mcal.utils.gaus_log_reader.check_normal_termination", false]], "check_normal_termination() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.check_normal_termination", false]], "check_reorganization_energy_completion() (in module mcal.mcal)": [[1, "mcal.mcal.check_reorganization_energy_completion", false]], "check_transfer_integral_completion() (in module mcal.mcal)": [[1, "mcal.mcal.check_transfer_integral_completion", false]], "cifreader (class in mcal.utils.cif_reader)": [[3, "mcal.utils.cif_reader.CifReader", false]], "close() (mcal.utils.gaus_log_reader.filereader method)": [[3, "mcal.utils.gaus_log_reader.FileReader.close", false]], "convert_cart_to_frac() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.convert_cart_to_frac", false]], "convert_frac_to_cart() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.convert_frac_to_cart", false]], "convert_xyz_to_gjf() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.convert_xyz_to_gjf", false]], "covalent_radii (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.COVALENT_RADII", false]], "create_chk_file() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.create_chk_file", false]], "create_cube_file() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.create_cube_file", false]], "create_monomer_file() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.create_monomer_file", false]], "create_reorg_gjf() (in module mcal.mcal)": [[1, "mcal.mcal.create_reorg_gjf", false]], "create_rwf_file() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.create_rwf_file", false]], "create_ti_gjf() (in module mcal.mcal)": [[1, "mcal.mcal.create_ti_gjf", false]], "custom_atomic_pair_transfer_analysis() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.custom_atomic_pair_transfer_analysis", false]], "demo() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.demo", false]], "diffusion_coefficient_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor", false]], "diffusion_coefficient_tensor_mc() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC", false]], "diffusion_coefficient_tensor_ode() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE", false]], "element_prop (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.ELEMENT_PROP", false]], "element_prop (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.ELEMENT_PROP", false]], "elementpropertiesisnotdefinederror": [[3, "mcal.utils.cif_reader.ElementPropertiesIsNotDefinedError", false]], "elements_num (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.ELEMENTS_NUM", false]], "ev (mcal.calculations.tcal.tcal attribute)": [[2, "mcal.calculations.tcal.Tcal.EV", false]], "expand_mols() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.expand_mols", false]], "export_gjf() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.export_gjf", false]], "export_mol_file() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.export_mol_file", false]], "export_unit_cell_file() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.export_unit_cell_file", false]], "export_xyz_file() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.export_xyz_file", false]], "extract_coordinates() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.extract_coordinates", false]], "extract_energy() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.extract_energy", false]], "extract_num() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.extract_num", false]], "fileio (class in mcal.utils.cif_reader)": [[3, "mcal.utils.cif_reader.FileIO", false]], "filereader (class in mcal.utils.gaus_log_reader)": [[3, "mcal.utils.gaus_log_reader.FileReader", false]], "gaustermerror": [[2, "mcal.calculations.rcal.GausTermError", false]], "gjfmaker (class in mcal.utils.gjf_maker)": [[3, "mcal.utils.gjf_maker.GjfMaker", false]], "main() (in module mcal.calculations.rcal)": [[2, "mcal.calculations.rcal.main", false]], "main() (in module mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.main", false]], "main() (in module mcal.mcal)": [[1, "mcal.mcal.main", false]], "marcus_rate() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.marcus_rate", false]], "mcal": [[1, "module-mcal", false]], "mcal.calculations": [[2, "module-mcal.calculations", false]], "mcal.calculations.hopping_mobility_model": [[2, "module-mcal.calculations.hopping_mobility_model", false]], "mcal.calculations.rcal": [[2, "module-mcal.calculations.rcal", false]], "mcal.calculations.tcal": [[2, "module-mcal.calculations.tcal", false]], "mcal.mcal": [[1, "module-mcal.mcal", false]], "mcal.utils": [[3, "module-mcal.utils", false]], "mcal.utils.cif_reader": [[3, "module-mcal.utils.cif_reader", false]], "mcal.utils.gaus_log_reader": [[3, "module-mcal.utils.gaus_log_reader", false]], "mcal.utils.gjf_maker": [[3, "module-mcal.utils.gjf_maker", false]], "mobility_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.mobility_tensor", false]], "module": [[1, "module-mcal", false], [1, "module-mcal.mcal", false], [2, "module-mcal.calculations", false], [2, "module-mcal.calculations.hopping_mobility_model", false], [2, "module-mcal.calculations.rcal", false], [2, "module-mcal.calculations.tcal", false], [3, "module-mcal.utils", false], [3, "module-mcal.utils.cif_reader", false], [3, "module-mcal.utils.gaus_log_reader", false], [3, "module-mcal.utils.gjf_maker", false]], "opt() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.opt", false]], "osctypeerror": [[1, "mcal.mcal.OSCTypeError", false], [2, "mcal.calculations.rcal.OSCTypeError", false]], "output_csv() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.output_csv", false]], "output_detail() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.output_detail", false]], "pairanalysis (class in mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.PairAnalysis", false]], "parent_dir (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.parent_dir", false]], "parent_dir (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.parent_dir", false]], "print_apta() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_apta", false]], "print_element_pairs() (mcal.calculations.tcal.pairanalysis method)": [[2, "mcal.calculations.tcal.PairAnalysis.print_element_pairs", false]], "print_largest_pairs() (mcal.calculations.tcal.pairanalysis method)": [[2, "mcal.calculations.tcal.PairAnalysis.print_largest_pairs", false]], "print_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.print_matrix", false]], "print_mobility() (in module mcal.mcal)": [[1, "mcal.mcal.print_mobility", false]], "print_reorg_energy() (in module mcal.mcal)": [[1, "mcal.mcal.print_reorg_energy", false]], "print_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.print_tensor", false]], "print_tensor() (in module mcal.mcal)": [[1, "mcal.mcal.print_tensor", false]], "print_timestamp() (mcal.calculations.rcal.rcal static method)": [[2, "mcal.calculations.rcal.Rcal.print_timestamp", false]], "print_timestamp() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.print_timestamp", false]], "print_tranfer_integral_diff_levels() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_tranfer_integral_diff_levels", false]], "print_transfer_integral() (in module mcal.mcal)": [[1, "mcal.mcal.print_transfer_integral", false]], "print_transfer_integrals() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_transfer_integrals", false]], "rcal (class in mcal.calculations.rcal)": [[2, "mcal.calculations.rcal.Rcal", false]], "read_dimer() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_dimer", false]], "read_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.read_matrix", false]], "read_monomer1() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_monomer1", false]], "read_monomer2() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_monomer2", false]], "read_pickle() (in module mcal.mcal)": [[1, "mcal.mcal.read_pickle", false]], "read_symmetric_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.read_symmetric_matrix", false]], "remove_duplicates() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.remove_duplicates", false]], "reset_variable() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.reset_variable", false]], "reversed_readline() (mcal.utils.gaus_log_reader.filereader method)": [[3, "mcal.utils.gaus_log_reader.FileReader.reversed_readline", false]], "run_gaussian() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.run_gaussian", false]], "set_charge_spin() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_charge_spin", false]], "set_coordinates() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_coordinates", false]], "set_function() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_function", false]], "set_resource() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_resource", false]], "set_symbols() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_symbols", false]], "set_title() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_title", false]], "symmetryisnotdefinederror": [[3, "mcal.utils.cif_reader.SymmetryIsNotDefinedError", false]], "tcal (class in mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.Tcal", false]], "zvalueisnotmatcherror": [[3, "mcal.utils.cif_reader.ZValueIsNotMatchError", false]]}, "objects": {"": [[1, 0, 0, "-", "mcal"]], "mcal": [[2, 0, 0, "-", "calculations"], [1, 0, 0, "-", "mcal"], [3, 0, 0, "-", "utils"]], "mcal.calculations": [[2, 0, 0, "-", "hopping_mobility_model"], [2, 0, 0, "-", "rcal"], [2, 0, 0, "-", "tcal"]], "mcal.calculations.hopping_mobility_model": [[2, 1, 1, "", "cal_pinv"], [2, 1, 1, "", "demo"], [2, 1, 1, "", "diffusion_coefficient_tensor"], [2, 1, 1, "", "diffusion_coefficient_tensor_MC"], [2, 1, 1, "", "diffusion_coefficient_tensor_ODE"], [2, 1, 1, "", "marcus_rate"], [2, 1, 1, "", "mobility_tensor"], [2, 1, 1, "", "print_tensor"]], "mcal.calculations.rcal": [[2, 2, 1, "", "GausTermError"], [2, 2, 1, "", "OSCTypeError"], [2, 3, 1, "", "Rcal"], [2, 1, 1, "", "main"]], "mcal.calculations.rcal.Rcal": [[2, 4, 1, "", "calc_reorganization"], [2, 4, 1, "", "check_error_term"], [2, 4, 1, "", "check_extension_log"], [2, 4, 1, "", "extract_energy"], [2, 4, 1, "", "print_timestamp"]], "mcal.calculations.tcal": [[2, 3, 1, "", "PairAnalysis"], [2, 3, 1, "", "Tcal"], [2, 1, 1, "", "main"]], "mcal.calculations.tcal.PairAnalysis": [[2, 4, 1, "", "print_element_pairs"], [2, 4, 1, "", "print_largest_pairs"]], "mcal.calculations.tcal.Tcal": [[2, 5, 1, "", "EV"], [2, 4, 1, "", "atomic_pair_transfer_analysis"], [2, 4, 1, "", "cal_transfer_integrals"], [2, 4, 1, "", "check_extension_log"], [2, 4, 1, "", "check_normal_termination"], [2, 4, 1, "", "convert_xyz_to_gjf"], [2, 4, 1, "", "create_cube_file"], [2, 4, 1, "", "create_monomer_file"], [2, 4, 1, "", "custom_atomic_pair_transfer_analysis"], [2, 4, 1, "", "extract_coordinates"], [2, 4, 1, "", "extract_num"], [2, 4, 1, "", "output_csv"], [2, 4, 1, "", "print_apta"], [2, 4, 1, "", "print_matrix"], [2, 4, 1, "", "print_timestamp"], [2, 4, 1, "", "print_tranfer_integral_diff_levels"], [2, 4, 1, "", "print_transfer_integrals"], [2, 4, 1, "", "read_dimer"], [2, 4, 1, "", "read_matrix"], [2, 4, 1, "", "read_monomer1"], [2, 4, 1, "", "read_monomer2"], [2, 4, 1, "", "read_symmetric_matrix"], [2, 4, 1, "", "run_gaussian"]], "mcal.mcal": [[1, 2, 1, "", "OSCTypeError"], [1, 1, 1, "", "atom_weight"], [1, 1, 1, "", "cal_cen_of_weight"], [1, 1, 1, "", "cal_distance_between_cen_of_weight"], [1, 1, 1, "", "cal_eigenvalue_decomposition"], [1, 1, 1, "", "cal_min_distance"], [1, 1, 1, "", "cal_moment_of_inertia"], [1, 1, 1, "", "check_reorganization_energy_completion"], [1, 1, 1, "", "check_transfer_integral_completion"], [1, 1, 1, "", "create_reorg_gjf"], [1, 1, 1, "", "create_ti_gjf"], [1, 1, 1, "", "main"], [1, 1, 1, "", "print_mobility"], [1, 1, 1, "", "print_reorg_energy"], [1, 1, 1, "", "print_tensor"], [1, 1, 1, "", "print_transfer_integral"], [1, 1, 1, "", "read_pickle"]], "mcal.utils": [[3, 0, 0, "-", "cif_reader"], [3, 0, 0, "-", "gaus_log_reader"], [3, 0, 0, "-", "gjf_maker"]], "mcal.utils.cif_reader": [[3, 3, 1, "", "CifReader"], [3, 2, 1, "", "ElementPropertiesIsNotDefinedError"], [3, 3, 1, "", "FileIO"], [3, 2, 1, "", "SymmetryIsNotDefinedError"], [3, 2, 1, "", "ZValueIsNotMatchError"]], "mcal.utils.cif_reader.CifReader": [[3, 5, 1, "", "ATOMIC_WEIGHTS"], [3, 5, 1, "", "COVALENT_RADII"], [3, 5, 1, "", "ELEMENT_PROP"], [3, 4, 1, "", "calc_cen_of_weight"], [3, 4, 1, "", "convert_cart_to_frac"], [3, 4, 1, "", "convert_frac_to_cart"], [3, 4, 1, "", "expand_mols"], [3, 4, 1, "", "export_unit_cell_file"], [3, 5, 1, "", "parent_dir"], [3, 4, 1, "", "remove_duplicates"]], "mcal.utils.cif_reader.FileIO": [[3, 4, 1, "", "add_adjacency_mat"], [3, 4, 1, "", "add_coordinates"], [3, 4, 1, "", "add_symbols"], [3, 4, 1, "", "export_mol_file"], [3, 4, 1, "", "export_xyz_file"]], "mcal.utils.gaus_log_reader": [[3, 3, 1, "", "FileReader"], [3, 1, 1, "", "check_normal_termination"]], "mcal.utils.gaus_log_reader.FileReader": [[3, 4, 1, "", "close"], [3, 4, 1, "", "reversed_readline"]], "mcal.utils.gjf_maker": [[3, 3, 1, "", "GjfMaker"]], "mcal.utils.gjf_maker.GjfMaker": [[3, 5, 1, "", "ELEMENTS_NUM"], [3, 5, 1, "", "ELEMENT_PROP"], [3, 4, 1, "", "add_link"], [3, 4, 1, "", "add_root"], [3, 4, 1, "", "create_chk_file"], [3, 4, 1, "", "create_rwf_file"], [3, 4, 1, "", "export_gjf"], [3, 4, 1, "", "opt"], [3, 4, 1, "", "output_detail"], [3, 5, 1, "", "parent_dir"], [3, 4, 1, "", "reset_variable"], [3, 4, 1, "", "set_charge_spin"], [3, 4, 1, "", "set_coordinates"], [3, 4, 1, "", "set_function"], [3, 4, 1, "", "set_resource"], [3, 4, 1, "", "set_symbols"], [3, 4, 1, "", "set_title"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "exception", "Python exception"], "3": ["py", "class", "Python class"], "4": ["py", "method", "Python method"], "5": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:exception", "3": "py:class", "4": "py:method", "5": "py:attribute"}, "terms": {"": [2, 3], "0": [2, 3], "00": 3, "0000": 3, "0001": 3, "0026": 3, "007": 3, "008": 3, "0080": 3, "01": 3, "011": 3, "0122": 3, "014": 3, "0140": 3, "02": 3, "03": 3, "0300": 3, "04": 3, "0400": 3, "05": [2, 3], "06": [2, 3], "07": 3, "078": 3, "08": 3, "085": 3, "09": [0, 2], "098": 3, "1": [1, 2, 3], "10": [0, 2, 3], "100": [2, 3], "10000": 2, "101": 3, "102": 3, "103": 3, "104": 3, "105": 3, "106": 3, "107": 3, "108": 3, "109": 3, "11": 3, "110": 3, "111": 3, "112": 3, "113": 3, "114": 3, "115": 3, "116": 3, "117": 3, "118": 3, "119": 3, "12": 3, "120": 3, "121": 3, "126": 3, "127": 3, "13": 3, "131": 3, "132": 3, "137": 3, "138": 3, "14": 3, "140": 3, "144": 3, "15": 3, "150": 3, "151": 3, "157": 3, "158": 3, "16": [0, 1, 2, 3], "162": 3, "164": 3, "167": 3, "168": 3, "16gb": [0, 1], "17": 3, "173": 3, "174": 3, "178": 3, "18": 3, "180": 3, "183": 3, "186": 3, "19": 3, "190": 3, "192": 3, "195": 3, "196": 3, "1e": 2, "1st": 2, "2": [0, 1, 2, 3], "20": 3, "200": [2, 3], "2000": 3, "2025": [2, 3], "204": 3, "207": 3, "208": 3, "21": 3, "22": 3, "224": 3, "23": 3, "231": 3, "232": 3, "238": 3, "24": 3, "25": 3, "26": 3, "27": 3, "27211": 2, "28": 3, "29": 3, "2nd": 2, "3": [0, 2, 3], "30": 3, "300": 2, "305": 3, "31": 3, "311g": [0, 1], "31g": [0, 1, 2], "32": [0, 3], "33": 3, "34": 3, "35": 3, "36": 3, "37": 3, "38": 3, "38456571948": 2, "39": 3, "3x3": 2, "3x3x3": [0, 1], "4": [0, 1, 2, 3], "40": [2, 3], "41": 3, "42": 3, "43": 3, "44": 3, "45": 3, "46": 3, "468": 3, "47": 3, "48": 3, "49": 3, "5": 3, "50": 3, "51": 3, "52": 3, "53": 3, "54": 3, "546": 3, "55": 3, "56": 3, "57": 3, "58": 3, "59": 3, "5x5x5": [0, 1], "6": [0, 1, 2, 3], "60": 3, "61": 3, "62": 3, "63": 3, "64": 3, "65": 3, "66": 3, "67": 3, "68": 3, "69": 3, "693": 3, "7": 3, "70": 3, "71": 3, "72": 3, "723": 3, "73": 3, "74": 3, "75": 3, "76": 3, "77": 3, "78": 3, "79": 3, "798": 3, "7x7x7": 0, "8": [0, 1, 3], "80": 3, "81": 3, "8192": 3, "82": 3, "83": 3, "84": 3, "845": 3, "85": 3, "86": 3, "867": 3, "87": 3, "88": 3, "89": 3, "9": [0, 2, 3], "90": 3, "904": 3, "906": 3, "91": 3, "92": 3, "922": 3, "93": 3, "933": 3, "938": 3, "94": 3, "9400": 3, "942": 3, "95": 3, "956": 3, "96": 3, "97": 3, "971": 3, "974": 3, "98": 3, "9800": 3, "982": 3, "99": 3, "996": 3, "998": 3, "999": 3, "A": 3, "As": 3, "At": 3, "Be": 3, "For": [0, 3], "If": [2, 3], "In": 3, "It": 0, "No": 3, "The": [0, 2, 3], "With": 1, "_description_": 2, "_io": 2, "a_transf": 2, "ac": [0, 3], "add": 3, "add_adjacency_mat": [1, 3], "add_coordin": [1, 3], "add_link": [1, 3], "add_root": [1, 3], "add_symbol": [1, 3], "adjac": 3, "adjacency_mat": 3, "after": 0, "ag": 3, "al": 3, "algorithm": 2, "all": [0, 1, 2], "am": 3, "amount": 0, "analysi": 2, "analyz": 2, "analyze_orb1": 2, "analyze_orb2": 2, "analyze_orbit": 2, "ani": [1, 2, 3], "anisotropi": [0, 1], "anoth": 1, "apta": 2, "ar": [0, 1, 3], "around": [0, 3], "arrai": [2, 3], "array_lik": 2, "atom": [1, 2, 3], "atom_weight": [1, 4], "atomic_pair_transfer_analysi": [1, 2], "atomic_weight": [1, 3], "au": 3, "awai": 3, "axi": 2, "b": [2, 3], "b3lyp": [0, 1, 2], "ba": 3, "base": [1, 2, 3], "basenam": 1, "basi": 0, "basic": 1, "beta": 3, "between": [0, 1], "bh": 3, "bi": 3, "bismuth": 3, "bk": 3, "bond": 3, "bool": [1, 2, 3], "box": 2, "br": 3, "bra": 2, "break": [2, 3], "buffer_s": 3, "c": [1, 2, 3], "ca": 3, "cal_cen_of_weight": [1, 4], "cal_distance_between_cen_of_weight": [1, 4], "cal_eigenvalue_decomposit": [1, 4], "cal_min_dist": [1, 4], "cal_moment_of_inertia": [1, 4], "cal_pinv": [1, 2], "cal_transfer_integr": [1, 2], "calc_cen_of_weight": [1, 3], "calc_reorgan": [1, 2], "calcul": [1, 3, 4], "can": 0, "carlo": [0, 1, 2], "cart_coord": 3, "cartesian": 3, "cd": 3, "ce": 3, "cell": [0, 2, 3], "cellsiz": 1, "center": [0, 1, 3], "central": 0, "cf": 3, "charg": 3, "check": [1, 2, 3], "check_error_term": [1, 2], "check_extension_log": [1, 2], "check_normal_termin": [1, 2, 3], "check_reorganization_energy_complet": [1, 4], "check_transfer_integral_complet": [1, 4], "chemic": 0, "chk": 3, "chk_rwf_name": 3, "cif": [0, 1, 3], "cif_filenam": 0, "cif_path": 3, "cif_path_without_ext": 1, "cif_read": [1, 4], "cifread": [1, 3], "cl": 3, "class": [2, 3], "close": [1, 3], "cm": 3, "cn": 3, "co": 3, "code": 2, "coeffici": 2, "column": [2, 3], "command": 2, "comment": 3, "compar": 1, "complet": 1, "comput": 0, "consid": [0, 1], "consum": 0, "contain": [1, 3], "content": 4, "continu": [0, 1], "convert": [2, 3], "convert_cart_to_frac": [1, 3], "convert_frac_to_cart": [1, 3], "convert_xyz_to_gjf": [1, 2], "coordin": [1, 2, 3], "coordinates1": 1, "coordinates2": 1, "coords1": 1, "coords2": 1, "correctli": 3, "covalent_radii": [1, 3], "covalent_radiu": 3, "cpu": [1, 3], "cpu_num": 3, "cr": 3, "creat": [0, 1, 2, 3], "create_chk_fil": [1, 3], "create_cube_fil": [1, 2], "create_monomer_fil": [1, 2], "create_reorg_gjf": [1, 4], "create_rwf_fil": [1, 3], "create_ti_gjf": [1, 4], "crystal": [0, 1, 3], "csv": 2, "cu": 3, "cube": 2, "custom_atomic_pair_transfer_analysi": [1, 2], "cutoff": 2, "cycl": 3, "d": [0, 1, 2, 3], "db": 3, "decomposit": [1, 2], "default": [0, 1, 2, 3], "defin": 3, "demo": [1, 2], "depend": 0, "detail": [0, 2, 3], "detect": 3, "determin": 0, "deuterium": 3, "dict": [1, 3], "dictionari": [1, 3], "differ": [0, 1], "differenti": [0, 2], "diffus": 2, "diffusion_coefficient_tensor": [1, 2], "diffusion_coefficient_tensor_mc": [1, 2], "diffusion_coefficient_tensor_od": [1, 2], "dimer": [1, 2], "direct": [0, 3], "directori": [1, 3], "disabl": 0, "distanc": [0, 1], "document": 3, "doubl": 2, "dtype": [1, 2, 3], "dummi": 3, "duplic": 3, "dy": 3, "e": 3, "each": 0, "eigenvalu": [0, 1, 2], "eigenvector": [0, 1], "electron": 0, "element": [2, 3], "element_prop": [1, 3], "elementpropertiesisnotdefinederror": [1, 3], "elements_num": [1, 3], "email": 0, "enabl": 0, "end": 3, "energi": [0, 1, 2], "ensur": 0, "environ": 0, "equat": [0, 2], "er": 3, "error": 2, "etc": 3, "eu": 3, "ev": [1, 2], "exampl": [1, 2, 3], "except": [1, 2, 3], "execut": [0, 2], "exist": [0, 1], "expand": [0, 1, 3], "expand_mol": [1, 3], "expand_rang": 3, "export": 3, "export_gjf": [1, 3], "export_mol_fil": [1, 3], "export_unit_cell_fil": [1, 3], "export_xyz_fil": [1, 3], "express": 2, "extens": [1, 2], "extension_log": 1, "extract": [2, 3], "extract_coordin": [1, 2], "extract_energi": [1, 2], "extract_num": [1, 2], "f": [2, 3], "fals": [2, 3], "faster": 0, "fe": 3, "file": [0, 1, 2, 3], "file_nam": [1, 2, 3], "file_path": 3, "fileio": [1, 3], "fileread": [1, 3], "fl": 3, "flerovium": 3, "float": [1, 2, 3], "float64": [1, 2, 3], "fm": 3, "fock": 2, "format": 3, "fr": 3, "frac_coord": 3, "fraction": 3, "from": [0, 1, 2, 3], "fullcal": 1, "function": [2, 3], "g16": 2, "ga": 3, "gau_com": 2, "gaus_log_read": [1, 4], "gaussian": [0, 1, 2, 3], "gaussian_command": 2, "gaustermerror": [1, 2], "gb": [0, 1, 2, 3], "gd": 3, "ge": 3, "gener": 3, "get": 1, "gillespi": 2, "git": 3, "github": 0, "given": 3, "gjf": [1, 2, 3], "gjf_basenam": 1, "gjf_file": [1, 2], "gjf_maker": [1, 4], "gjfmaker": [1, 3], "group": 3, "h": [0, 3], "he": 3, "header": 3, "header1": 3, "header2": 3, "helium": 3, "help": 0, "hf": 3, "hg": 3, "high": 1, "hiroyuki": 0, "ho": 3, "homo": [0, 2], "hop": 2, "hop_mcal": 1, "hopping_mobility_model": [1, 4], "hydrogen": 3, "i": [0, 1, 2, 3], "idx": 2, "import": 2, "includ": 2, "increas": 0, "index": [0, 3], "inertia": [0, 1], "inform": 3, "inner": 3, "input": 2, "int": [1, 2, 3], "integ": 2, "integr": [0, 1, 2], "intermolecular": 2, "interrupt": 0, "invers": 2, "ion": [1, 2], "ir": 3, "is_matrix": 2, "is_output_detail": 2, "j": [2, 3], "jp": 0, "k": [2, 3], "kei": 3, "ket": 2, "kinet": [0, 1], "koki": 0, "kr": 3, "la": 3, "laboratori": 0, "larg": 0, "larger": 0, "largest": 2, "last": 2, "lattic": 2, "lead": 3, "level": 0, "li": 3, "librari": 0, "like": 2, "line": [2, 3], "link": 3, "list": [1, 2, 3], "liter": [1, 2, 3], "lithium": 3, "livermorium": 3, "log": [0, 1, 2, 3], "log_fil": 3, "lr": 3, "lu": 3, "lumo": [0, 2], "lv": 3, "m": 1, "mai": 3, "main": [1, 2, 4], "make": 0, "manag": 3, "marcus_r": [1, 2], "match": 3, "matrix": [2, 3], "matsui": 0, "max_rat": 2, "max_step": 2, "maximum": 2, "mc": [1, 3], "md": 3, "mean": 2, "mem": [1, 2], "mem_num": 3, "mem_unit": 3, "memori": [1, 2, 3], "messag": [1, 2], "method": 1, "mg": 3, "minimum": 1, "mit": 0, "mn": 3, "mo": [2, 3], "mobil": [0, 1, 2], "mobility_tensor": [1, 2], "modul": [0, 4], "mol": 3, "molecul": [0, 2, 3], "molecular": 3, "moment": [0, 1], "monom": [1, 2], "monomer1": 1, "monomer1_atom_num": 2, "monomer2": 1, "monomolecular": 3, "mont": [0, 1, 2], "more": 0, "moscovium": 3, "msg": [1, 2], "mt": 3, "mu": 1, "must": 0, "n": [0, 1, 2, 3], "n_basi": 2, "n_bsuse": 2, "na": 3, "name": [1, 2, 3], "nan": 3, "nb": 3, "nd": 3, "ndarrai": [1, 2, 3], "ne": 3, "neg": 2, "neighbor": 1, "neighbor_mol": 1, "nest": 3, "neutral": [1, 2], "newer": 0, "nh": 3, "nhomo": 2, "ni": 3, "nlevel": 2, "nlumo": 2, "none": [1, 2, 3], "normal": [0, 1, 3], "np": [1, 2, 3], "nprocshar": 2, "number": [1, 2, 3], "numer": 2, "numpi": [0, 2], "o": 3, "object": [2, 3], "od": [1, 2], "offset": 3, "og": 3, "oganesson": 3, "one": [1, 2, 3], "onli": 2, "only_read": 2, "open": 2, "opt": [1, 3], "opt_ion": [1, 2], "opt_neutr": [1, 2], "optim": 3, "option": [1, 2, 3], "orbit": 2, "ordinari": [0, 2], "organ": [0, 2], "origin": 3, "osc_typ": [0, 1, 2], "osctypeerror": [1, 2, 4], "other": 2, "otherwis": 3, "outer": 3, "output": [2, 3], "output_apta": 2, "output_csv": [1, 2], "output_detail": [1, 3], "output_matrix": 2, "output_ti_diff_level": 2, "overlap": 2, "ozawa": 0, "p": [1, 2, 3], "pa": 3, "packag": [0, 4], "page": 0, "pair": [0, 2], "pairanalysi": [1, 2], "panda": 0, "paramet": [1, 2, 3], "parent_dir": [1, 3], "particl": 2, "path": [0, 1, 3], "pattern": 2, "pb": 3, "pd": 3, "period": 3, "pickl": 1, "pip": 0, "pkl": [0, 1], "pkl_filenam": 0, "pleas": 0, "pm": 3, "po": 3, "posixpath": 3, "pr": 3, "precis": 1, "print": [1, 2, 3], "print_apta": [1, 2], "print_element_pair": [1, 2], "print_largest_pair": [1, 2], "print_matrix": [1, 2], "print_mobl": [1, 4], "print_reorg_energi": [1, 4], "print_tensor": [1, 2, 4], "print_timestamp": [1, 2], "print_tranfer_integral_diff_level": [1, 2], "print_transfer_integr": [1, 2, 4], "process": 0, "produc": 3, "project": 0, "properti": 3, "protactinium": 3, "pseudo": 2, "pt": 3, "pu": 3, "py": [1, 2], "python": [0, 1], "quantum": 0, "r": [1, 2], "ra": 3, "rais": [2, 3], "rang": [0, 1], "rate": 2, "rb": 3, "rcal": [1, 4], "rcond": 2, "re": [2, 3], "read": [1, 2, 3], "read_dim": [1, 2], "read_matrix": [1, 2], "read_monomer1": [1, 2], "read_monomer2": [1, 2], "read_pickl": [1, 4], "read_symmetric_matrix": [1, 2], "reader": [2, 3], "readlin": 2, "regular": 2, "rel": 3, "releas": 0, "remov": 3, "remove_dupl": [1, 3], "remove_radical_flag": 3, "reorg_energi": 1, "reorgan": [0, 1, 2], "replac": 0, "repres": 3, "research": 0, "reset": 3, "reset_vari": [1, 3], "resourc": 1, "result": [1, 2], "resum": 1, "return": [1, 2, 3], "returncod": 2, "reversed_readlin": [1, 3], "rf": 3, "rg": 3, "rh": 3, "rn": 3, "roel": 0, "root": 3, "row": [2, 3], "rp": 1, "ru": 3, "run": [0, 1, 2], "run_gaussian": [1, 2], "rwf": 3, "sampl": [2, 3], "save": [0, 1, 3], "save_dir": [1, 3], "sb": 3, "sc": 3, "se": 3, "search": [0, 2], "see": 0, "semiconductor": [0, 1, 2], "set": [1, 3], "set_charge_spin": [1, 3], "set_coordin": [1, 3], "set_funct": [1, 3], "set_resourc": [1, 3], "set_symbol": [1, 3], "set_titl": [1, 3], "sg": 3, "shape": 3, "should": 2, "si": 3, "significantli": 0, "sim_typ": 1, "simul": [1, 2], "singular": 2, "size": [0, 2], "skip": [1, 2], "skip_cal": 2, "skip_monomer_num": 2, "skip_specified_c": 2, "sm": 3, "small": 2, "smaller": 0, "sn": 3, "solut": 2, "specifi": [0, 2], "speedup": [0, 1], "spin": 3, "sr": 3, "src": 3, "static": 2, "step": 2, "str": [1, 2, 3], "string": 2, "structur": [0, 3], "subaru": 3, "submodul": 4, "subpackag": 4, "subprocess": 2, "success": 2, "suffici": 0, "supercel": [0, 1], "sure": 0, "symbol": [1, 3], "symbols1": 1, "symbols2": 1, "symmetr": 2, "symmetri": 3, "symmetrix": 2, "symmetryisnotdefinederror": [1, 3], "system": 0, "t": [2, 3], "ta": 3, "target": 2, "tb": 3, "tc": 3, "tcal": [1, 4], "te": 3, "temperatur": 2, "tennessin": 3, "tensor": [0, 1, 2], "term": 2, "termin": [0, 1, 2, 3], "textiowrapp": 2, "th": [2, 3], "thi": [0, 2, 3], "thorium": 3, "ti": 3, "tight": 3, "timestamp": 2, "titl": 3, "tl": 3, "tm": 3, "tol": 3, "toler": 3, "tool": 0, "total": 2, "transfer": [0, 1, 2], "true": [1, 2, 3], "tupl": [1, 2, 3], "two": 1, "txt": 3, "type": [0, 1, 2, 3], "u": [0, 3], "under": 0, "union": 1, "uniqu": [1, 3], "unique_mol": 1, "unit": [0, 2, 3], "univers": 0, "uranium": 3, "us": [0, 1, 2, 3], "usag": 1, "user": 3, "util": [1, 4], "v": 3, "valu": [1, 2, 3], "valueerror": 2, "vari": 0, "variabl": 3, "vdw_radiu": 3, "vector": [1, 2], "w": 3, "wa": 2, "weight": [0, 1, 3], "when": 3, "whether": 2, "while": [2, 3], "widen": [0, 1], "within": 3, "without": [0, 1], "x": 3, "xe": 3, "xxx": [0, 1], "xxx_result": [0, 1], "xyz": [2, 3], "y": 3, "yamagata": 0, "yb": 3, "you": 0, "your": 0, "yu": 0, "yz": 0, "z": 3, "zero": 2, "zn": 3, "zr": 3, "zvalueisnotmatcherror": [1, 3]}, "titles": ["mcal 0.1.0 Documentation", "mcal package", "mcal.calculations package", "mcal.utils package", "mcal"], "titleterms": {"0": 0, "1": 0, "If": 0, "To": 0, "api": 0, "argument": 0, "author": 0, "basic": 0, "c": 0, "calcul": [0, 2], "cellsiz": 0, "cif_read": 3, "coeffici": 0, "compar": 0, "content": [1, 2, 3], "control": 0, "cpu": 0, "diffus": 0, "document": 0, "error": 0, "exampl": 0, "featur": 0, "fullcal": 0, "g": 0, "g09": 0, "gaus_log_read": 3, "gjf_maker": 3, "high": 0, "hopping_mobility_model": 2, "indic": 0, "instal": 0, "licens": 0, "m": 0, "manual": 0, "mc": 0, "mcal": [0, 1, 2, 3, 4], "mem": 0, "memori": 0, "method": 0, "midwai": 0, "modul": [1, 2, 3], "note": 0, "number": 0, "od": 0, "option": 0, "output": 0, "overview": 0, "p": 0, "packag": [1, 2, 3], "pickl": 0, "practic": 0, "precis": 0, "r": 0, "rcal": 2, "read": 0, "read_pickl": 0, "reduc": 0, "refer": 0, "requir": 0, "result": 0, "resum": 0, "reus": 0, "rp": 0, "set": 0, "shortag": 0, "standard": 0, "stop": 0, "submodul": [1, 2, 3], "subpackag": 1, "tabl": 0, "tcal": 2, "time": 0, "troubleshoot": 0, "usag": 0, "util": 3, "verifi": 0}})
1
+ Search.setIndex({"alltitles": {"--cellsize <number>": [[0, "cellsize-number"]], "--fullcal": [[0, "fullcal"]], "--mc": [[0, "mc"]], "--ode": [[0, "ode"]], "--resume": [[0, "resume"]], "-M, --method <method>": [[0, "m-method-method"]], "-c, --cpu <number>": [[0, "c-cpu-number"]], "-g, --g09": [[0, "g-g09"]], "-m, --mem <memory>": [[0, "m-mem-memory"]], "-p, --pickle": [[0, "p-pickle"]], "-r, --read": [[0, "r-read"]], "-rp, --read_pickle": [[0, "rp-read-pickle"]], "API Reference": [[0, "api-reference"], [0, null]], "Authors": [[0, "authors"]], "Basic Calculations": [[0, "basic-calculations"]], "Basic Examples": [[0, "basic-examples"]], "Basic Usage": [[0, "basic-usage"]], "Calculation Control": [[0, "calculation-control"]], "Calculation Settings": [[0, "calculation-settings"]], "Comparing Diffusion Coefficients": [[0, "comparing-diffusion-coefficients"]], "Diffusion Coefficient Calculation Methods": [[0, "diffusion-coefficient-calculation-methods"]], "Features": [[0, "features"]], "High-Precision Calculations": [[0, "high-precision-calculations"]], "If calculation stops midway": [[0, "if-calculation-stops-midway"]], "Indices and Tables": [[0, "indices-and-tables"]], "Installation": [[0, "installation"]], "License": [[0, "license"]], "Memory shortage error": [[0, "memory-shortage-error"]], "Module contents": [[1, "module-mcal"], [2, "module-mcal.calculations"], [3, "module-mcal.utils"]], "Notes": [[0, "notes"]], "Options": [[0, "options"]], "Output": [[0, "output"]], "Output Settings": [[0, "output-settings"]], "Overview": [[0, "overview"]], "Practical Usage Examples": [[0, "practical-usage-examples"]], "Required Arguments": [[0, "required-arguments"]], "Requirements": [[0, "requirements"]], "Reusing Results": [[0, "reusing-results"]], "Standard Output": [[0, "standard-output"]], "Submodules": [[1, "submodules"], [2, "submodules"], [3, "submodules"]], "Subpackages": [[1, "subpackages"]], "To reduce calculation time": [[0, "to-reduce-calculation-time"]], "Troubleshooting": [[0, "troubleshooting"]], "Verify Installation": [[0, "verify-installation"]], "mcal": [[4, null]], "mcal 0.1.1 Documentation": [[0, null]], "mcal Usage Manual": [[0, "mcal-usage-manual"]], "mcal package": [[1, null]], "mcal.calculations package": [[2, null]], "mcal.calculations.hopping_mobility_model module": [[2, "module-mcal.calculations.hopping_mobility_model"]], "mcal.calculations.rcal module": [[2, "module-mcal.calculations.rcal"]], "mcal.calculations.tcal module": [[2, "module-mcal.calculations.tcal"]], "mcal.mcal module": [[1, "module-mcal.mcal"]], "mcal.utils package": [[3, null]], "mcal.utils.cif_reader module": [[3, "module-mcal.utils.cif_reader"]], "mcal.utils.gaus_log_reader module": [[3, "module-mcal.utils.gaus_log_reader"]], "mcal.utils.gjf_maker module": [[3, "module-mcal.utils.gjf_maker"]]}, "docnames": ["index", "mcal", "mcal.calculations", "mcal.utils", "modules"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["index.rst", "mcal.rst", "mcal.calculations.rst", "mcal.utils.rst", "modules.rst"], "indexentries": {"add_adjacency_mat() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_adjacency_mat", false]], "add_coordinates() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_coordinates", false]], "add_link() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.add_link", false]], "add_root() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.add_root", false]], "add_symbols() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.add_symbols", false]], "atom_weight() (in module mcal.mcal)": [[1, "mcal.mcal.atom_weight", false]], "atomic_pair_transfer_analysis() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.atomic_pair_transfer_analysis", false]], "atomic_weights (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.ATOMIC_WEIGHTS", false]], "cal_cen_of_weight() (in module mcal.mcal)": [[1, "mcal.mcal.cal_cen_of_weight", false]], "cal_distance_between_cen_of_weight() (in module mcal.mcal)": [[1, "mcal.mcal.cal_distance_between_cen_of_weight", false]], "cal_eigenvalue_decomposition() (in module mcal.mcal)": [[1, "mcal.mcal.cal_eigenvalue_decomposition", false]], "cal_min_distance() (in module mcal.mcal)": [[1, "mcal.mcal.cal_min_distance", false]], "cal_moment_of_inertia() (in module mcal.mcal)": [[1, "mcal.mcal.cal_moment_of_inertia", false]], "cal_pinv() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.cal_pinv", false]], "cal_transfer_integrals() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.cal_transfer_integrals", false]], "calc_cen_of_weight() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.calc_cen_of_weight", false]], "calc_reorganization() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.calc_reorganization", false]], "check_error_term() (mcal.calculations.rcal.rcal static method)": [[2, "mcal.calculations.rcal.Rcal.check_error_term", false]], "check_extension_log() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.check_extension_log", false]], "check_extension_log() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.check_extension_log", false]], "check_normal_termination() (in module mcal.utils.gaus_log_reader)": [[3, "mcal.utils.gaus_log_reader.check_normal_termination", false]], "check_normal_termination() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.check_normal_termination", false]], "check_reorganization_energy_completion() (in module mcal.mcal)": [[1, "mcal.mcal.check_reorganization_energy_completion", false]], "check_transfer_integral_completion() (in module mcal.mcal)": [[1, "mcal.mcal.check_transfer_integral_completion", false]], "cifreader (class in mcal.utils.cif_reader)": [[3, "mcal.utils.cif_reader.CifReader", false]], "close() (mcal.utils.gaus_log_reader.filereader method)": [[3, "mcal.utils.gaus_log_reader.FileReader.close", false]], "convert_cart_to_frac() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.convert_cart_to_frac", false]], "convert_frac_to_cart() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.convert_frac_to_cart", false]], "convert_xyz_to_gjf() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.convert_xyz_to_gjf", false]], "covalent_radii (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.COVALENT_RADII", false]], "create_chk_file() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.create_chk_file", false]], "create_cube_file() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.create_cube_file", false]], "create_monomer_file() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.create_monomer_file", false]], "create_reorg_gjf() (in module mcal.mcal)": [[1, "mcal.mcal.create_reorg_gjf", false]], "create_rwf_file() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.create_rwf_file", false]], "create_ti_gjf() (in module mcal.mcal)": [[1, "mcal.mcal.create_ti_gjf", false]], "custom_atomic_pair_transfer_analysis() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.custom_atomic_pair_transfer_analysis", false]], "demo() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.demo", false]], "diffusion_coefficient_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor", false]], "diffusion_coefficient_tensor_mc() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC", false]], "diffusion_coefficient_tensor_ode() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE", false]], "element_prop (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.ELEMENT_PROP", false]], "element_prop (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.ELEMENT_PROP", false]], "elementpropertiesisnotdefinederror": [[3, "mcal.utils.cif_reader.ElementPropertiesIsNotDefinedError", false]], "elements_num (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.ELEMENTS_NUM", false]], "ev (mcal.calculations.tcal.tcal attribute)": [[2, "mcal.calculations.tcal.Tcal.EV", false]], "expand_mols() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.expand_mols", false]], "export_gjf() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.export_gjf", false]], "export_mol_file() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.export_mol_file", false]], "export_unit_cell_file() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.export_unit_cell_file", false]], "export_xyz_file() (mcal.utils.cif_reader.fileio method)": [[3, "mcal.utils.cif_reader.FileIO.export_xyz_file", false]], "extract_coordinates() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.extract_coordinates", false]], "extract_energy() (mcal.calculations.rcal.rcal method)": [[2, "mcal.calculations.rcal.Rcal.extract_energy", false]], "extract_num() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.extract_num", false]], "fileio (class in mcal.utils.cif_reader)": [[3, "mcal.utils.cif_reader.FileIO", false]], "filereader (class in mcal.utils.gaus_log_reader)": [[3, "mcal.utils.gaus_log_reader.FileReader", false]], "gaustermerror": [[2, "mcal.calculations.rcal.GausTermError", false]], "gjfmaker (class in mcal.utils.gjf_maker)": [[3, "mcal.utils.gjf_maker.GjfMaker", false]], "main() (in module mcal.calculations.rcal)": [[2, "mcal.calculations.rcal.main", false]], "main() (in module mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.main", false]], "main() (in module mcal.mcal)": [[1, "mcal.mcal.main", false]], "marcus_rate() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.marcus_rate", false]], "mcal": [[1, "module-mcal", false]], "mcal.calculations": [[2, "module-mcal.calculations", false]], "mcal.calculations.hopping_mobility_model": [[2, "module-mcal.calculations.hopping_mobility_model", false]], "mcal.calculations.rcal": [[2, "module-mcal.calculations.rcal", false]], "mcal.calculations.tcal": [[2, "module-mcal.calculations.tcal", false]], "mcal.mcal": [[1, "module-mcal.mcal", false]], "mcal.utils": [[3, "module-mcal.utils", false]], "mcal.utils.cif_reader": [[3, "module-mcal.utils.cif_reader", false]], "mcal.utils.gaus_log_reader": [[3, "module-mcal.utils.gaus_log_reader", false]], "mcal.utils.gjf_maker": [[3, "module-mcal.utils.gjf_maker", false]], "mobility_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.mobility_tensor", false]], "module": [[1, "module-mcal", false], [1, "module-mcal.mcal", false], [2, "module-mcal.calculations", false], [2, "module-mcal.calculations.hopping_mobility_model", false], [2, "module-mcal.calculations.rcal", false], [2, "module-mcal.calculations.tcal", false], [3, "module-mcal.utils", false], [3, "module-mcal.utils.cif_reader", false], [3, "module-mcal.utils.gaus_log_reader", false], [3, "module-mcal.utils.gjf_maker", false]], "opt() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.opt", false]], "osctypeerror": [[1, "mcal.mcal.OSCTypeError", false], [2, "mcal.calculations.rcal.OSCTypeError", false]], "output_csv() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.output_csv", false]], "output_detail() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.output_detail", false]], "pairanalysis (class in mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.PairAnalysis", false]], "parent_dir (mcal.utils.cif_reader.cifreader attribute)": [[3, "mcal.utils.cif_reader.CifReader.parent_dir", false]], "parent_dir (mcal.utils.gjf_maker.gjfmaker attribute)": [[3, "mcal.utils.gjf_maker.GjfMaker.parent_dir", false]], "print_apta() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_apta", false]], "print_element_pairs() (mcal.calculations.tcal.pairanalysis method)": [[2, "mcal.calculations.tcal.PairAnalysis.print_element_pairs", false]], "print_largest_pairs() (mcal.calculations.tcal.pairanalysis method)": [[2, "mcal.calculations.tcal.PairAnalysis.print_largest_pairs", false]], "print_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.print_matrix", false]], "print_mobility() (in module mcal.mcal)": [[1, "mcal.mcal.print_mobility", false]], "print_reorg_energy() (in module mcal.mcal)": [[1, "mcal.mcal.print_reorg_energy", false]], "print_tensor() (in module mcal.calculations.hopping_mobility_model)": [[2, "mcal.calculations.hopping_mobility_model.print_tensor", false]], "print_tensor() (in module mcal.mcal)": [[1, "mcal.mcal.print_tensor", false]], "print_timestamp() (mcal.calculations.rcal.rcal static method)": [[2, "mcal.calculations.rcal.Rcal.print_timestamp", false]], "print_timestamp() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.print_timestamp", false]], "print_tranfer_integral_diff_levels() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_tranfer_integral_diff_levels", false]], "print_transfer_integral() (in module mcal.mcal)": [[1, "mcal.mcal.print_transfer_integral", false]], "print_transfer_integrals() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.print_transfer_integrals", false]], "rcal (class in mcal.calculations.rcal)": [[2, "mcal.calculations.rcal.Rcal", false]], "read_dimer() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_dimer", false]], "read_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.read_matrix", false]], "read_monomer1() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_monomer1", false]], "read_monomer2() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.read_monomer2", false]], "read_pickle() (in module mcal.mcal)": [[1, "mcal.mcal.read_pickle", false]], "read_symmetric_matrix() (mcal.calculations.tcal.tcal static method)": [[2, "mcal.calculations.tcal.Tcal.read_symmetric_matrix", false]], "remove_duplicates() (mcal.utils.cif_reader.cifreader method)": [[3, "mcal.utils.cif_reader.CifReader.remove_duplicates", false]], "reset_variable() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.reset_variable", false]], "reversed_readline() (mcal.utils.gaus_log_reader.filereader method)": [[3, "mcal.utils.gaus_log_reader.FileReader.reversed_readline", false]], "run_gaussian() (mcal.calculations.tcal.tcal method)": [[2, "mcal.calculations.tcal.Tcal.run_gaussian", false]], "set_charge_spin() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_charge_spin", false]], "set_coordinates() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_coordinates", false]], "set_function() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_function", false]], "set_resource() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_resource", false]], "set_symbols() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_symbols", false]], "set_title() (mcal.utils.gjf_maker.gjfmaker method)": [[3, "mcal.utils.gjf_maker.GjfMaker.set_title", false]], "symmetryisnotdefinederror": [[3, "mcal.utils.cif_reader.SymmetryIsNotDefinedError", false]], "tcal (class in mcal.calculations.tcal)": [[2, "mcal.calculations.tcal.Tcal", false]], "zvalueisnotmatcherror": [[3, "mcal.utils.cif_reader.ZValueIsNotMatchError", false]]}, "objects": {"": [[1, 0, 0, "-", "mcal"]], "mcal": [[2, 0, 0, "-", "calculations"], [1, 0, 0, "-", "mcal"], [3, 0, 0, "-", "utils"]], "mcal.calculations": [[2, 0, 0, "-", "hopping_mobility_model"], [2, 0, 0, "-", "rcal"], [2, 0, 0, "-", "tcal"]], "mcal.calculations.hopping_mobility_model": [[2, 1, 1, "", "cal_pinv"], [2, 1, 1, "", "demo"], [2, 1, 1, "", "diffusion_coefficient_tensor"], [2, 1, 1, "", "diffusion_coefficient_tensor_MC"], [2, 1, 1, "", "diffusion_coefficient_tensor_ODE"], [2, 1, 1, "", "marcus_rate"], [2, 1, 1, "", "mobility_tensor"], [2, 1, 1, "", "print_tensor"]], "mcal.calculations.rcal": [[2, 2, 1, "", "GausTermError"], [2, 2, 1, "", "OSCTypeError"], [2, 3, 1, "", "Rcal"], [2, 1, 1, "", "main"]], "mcal.calculations.rcal.Rcal": [[2, 4, 1, "", "calc_reorganization"], [2, 4, 1, "", "check_error_term"], [2, 4, 1, "", "check_extension_log"], [2, 4, 1, "", "extract_energy"], [2, 4, 1, "", "print_timestamp"]], "mcal.calculations.tcal": [[2, 3, 1, "", "PairAnalysis"], [2, 3, 1, "", "Tcal"], [2, 1, 1, "", "main"]], "mcal.calculations.tcal.PairAnalysis": [[2, 4, 1, "", "print_element_pairs"], [2, 4, 1, "", "print_largest_pairs"]], "mcal.calculations.tcal.Tcal": [[2, 5, 1, "", "EV"], [2, 4, 1, "", "atomic_pair_transfer_analysis"], [2, 4, 1, "", "cal_transfer_integrals"], [2, 4, 1, "", "check_extension_log"], [2, 4, 1, "", "check_normal_termination"], [2, 4, 1, "", "convert_xyz_to_gjf"], [2, 4, 1, "", "create_cube_file"], [2, 4, 1, "", "create_monomer_file"], [2, 4, 1, "", "custom_atomic_pair_transfer_analysis"], [2, 4, 1, "", "extract_coordinates"], [2, 4, 1, "", "extract_num"], [2, 4, 1, "", "output_csv"], [2, 4, 1, "", "print_apta"], [2, 4, 1, "", "print_matrix"], [2, 4, 1, "", "print_timestamp"], [2, 4, 1, "", "print_tranfer_integral_diff_levels"], [2, 4, 1, "", "print_transfer_integrals"], [2, 4, 1, "", "read_dimer"], [2, 4, 1, "", "read_matrix"], [2, 4, 1, "", "read_monomer1"], [2, 4, 1, "", "read_monomer2"], [2, 4, 1, "", "read_symmetric_matrix"], [2, 4, 1, "", "run_gaussian"]], "mcal.mcal": [[1, 2, 1, "", "OSCTypeError"], [1, 1, 1, "", "atom_weight"], [1, 1, 1, "", "cal_cen_of_weight"], [1, 1, 1, "", "cal_distance_between_cen_of_weight"], [1, 1, 1, "", "cal_eigenvalue_decomposition"], [1, 1, 1, "", "cal_min_distance"], [1, 1, 1, "", "cal_moment_of_inertia"], [1, 1, 1, "", "check_reorganization_energy_completion"], [1, 1, 1, "", "check_transfer_integral_completion"], [1, 1, 1, "", "create_reorg_gjf"], [1, 1, 1, "", "create_ti_gjf"], [1, 1, 1, "", "main"], [1, 1, 1, "", "print_mobility"], [1, 1, 1, "", "print_reorg_energy"], [1, 1, 1, "", "print_tensor"], [1, 1, 1, "", "print_transfer_integral"], [1, 1, 1, "", "read_pickle"]], "mcal.utils": [[3, 0, 0, "-", "cif_reader"], [3, 0, 0, "-", "gaus_log_reader"], [3, 0, 0, "-", "gjf_maker"]], "mcal.utils.cif_reader": [[3, 3, 1, "", "CifReader"], [3, 2, 1, "", "ElementPropertiesIsNotDefinedError"], [3, 3, 1, "", "FileIO"], [3, 2, 1, "", "SymmetryIsNotDefinedError"], [3, 2, 1, "", "ZValueIsNotMatchError"]], "mcal.utils.cif_reader.CifReader": [[3, 5, 1, "", "ATOMIC_WEIGHTS"], [3, 5, 1, "", "COVALENT_RADII"], [3, 5, 1, "", "ELEMENT_PROP"], [3, 4, 1, "", "calc_cen_of_weight"], [3, 4, 1, "", "convert_cart_to_frac"], [3, 4, 1, "", "convert_frac_to_cart"], [3, 4, 1, "", "expand_mols"], [3, 4, 1, "", "export_unit_cell_file"], [3, 5, 1, "", "parent_dir"], [3, 4, 1, "", "remove_duplicates"]], "mcal.utils.cif_reader.FileIO": [[3, 4, 1, "", "add_adjacency_mat"], [3, 4, 1, "", "add_coordinates"], [3, 4, 1, "", "add_symbols"], [3, 4, 1, "", "export_mol_file"], [3, 4, 1, "", "export_xyz_file"]], "mcal.utils.gaus_log_reader": [[3, 3, 1, "", "FileReader"], [3, 1, 1, "", "check_normal_termination"]], "mcal.utils.gaus_log_reader.FileReader": [[3, 4, 1, "", "close"], [3, 4, 1, "", "reversed_readline"]], "mcal.utils.gjf_maker": [[3, 3, 1, "", "GjfMaker"]], "mcal.utils.gjf_maker.GjfMaker": [[3, 5, 1, "", "ELEMENTS_NUM"], [3, 5, 1, "", "ELEMENT_PROP"], [3, 4, 1, "", "add_link"], [3, 4, 1, "", "add_root"], [3, 4, 1, "", "create_chk_file"], [3, 4, 1, "", "create_rwf_file"], [3, 4, 1, "", "export_gjf"], [3, 4, 1, "", "opt"], [3, 4, 1, "", "output_detail"], [3, 5, 1, "", "parent_dir"], [3, 4, 1, "", "reset_variable"], [3, 4, 1, "", "set_charge_spin"], [3, 4, 1, "", "set_coordinates"], [3, 4, 1, "", "set_function"], [3, 4, 1, "", "set_resource"], [3, 4, 1, "", "set_symbols"], [3, 4, 1, "", "set_title"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "exception", "Python exception"], "3": ["py", "class", "Python class"], "4": ["py", "method", "Python method"], "5": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:exception", "3": "py:class", "4": "py:method", "5": "py:attribute"}, "terms": {"": [2, 3], "0": [2, 3], "00": 3, "0000": 3, "0001": 3, "0026": 3, "007": 3, "008": 3, "0080": 3, "01": 3, "011": 3, "0122": 3, "014": 3, "0140": 3, "02": 3, "03": 3, "0300": 3, "04": 3, "0400": 3, "05": [2, 3], "06": [2, 3], "07": 3, "078": 3, "08": 3, "085": 3, "09": [0, 2], "098": 3, "1": [1, 2, 3], "10": [0, 2, 3], "100": [2, 3], "10000": 2, "101": 3, "102": 3, "103": 3, "104": 3, "105": 3, "106": 3, "107": 3, "108": 3, "109": 3, "11": 3, "110": 3, "111": 3, "112": 3, "113": 3, "114": 3, "115": 3, "116": 3, "117": 3, "118": 3, "119": 3, "12": 3, "120": 3, "121": 3, "126": 3, "127": 3, "13": 3, "131": 3, "132": 3, "137": 3, "138": 3, "14": 3, "140": 3, "144": 3, "15": 3, "150": 3, "151": 3, "157": 3, "158": 3, "16": [0, 1, 2, 3], "162": 3, "164": 3, "167": 3, "168": 3, "16gb": [0, 1], "17": 3, "173": 3, "174": 3, "178": 3, "18": 3, "180": 3, "183": 3, "186": 3, "19": 3, "190": 3, "192": 3, "195": 3, "196": 3, "1e": 2, "1st": 2, "2": [0, 1, 2, 3], "20": 3, "200": [2, 3], "2000": 3, "2025": [2, 3], "204": 3, "207": 3, "208": 3, "21": 3, "22": 3, "224": 3, "23": 3, "231": 3, "232": 3, "238": 3, "24": 3, "25": 3, "26": 3, "27": 3, "27211": 2, "28": 3, "29": 3, "2nd": 2, "3": [0, 2, 3], "30": 3, "300": 2, "305": 3, "31": 3, "311g": [0, 1], "31g": [0, 1, 2], "32": [0, 3], "33": 3, "34": 3, "35": 3, "36": 3, "37": 3, "38": 3, "38456571948": 2, "39": 3, "3x3": 2, "3x3x3": [0, 1], "4": [0, 1, 2, 3], "40": [2, 3], "41": 3, "42": 3, "43": 3, "44": 3, "45": 3, "46": 3, "468": 3, "47": 3, "48": 3, "49": 3, "5": 3, "50": 3, "51": 3, "52": 3, "53": 3, "54": 3, "546": 3, "55": 3, "56": 3, "57": 3, "58": 3, "59": 3, "5x5x5": [0, 1], "6": [0, 1, 2, 3], "60": 3, "61": 3, "62": 3, "63": 3, "64": 3, "65": 3, "66": 3, "67": 3, "68": 3, "69": 3, "693": 3, "7": 3, "70": 3, "71": 3, "72": 3, "723": 3, "73": 3, "74": 3, "75": 3, "76": 3, "77": 3, "78": 3, "79": 3, "798": 3, "7x7x7": 0, "8": [0, 1, 3], "80": 3, "81": 3, "8192": 3, "82": 3, "83": 3, "84": 3, "845": 3, "85": 3, "86": 3, "867": 3, "87": 3, "88": 3, "89": 3, "9": [0, 2, 3], "90": 3, "904": 3, "906": 3, "91": 3, "92": 3, "922": 3, "93": 3, "933": 3, "938": 3, "94": 3, "9400": 3, "942": 3, "95": 3, "956": 3, "96": 3, "97": 3, "971": 3, "974": 3, "98": 3, "9800": 3, "982": 3, "99": 3, "996": 3, "998": 3, "999": 3, "A": 3, "As": 3, "At": 3, "Be": 3, "For": [0, 3], "If": [2, 3], "In": 3, "It": 0, "No": 3, "The": [0, 2, 3], "With": 1, "_description_": 2, "_io": 2, "a_transf": 2, "ac": [0, 3], "add": 3, "add_adjacency_mat": [1, 3], "add_coordin": [1, 3], "add_link": [1, 3], "add_root": [1, 3], "add_symbol": [1, 3], "adjac": 3, "adjacency_mat": 3, "after": 0, "ag": 3, "al": 3, "algorithm": 2, "all": [0, 1, 2], "am": 3, "amount": 0, "analysi": 2, "analyz": 2, "analyze_orb1": 2, "analyze_orb2": 2, "analyze_orbit": 2, "ani": [1, 2, 3], "anisotropi": [0, 1], "anoth": 1, "apta": 2, "ar": [0, 1, 3], "around": [0, 3], "arrai": [2, 3], "array_lik": 2, "atom": [1, 2, 3], "atom_weight": [1, 4], "atomic_pair_transfer_analysi": [1, 2], "atomic_weight": [1, 3], "au": 3, "awai": 3, "axi": 2, "b": [2, 3], "b3lyp": [0, 1, 2], "ba": 3, "base": [1, 2, 3], "basenam": 1, "basi": 0, "basic": 1, "beta": 3, "between": [0, 1], "bh": 3, "bi": 3, "bismuth": 3, "bk": 3, "bond": 3, "bool": [1, 2, 3], "box": 2, "br": 3, "bra": 2, "break": [2, 3], "buffer_s": 3, "c": [1, 2, 3], "ca": 3, "cal_cen_of_weight": [1, 4], "cal_distance_between_cen_of_weight": [1, 4], "cal_eigenvalue_decomposit": [1, 4], "cal_min_dist": [1, 4], "cal_moment_of_inertia": [1, 4], "cal_pinv": [1, 2], "cal_transfer_integr": [1, 2], "calc_cen_of_weight": [1, 3], "calc_reorgan": [1, 2], "calcul": [1, 3, 4], "can": 0, "carlo": [0, 1, 2], "cart_coord": 3, "cartesian": 3, "cd": 3, "ce": 3, "cell": [0, 2, 3], "cellsiz": 1, "center": [0, 1, 3], "central": 0, "cf": 3, "charg": 3, "check": [1, 2, 3], "check_error_term": [1, 2], "check_extension_log": [1, 2], "check_normal_termin": [1, 2, 3], "check_reorganization_energy_complet": [1, 4], "check_transfer_integral_complet": [1, 4], "chemic": 0, "chk": 3, "chk_rwf_name": 3, "cif": [0, 1, 3], "cif_filenam": 0, "cif_path": 3, "cif_path_without_ext": 1, "cif_read": [1, 4], "cifread": [1, 3], "cl": 3, "class": [2, 3], "close": [1, 3], "cm": 3, "cn": 3, "co": 3, "code": 2, "coeffici": 2, "column": [2, 3], "command": 2, "comment": 3, "compar": 1, "complet": 1, "comput": 0, "consid": [0, 1], "consum": 0, "contain": [1, 3], "content": 4, "continu": [0, 1], "convert": [2, 3], "convert_cart_to_frac": [1, 3], "convert_frac_to_cart": [1, 3], "convert_xyz_to_gjf": [1, 2], "coordin": [1, 2, 3], "coordinates1": 1, "coordinates2": 1, "coords1": 1, "coords2": 1, "correctli": 3, "covalent_radii": [1, 3], "covalent_radiu": 3, "cpu": [1, 3], "cpu_num": 3, "cr": 3, "creat": [0, 1, 2, 3], "create_chk_fil": [1, 3], "create_cube_fil": [1, 2], "create_monomer_fil": [1, 2], "create_reorg_gjf": [1, 4], "create_rwf_fil": [1, 3], "create_ti_gjf": [1, 4], "crystal": [0, 1, 3], "csv": 2, "cu": 3, "cube": 2, "custom_atomic_pair_transfer_analysi": [1, 2], "cutoff": 2, "cycl": 3, "d": [0, 1, 2, 3], "db": 3, "decomposit": [1, 2], "default": [0, 1, 2, 3], "defin": 3, "demo": [1, 2], "depend": 0, "detail": [0, 2, 3], "detect": 3, "determin": 0, "deuterium": 3, "dict": [1, 3], "dictionari": [1, 3], "differ": [0, 1], "differenti": [0, 2], "diffus": 2, "diffusion_coefficient_tensor": [1, 2], "diffusion_coefficient_tensor_mc": [1, 2], "diffusion_coefficient_tensor_od": [1, 2], "dimer": [1, 2], "direct": [0, 3], "directori": [1, 3], "disabl": 0, "distanc": [0, 1], "document": 3, "doubl": 2, "dtype": [1, 2, 3], "dummi": 3, "duplic": 3, "dy": 3, "e": 3, "each": 0, "eigenvalu": [0, 1, 2], "eigenvector": [0, 1], "electron": 0, "element": [2, 3], "element_prop": [1, 3], "elementpropertiesisnotdefinederror": [1, 3], "elements_num": [1, 3], "email": 0, "enabl": 0, "end": 3, "energi": [0, 1, 2], "ensur": 0, "environ": 0, "equat": [0, 2], "er": 3, "error": 2, "etc": 3, "eu": 3, "ev": [1, 2], "exampl": [1, 2, 3], "except": [1, 2, 3], "execut": [0, 2], "exist": [0, 1], "expand": [0, 1, 3], "expand_mol": [1, 3], "expand_rang": 3, "export": 3, "export_gjf": [1, 3], "export_mol_fil": [1, 3], "export_unit_cell_fil": [1, 3], "export_xyz_fil": [1, 3], "express": 2, "extens": [1, 2], "extension_log": 1, "extract": [2, 3], "extract_coordin": [1, 2], "extract_energi": [1, 2], "extract_num": [1, 2], "f": [2, 3], "fals": [2, 3], "faster": 0, "fe": 3, "file": [0, 1, 2, 3], "file_nam": [1, 2, 3], "file_path": 3, "fileio": [1, 3], "fileread": [1, 3], "fl": 3, "flerovium": 3, "float": [1, 2, 3], "float64": [1, 2, 3], "fm": 3, "fock": 2, "format": 3, "fr": 3, "frac_coord": 3, "fraction": 3, "from": [0, 1, 2, 3], "fullcal": 1, "function": [2, 3], "g16": 2, "ga": 3, "gau_com": 2, "gaus_log_read": [1, 4], "gaussian": [0, 1, 2, 3], "gaussian_command": 2, "gaustermerror": [1, 2], "gb": [0, 1, 2, 3], "gd": 3, "ge": 3, "gener": 3, "get": 1, "gillespi": 2, "git": 3, "github": 0, "given": 3, "gjf": [1, 2, 3], "gjf_basenam": 1, "gjf_file": [1, 2], "gjf_maker": [1, 4], "gjfmaker": [1, 3], "group": 3, "h": [0, 3], "he": 3, "header": 3, "header1": 3, "header2": 3, "helium": 3, "help": 0, "hf": 3, "hg": 3, "high": 1, "hiroyuki": 0, "ho": 3, "homo": [0, 2], "hop": 2, "hop_mcal": 1, "hopping_mobility_model": [1, 4], "hydrogen": 3, "i": [0, 1, 2, 3], "idx": 2, "import": 2, "includ": 2, "increas": 0, "index": [0, 3], "inertia": [0, 1], "inform": 3, "inner": 3, "input": 2, "int": [1, 2, 3], "integ": 2, "integr": [0, 1, 2], "intermolecular": 2, "interrupt": 0, "invers": 2, "ion": [1, 2], "ir": 3, "is_matrix": 2, "is_output_detail": 2, "j": [2, 3], "jp": 0, "k": [2, 3], "kei": 3, "ket": 2, "kinet": [0, 1], "koki": 0, "kr": 3, "la": 3, "laboratori": 0, "larg": 0, "larger": 0, "largest": 2, "last": 2, "lattic": 2, "lead": 3, "level": 0, "li": 3, "librari": 0, "like": 2, "line": [2, 3], "link": 3, "list": [1, 2, 3], "liter": [1, 2, 3], "lithium": 3, "livermorium": 3, "log": [0, 1, 2, 3], "log_fil": 3, "lr": 3, "lu": 3, "lumo": [0, 2], "lv": 3, "m": 1, "mai": 3, "main": [1, 2, 4], "make": 0, "manag": 3, "marcus_r": [1, 2], "match": 3, "matrix": [2, 3], "matsui": 0, "max_rat": 2, "max_step": 2, "maximum": 2, "mc": [1, 3], "md": 3, "mean": 2, "mem": [1, 2], "mem_num": 3, "mem_unit": 3, "memori": [1, 2, 3], "messag": [1, 2], "method": 1, "mg": 3, "minimum": 1, "mit": 0, "mn": 3, "mo": [2, 3], "mobil": [0, 1, 2], "mobility_tensor": [1, 2], "modul": [0, 4], "mol": 3, "molecul": [0, 2, 3], "molecular": 3, "moment": [0, 1], "monom": [1, 2], "monomer1": 1, "monomer1_atom_num": 2, "monomer2": 1, "monomolecular": 3, "mont": [0, 1, 2], "more": 0, "moscovium": 3, "msg": [1, 2], "mt": 3, "mu": 1, "must": 0, "n": [0, 1, 2, 3], "n_basi": 2, "n_bsuse": 2, "na": 3, "name": [1, 2, 3], "nan": 3, "nb": 3, "nd": 3, "ndarrai": [1, 2, 3], "ne": 3, "neg": 2, "neighbor": 1, "neighbor_mol": 1, "nest": 3, "neutral": [1, 2], "newer": 0, "nh": 3, "nhomo": 2, "ni": 3, "nlevel": 2, "nlumo": 2, "none": [1, 2, 3], "normal": [0, 1, 3], "np": [1, 2, 3], "nprocshar": 2, "number": [1, 2, 3], "numer": 2, "numpi": [0, 2], "o": 3, "object": [2, 3], "od": [1, 2], "offset": 3, "og": 3, "oganesson": 3, "one": [1, 2, 3], "onli": 2, "only_read": 2, "open": 2, "opt": [1, 3], "opt_ion": [1, 2], "opt_neutr": [1, 2], "optim": 3, "option": [1, 2, 3], "orbit": 2, "ordinari": [0, 2], "organ": [0, 2], "origin": 3, "osc_typ": [0, 1, 2], "osctypeerror": [1, 2, 4], "other": 2, "otherwis": 3, "outer": 3, "output": [2, 3], "output_apta": 2, "output_csv": [1, 2], "output_detail": [1, 3], "output_matrix": 2, "output_ti_diff_level": 2, "overlap": 2, "ozawa": 0, "p": [1, 2, 3], "pa": 3, "packag": [0, 4], "page": 0, "pair": [0, 2], "pairanalysi": [1, 2], "panda": 0, "paramet": [1, 2, 3], "parent_dir": [1, 3], "particl": 2, "path": [0, 1, 3], "pattern": 2, "pb": 3, "pd": 3, "period": 3, "pickl": 1, "pip": 0, "pkl": [0, 1], "pkl_filenam": 0, "pleas": 0, "pm": 3, "po": 3, "posixpath": 3, "pr": 3, "precis": 1, "print": [1, 2, 3], "print_apta": [1, 2], "print_element_pair": [1, 2], "print_largest_pair": [1, 2], "print_matrix": [1, 2], "print_mobl": [1, 4], "print_reorg_energi": [1, 4], "print_tensor": [1, 2, 4], "print_timestamp": [1, 2], "print_tranfer_integral_diff_level": [1, 2], "print_transfer_integr": [1, 2, 4], "process": 0, "produc": 3, "project": 0, "properti": 3, "protactinium": 3, "pseudo": 2, "pt": 3, "pu": 3, "py": [1, 2], "python": [0, 1], "quantum": 0, "r": [1, 2], "ra": 3, "rais": [2, 3], "rang": [0, 1], "rate": 2, "rb": 3, "rcal": [1, 4], "rcond": 2, "re": [2, 3], "read": [1, 2, 3], "read_dim": [1, 2], "read_matrix": [1, 2], "read_monomer1": [1, 2], "read_monomer2": [1, 2], "read_pickl": [1, 4], "read_symmetric_matrix": [1, 2], "reader": [2, 3], "readlin": 2, "regular": 2, "rel": 3, "releas": 0, "remov": 3, "remove_dupl": [1, 3], "remove_radical_flag": 3, "reorg_energi": 1, "reorgan": [0, 1, 2], "replac": 0, "repres": 3, "research": 0, "reset": 3, "reset_vari": [1, 3], "resourc": 1, "result": [1, 2], "resum": 1, "return": [1, 2, 3], "returncod": 2, "reversed_readlin": [1, 3], "rf": 3, "rg": 3, "rh": 3, "rn": 3, "roel": 0, "root": 3, "row": [2, 3], "rp": 1, "ru": 3, "run": [0, 1, 2], "run_gaussian": [1, 2], "rwf": 3, "sampl": [2, 3], "save": [0, 1, 3], "save_dir": [1, 3], "sb": 3, "sc": 3, "se": 3, "search": [0, 2], "see": 0, "semiconductor": [0, 1, 2], "set": [1, 3], "set_charge_spin": [1, 3], "set_coordin": [1, 3], "set_funct": [1, 3], "set_resourc": [1, 3], "set_symbol": [1, 3], "set_titl": [1, 3], "sg": 3, "shape": 3, "should": 2, "si": 3, "significantli": 0, "sim_typ": 1, "simul": [1, 2], "singular": 2, "size": [0, 2], "skip": [1, 2], "skip_cal": 2, "skip_monomer_num": 2, "skip_specified_c": 2, "sm": 3, "small": 2, "smaller": 0, "sn": 3, "solut": 2, "specifi": [0, 2], "speedup": [0, 1], "spin": 3, "sr": 3, "src": 3, "static": 2, "step": 2, "str": [1, 2, 3], "string": 2, "structur": [0, 3], "subaru": 3, "submodul": 4, "subpackag": 4, "subprocess": 2, "success": 2, "suffici": 0, "supercel": [0, 1], "sure": 0, "symbol": [1, 3], "symbols1": 1, "symbols2": 1, "symmetr": 2, "symmetri": 3, "symmetrix": 2, "symmetryisnotdefinederror": [1, 3], "system": 0, "t": [2, 3], "ta": 3, "target": 2, "tb": 3, "tc": 3, "tcal": [1, 4], "te": 3, "temperatur": 2, "tennessin": 3, "tensor": [0, 1, 2], "term": 2, "termin": [0, 1, 2, 3], "textiowrapp": 2, "th": [2, 3], "thi": [0, 2, 3], "thorium": 3, "ti": 3, "tight": 3, "timestamp": 2, "titl": 3, "tl": 3, "tm": 3, "tol": 3, "toler": 3, "tool": 0, "total": 2, "transfer": [0, 1, 2], "true": [1, 2, 3], "tupl": [1, 2, 3], "two": 1, "txt": 3, "type": [0, 1, 2, 3], "u": [0, 3], "under": 0, "union": 1, "uniqu": [1, 3], "unique_mol": 1, "unit": [0, 2, 3], "univers": 0, "uranium": 3, "us": [0, 1, 2, 3], "usag": 1, "user": 3, "util": [1, 4], "v": 3, "valu": [1, 2, 3], "valueerror": 2, "vari": 0, "variabl": 3, "vdw_radiu": 3, "vector": [1, 2], "w": 3, "wa": 2, "weight": [0, 1, 3], "when": 3, "whether": 2, "while": [2, 3], "widen": [0, 1], "within": 3, "without": [0, 1], "x": 3, "xe": 3, "xxx": [0, 1], "xxx_result": [0, 1], "xyz": [2, 3], "y": 3, "yamagata": 0, "yb": 3, "you": 0, "your": 0, "yu": 0, "yz": 0, "z": 3, "zero": 2, "zn": 3, "zr": 3, "zvalueisnotmatcherror": [1, 3]}, "titles": ["mcal 0.1.1 Documentation", "mcal package", "mcal.calculations package", "mcal.utils package", "mcal"], "titleterms": {"0": 0, "1": 0, "If": 0, "To": 0, "api": 0, "argument": 0, "author": 0, "basic": 0, "c": 0, "calcul": [0, 2], "cellsiz": 0, "cif_read": 3, "coeffici": 0, "compar": 0, "content": [1, 2, 3], "control": 0, "cpu": 0, "diffus": 0, "document": 0, "error": 0, "exampl": 0, "featur": 0, "fullcal": 0, "g": 0, "g09": 0, "gaus_log_read": 3, "gjf_maker": 3, "high": 0, "hopping_mobility_model": 2, "indic": 0, "instal": 0, "licens": 0, "m": 0, "manual": 0, "mc": 0, "mcal": [0, 1, 2, 3, 4], "mem": 0, "memori": 0, "method": 0, "midwai": 0, "modul": [1, 2, 3], "note": 0, "number": 0, "od": 0, "option": 0, "output": 0, "overview": 0, "p": 0, "packag": [1, 2, 3], "pickl": 0, "practic": 0, "precis": 0, "r": 0, "rcal": 2, "read": 0, "read_pickl": 0, "reduc": 0, "refer": 0, "requir": 0, "result": 0, "resum": 0, "reus": 0, "rp": 0, "set": 0, "shortag": 0, "standard": 0, "stop": 0, "submodul": [1, 2, 3], "subpackag": 1, "tabl": 0, "tcal": 2, "time": 0, "troubleshoot": 0, "usag": 0, "util": 3, "verifi": 0}})
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "yu-mcal"
3
- version = "0.1.0"
3
+ version = "0.1.1"
4
4
  description = "Program for the calculation of mobility tensor for organic semiconductor crystals"
5
5
  requires-python = ">=3.9"
6
6
  dependencies = [
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/mcal.py RENAMED
@@ -139,9 +139,9 @@ def main():
139
139
  filename = cif_file.stem
140
140
  cif_path_without_ext = f'{directory}/{filename}'
141
141
 
142
- print('---------------------------------------')
143
- print(' mcal 0.1.0 (2025/12/30) by Matsui Lab. ')
144
- print('---------------------------------------')
142
+ print('----------------------------------------')
143
+ print(' mcal 0.1.1 (2026/01/08) by Matsui Lab. ')
144
+ print('----------------------------------------')
145
145
 
146
146
  if args.read_pickle:
147
147
  read_pickle(args.file)
@@ -312,27 +312,27 @@ def main():
312
312
  hop.append((s, t, i, j, k, marcus_rate(ti, reorg_energy)))
313
313
 
314
314
  diffusion_coef_tensor = diffusion_coefficient_tensor(cif_reader.lattice * 1e-8, hop)
315
- print_tensor(diffusion_coef_tensor, msg="Diffusion coefficient tensor")
315
+ print_tensor(diffusion_coef_tensor, msg="Diffusion coefficient tensor (cm^2/s)")
316
316
  mu = mobility_tensor(diffusion_coef_tensor)
317
- print_tensor(mu)
317
+ print_tensor(mu, msg="Mobility tensor (cm^2/Vs)")
318
318
  value, vector = cal_eigenvalue_decomposition(mu)
319
319
  print_mobility(value, vector)
320
320
 
321
321
  ##### Simulate mobility tensor calculation using Monte Carlo method #####
322
322
  if args.mc:
323
323
  D_MC = diffusion_coefficient_tensor_MC(cif_reader.lattice * 1e-8, hop)
324
- print_tensor(D_MC, msg="Diffusion coefficient tensor (MC)")
324
+ print_tensor(D_MC, msg="Diffusion coefficient tensor (cm^2/s) (MC)")
325
325
  mu_MC = mobility_tensor(D_MC)
326
- print_tensor(mu_MC, msg="Mobility tensor (MC)")
326
+ print_tensor(mu_MC, msg="Mobility tensor (cm^2/Vs) (MC)")
327
327
  value_MC, vector_MC = cal_eigenvalue_decomposition(mu_MC)
328
328
  print_mobility(value_MC, vector_MC, sim_type='MC')
329
329
 
330
330
  ##### Simulate mobility tensor calculation using Ordinary Differential Equation method #####
331
331
  if args.ode:
332
332
  D_ODE = diffusion_coefficient_tensor_ODE(cif_reader.lattice * 1e-8, hop)
333
- print_tensor(D_ODE, msg="Diffusion coefficient tensor (ODE)")
333
+ print_tensor(D_ODE, msg="Diffusion coefficient tensor (cm^2/s) (ODE)")
334
334
  mu_ODE = mobility_tensor(D_ODE)
335
- print_tensor(mu_ODE, msg="Mobility tensor (ODE)")
335
+ print_tensor(mu_ODE, msg="Mobility tensor (cm^2/Vs) (ODE)")
336
336
  value_ODE, vector_ODE = cal_eigenvalue_decomposition(mu_ODE)
337
337
  print_mobility(value_ODE, vector_ODE, sim_type='ODE')
338
338
 
@@ -355,14 +355,18 @@ def main():
355
355
  Tcal.print_timestamp()
356
356
  end_time = time()
357
357
  elapsed_time = end_time - start_time
358
+ elapsed_time_h = int(elapsed_time // 3600)
359
+ elapsed_time_min = int((elapsed_time - elapsed_time_h * 3600) // 60)
360
+ elapsed_time_sec = int(elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60)
361
+ elapsed_time_ms = (elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60 - elapsed_time_sec) * 1000
358
362
  if elapsed_time < 1:
359
- print(f'Elapsed Time: {elapsed_time*1000:.0f} ms')
363
+ print(f'Elapsed Time: {elapsed_time_ms:.0f} ms')
360
364
  elif elapsed_time < 60:
361
- print(f'Elapsed Time: {elapsed_time:.0f} s')
365
+ print(f'Elapsed Time: {elapsed_time_sec} sec')
362
366
  elif elapsed_time < 3600:
363
- print(f'Elapsed Time: {elapsed_time/60:.0f} min')
367
+ print(f'Elapsed Time: {elapsed_time_min} min {elapsed_time_sec} sec')
364
368
  else:
365
- print(f'Elapsed Time: {elapsed_time/3600:.0f} h')
369
+ print(f'Elapsed Time: {elapsed_time_h} h {elapsed_time_min} min {elapsed_time_sec} sec')
366
370
 
367
371
 
368
372
  def atom_weight(symbol: str) -> float:
@@ -728,8 +732,9 @@ def print_mobility(value: NDArray[np.float64], vector: NDArray[np.float64], sim_
728
732
  sim_type : str
729
733
  Simulation type (MC or ODE)
730
734
  """
731
- msg_value = 'Mobility value'
732
- msg_vector = 'Mobility vector'
735
+ msg_value = 'Mobility eigenvalues (cm^2/Vs)'
736
+ msg_vector = 'Mobility eigenvectors'
737
+ direction = ['x', 'y', 'z']
733
738
 
734
739
  if sim_type:
735
740
  msg_value += f' ({sim_type})'
@@ -746,8 +751,9 @@ def print_mobility(value: NDArray[np.float64], vector: NDArray[np.float64], sim_
746
751
  print('-' * (len(msg_vector)+2))
747
752
  print(f' {msg_vector} ')
748
753
  print('-' * (len(msg_vector)+2))
749
- for v in vector:
750
- print(f"{v[0]:12.6g} {v[1]:12.6g} {v[2]:12.6g}")
754
+ print(' vector1 vector2 vector3')
755
+ for v, d in zip(vector, direction):
756
+ print(f'{d} {v[0]:12.6g} {v[1]:12.6g} {v[2]:12.6g}')
751
757
  print()
752
758
 
753
759
 
@@ -822,9 +828,9 @@ def read_pickle(file_name: str):
822
828
  print(f'{s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell')
823
829
  print_transfer_integral(results['osc_type'], ti)
824
830
 
825
- print_tensor(results['diffusion_coefficient_tensor'], msg="Diffusion coefficient tensor")
831
+ print_tensor(results['diffusion_coefficient_tensor'], msg="Diffusion coefficient tensor (cm^2/s)")
826
832
 
827
- print_tensor(results['mobility_tensor'])
833
+ print_tensor(results['mobility_tensor'], msg="Mobility tensor (cm^2/Vs)")
828
834
 
829
835
  print_mobility(results['mobility_value'], results['mobility_vector'])
830
836
 
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/uv.lock RENAMED
@@ -1244,7 +1244,7 @@ wheels = [
1244
1244
 
1245
1245
  [[package]]
1246
1246
  name = "yu-mcal"
1247
- version = "0.1.0"
1247
+ version = "0.1.1"
1248
1248
  source = { editable = "." }
1249
1249
  dependencies = [
1250
1250
  { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
yu_mcal-0.1.0/docs/objects.inv DELETED
Binary file
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/.gitignore RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/.python-version RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/LICENSE RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/.nojekyll RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/basic.css RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/debug.css RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/file.png RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/minus.png RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs/_static/plus.png RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/Makefile RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/make.bat RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/docs-src/source/conf.py RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/requirements.txt RENAMED
File without changes
{yu_mcal-0.1.0 → yu_mcal-0.1.1}/src/mcal/__init__.py RENAMED
File without changes