yu-mcal 0.1.1__tar.gz → 0.1.3__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.
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/PKG-INFO +4 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/README.md +3 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/README_ja.md +3 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_sources/index.rst.txt +5 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/documentation_options.js +1 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/genindex.html +4 -4
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/index.html +11 -6
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/mcal.calculations.html +5 -5
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/mcal.html +4 -4
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/mcal.utils.html +4 -4
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/modules.html +5 -5
- yu_mcal-0.1.3/docs/objects.inv +8 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/py-modindex.html +4 -4
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/search.html +4 -4
- yu_mcal-0.1.3/docs/searchindex.js +1 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/index.rst +5 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/pyproject.toml +1 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/calculations/hopping_mobility_model.py +1 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/mcal.py +1 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/uv.lock +1 -1
- yu_mcal-0.1.1/docs/objects.inv +0 -0
- yu_mcal-0.1.1/docs/searchindex.js +0 -1
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/.gitignore +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/.python-version +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/LICENSE +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/.nojekyll +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_sources/mcal.calculations.rst.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_sources/mcal.rst.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_sources/mcal.utils.rst.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_sources/modules.rst.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/autodoc_pydantic.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/basic.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/debug.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/doctools.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/file.png +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/language_data.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/minus.png +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/plus.png +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/pygments.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/scripts/furo-extensions.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/scripts/furo.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/scripts/furo.js.LICENSE.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/scripts/furo.js.map +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/searchtools.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/skeleton.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/sphinx_highlight.js +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/styles/furo-extensions.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/styles/furo-extensions.css.map +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/styles/furo.css +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs/_static/styles/furo.css.map +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/Makefile +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/make.bat +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/conf.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/mcal.calculations.rst +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/mcal.rst +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/mcal.utils.rst +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/docs-src/source/modules.rst +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/requirements.txt +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/__init__.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/calculations/__init__.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/calculations/rcal.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/calculations/tcal.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/constants/element_properties.csv +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/utils/__init__.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/utils/cif_reader.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/utils/gaus_log_reader.py +0 -0
- {yu_mcal-0.1.1 → yu_mcal-0.1.3}/src/mcal/utils/gjf_maker.py +0 -0
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Name: yu-mcal
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Version: 0.1.
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Version: 0.1.3
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Summary: Program for the calculation of mobility tensor for organic semiconductor crystals
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Author: Koki Ozawa
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Author-email: Hiroyuki Matsui <h-matsui@yz.yamagata-u.ac.jp>
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Hiroyuki Matsui, Koki Ozawa
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Please replace [at] with @
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# Acknowledgements
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This work was supported by JSPS Grant-in-Aid for JSPS Fellows Grant Number JP25KJ0647.
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This project is released under the MIT License.
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For more details, see the `LICENSE file on GitHub <https://github.com/matsui-lab-yamagata/mcal/blob/main/LICENSE>`_.
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Acknowledgements
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================
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This project is released under the MIT License.
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For more details, see the `LICENSE file on GitHub <https://github.com/matsui-lab-yamagata/mcal/blob/main/LICENSE>`_.
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Acknowledgements
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================
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This work was supported by JSPS Grant-in-Aid for JSPS Fellows Grant Number JP25KJ0647.
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@@ -79,7 +79,7 @@ def demo():
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print(f"{d[0]:9.6f} {d[1]:9.6f} {d[2]:9.6f}")
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def cal_pinv(array: NDArray[np.float64], rcond: float = 1e-
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def cal_pinv(array: NDArray[np.float64], rcond: float = 1e-3) -> NDArray[np.float64]:
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"""Calculate pseudo-inverse matrix using eigenvalue decomposition
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Parameters
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cif_path_without_ext = f'{directory}/{filename}'
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print('----------------------------------------')
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print(' mcal 0.1.
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print(' mcal 0.1.3 (2026/01/20) by Matsui Lab. ')
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print('----------------------------------------')
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if args.read_pickle:
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@@ -1244,7 +1244,7 @@ wheels = [
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[[package]]
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name = "yu-mcal"
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version = "0.1.
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version = "0.1.3"
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source = { editable = "." }
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dependencies = [
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{ name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
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yu_mcal-0.1.1/docs/objects.inv
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@@ -1 +0,0 @@
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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, 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