==================================
mcal Documentation
==================================

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   :target: https://www.python.org
   :alt: Python

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   :alt: License: MIT

Overview
========

``mcal`` is a tool for calculating mobility tensors of organic semiconductors.
It calculates transfer integrals and reorganization energy from crystal structures (CIF files),
and determines mobility tensors considering anisotropy and path continuity.

Features
--------

* Read crystal structures from CIF files
* Quantum chemical calculations using Gaussian 09/16 or PySCF
* Calculation of transfer integrals
* Calculation of reorganization energy
* Computation of mobility tensors and eigenvalues

Requirements
============

* Python 3.9 or newer
* NumPy
* Pandas
* Matplotlib
* yu-tcal==4.0.3

Quantum Chemistry Calculation Tools
------------------------------------

At least one of the following is required:

* Gaussian 09 or 16
* PySCF (macOS / Linux / WSL2(Windows Subsystem for Linux))
* GPU4PySCF (macOS / Linux / WSL2(Windows Subsystem for Linux))

.. important::
   When using Gaussian, the path to Gaussian must be set in your environment.
   PySCF is supported on macOS / Linux. Windows users must use WSL2.

Installation
============

Using Gaussian 09 or 16 (without PySCF)
----------------------------------------

.. code-block:: bash

   pip install yu-mcal

Using PySCF (CPU only, macOS / Linux / WSL2)
---------------------------------------------

.. code-block:: bash

   pip install "yu-mcal[pyscf]"

Using GPU acceleration with PySCF (macOS / Linux / WSL2)
---------------------------------------------------------

1. Check your installed CUDA Toolkit version:

.. code-block:: bash

   nvcc --version

2. Install mcal with GPU acceleration:

If your CUDA Toolkit version is 12.x:

.. code-block:: bash

   pip install "yu-mcal[gpu4pyscf-cuda12]"

If your CUDA Toolkit version is 11.x:

.. code-block:: bash

   pip install "yu-mcal[gpu4pyscf-cuda11]"


Verify Installation
-------------------

After installation, you can verify by running:

.. code-block:: bash

   mcal --help

mcal Usage Manual
=================

Basic Usage
-----------

.. code-block:: bash

   mcal <cif_filename or pkl_filename> <osc_type> [options]

Required Arguments
~~~~~~~~~~~~~~~~~~

* ``cif_filename``: Path to the CIF file
* ``pkl_filename``: Path to the pickle file
* ``osc_type``: Organic semiconductor type

  * ``p``: p-type semiconductor (uses HOMO level)
  * ``n``: n-type semiconductor (uses LUMO level)

Basic Examples
~~~~~~~~~~~~~~

.. code-block:: bash

   # Calculate as p-type semiconductor
   mcal xxx.cif p

   # Calculate as n-type semiconductor
   mcal xxx.cif n

Options
-------

Calculation Settings
~~~~~~~~~~~~~~~~~~~~

``-M, --method <method>``
^^^^^^^^^^^^^^^^^^^^^^^^^^

Specify the calculation method (used in both Gaussian and PySCF calculations).

* **Default**: ``B3LYP/6-31G(d,p)``
* **Example**: ``mcal xxx.cif p -M "B3LYP/6-31G(d)"``

``-c, --cpu <number>``
^^^^^^^^^^^^^^^^^^^^^^

Specify the number of CPUs to use.

* **Default**: ``4``
* **Example**: ``mcal xxx.cif p -c 8``

``-m, --mem <memory>``
^^^^^^^^^^^^^^^^^^^^^^

Specify the amount of memory in GB.

* **Default**: ``10``
* **Example**: ``mcal xxx.cif p -m 16``

``-g, --g09``
^^^^^^^^^^^^^

Use Gaussian 09 (default is Gaussian 16).

* **Example**: ``mcal xxx.cif p -g``

PySCF Settings
~~~~~~~~~~~~~~

``--pyscf``
^^^^^^^^^^^^

Use PySCF instead of Gaussian for all calculations. Requires ``yu-mcal[pyscf]``.

* **Example**: ``mcal xxx.cif p --pyscf``

``--gpu4pyscf``
^^^^^^^^^^^^^^^^

Use GPU acceleration via gpu4pyscf. Automatically enables PySCF mode (no need to specify ``--pyscf``).
Requires ``yu-mcal[gpu4pyscf-cuda11]`` or ``yu-mcal[gpu4pyscf-cuda12]``.

* **Example**: ``mcal xxx.cif p --gpu4pyscf``

``--cart``
^^^^^^^^^^^

Use Cartesian basis functions instead of spherical harmonics (PySCF only).

* **Example**: ``mcal xxx.cif p --pyscf --cart``

Calculation Control
~~~~~~~~~~~~~~~~~~~

``-r, --read``
^^^^^^^^^^^^^^

Read results from existing files without executing calculations.
With Gaussian, reads from log files; with PySCF, reads from checkpoint (``.chk``) files.

* **Example**: ``mcal xxx.cif p -r``

``-rp, --read_pickle``
^^^^^^^^^^^^^^^^^^^^^^

Read results from existing pickle file without executing calculations.

* **Example**: ``mcal xxx_result.pkl p -rp``

``--resume``
^^^^^^^^^^^^

Resume calculation using existing results.
With Gaussian, checks log file termination; with PySCF, checks for existing checkpoint (``.chk``) files.

* **Example**: ``mcal xxx.cif p --resume``

``--fullcal``
^^^^^^^^^^^^^

Disable all speedup processing and calculate transfer integrals for all pairs from scratch.
The following two optimizations are disabled:

1. **Pair screening**: pairs are normally skipped based on moment of inertia and center-of-mass
   distance; ``--fullcal`` disables this screening.
2. **Monomer caching**: monomer SCF calculations for the same molecule type are normally skipped
   by reusing a previously computed result file; ``--fullcal`` forces all monomer calculations
   to be performed from scratch.

* **Example**: ``mcal xxx.cif p --fullcal``

``--no-monomer-cache``
^^^^^^^^^^^^^^^^^^^^^

Disable only monomer caching. Pair screening remains active.
All monomer SCF calculations are performed from scratch instead of reusing
previously computed result files.
When performing detailed transfer integral analysis using
`tcal <https://github.com/matsui-lab-yamagata/tcal>`_, it is recommended to use this option.

* **Example**: ``mcal xxx.cif p --no-monomer-cache``

``--cellsize <number>``
^^^^^^^^^^^^^^^^^^^^^^^

Specify the number of unit cells to expand in each direction around the central unit cell
for transfer integral calculations.

* **Default**: ``2`` (creates 5x5x5 supercell)
* **Examples**:

  * ``mcal xxx.cif p --cellsize 1`` (creates 3x3x3 supercell)
  * ``mcal xxx.cif p --cellsize 3`` (creates 7x7x7 supercell)

Output Settings
~~~~~~~~~~~~~~~

``-p, --pickle``
^^^^^^^^^^^^^^^^

Save calculation results to a pickle file.

* **Example**: ``mcal xxx.cif p -p``

``--plot-plane <plane>``
^^^^^^^^^^^^^^^^^^^^^^^^^

Plot mobility tensor as a 2D polar plot on specified crystallographic plane.

* **Available planes**: ``ab``, ``ac``, ``ba``, ``bc``, ``ca``, ``cb``
* **Default**: None (no plot generated)
* **Examples**:

  * ``mcal xxx.cif p --plot-plane ab`` (plot on ab-plane)
  * ``mcal xxx.cif p --plot-plane bc`` (plot on bc-plane)

Practical Usage Examples
-------------------------

Basic Calculations
~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Calculate mobility of p-type xxx
   mcal xxx.cif p

   # Use 8 CPUs and 16GB memory
   mcal xxx.cif p -c 8 -m 16

High-Precision Calculations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Calculate transfer integrals for all pairs (high precision, time-consuming)
   mcal xxx.cif p --fullcal

   # Use larger supercell to widen transfer integral calculation range
   mcal xxx.cif p --cellsize 3

   # Use different basis set
   mcal xxx.cif p -M "B3LYP/6-311G(d,p)"

PySCF Calculations
~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Calculate using PySCF (CPU)
   mcal xxx.cif p --pyscf

   # Calculate using PySCF with GPU acceleration (no --pyscf needed)
   mcal xxx.cif p --gpu4pyscf

   # Use 8 CPUs and 16GB memory with PySCF
   mcal xxx.cif p --pyscf -c 8 -m 16

   # Resume interrupted PySCF calculation
   mcal xxx.cif p --pyscf --resume

   # Read from existing PySCF checkpoint files
   mcal xxx.cif p --pyscf -r

Reusing Results
~~~~~~~~~~~~~~~

.. code-block:: bash

   # Read from existing calculation results
   mcal xxx.cif p -r

   # Read from existing pickle file
   mcal xxx_result.pkl p -rp

   # Resume interrupted calculation
   mcal xxx.cif p --resume

   # Save results to pickle file
   mcal xxx.cif p -p

Output
------

Standard Output
~~~~~~~~~~~~~~~

* Reorganization energy
* Transfer integrals for each pair
* Diffusion coefficient tensor
* Mobility tensor
* Eigenvalues and eigenvectors of mobility

Generated Files
~~~~~~~~~~~~~~~

Reorganization Energy Files
^^^^^^^^^^^^^^^^^^^^^^^^^^^

The following files are generated during reorganization energy calculation
(``c`` = cation for p-type, ``a`` = anion for n-type):

**Gaussian:**

* ``xxx_opt_n.gjf`` / ``xxx_opt_n.log`` — geometry optimization of neutral molecule
* ``xxx_c.gjf`` / ``xxx_c.log`` (or ``xxx_a``) — SP energy of ion at neutral geometry
* ``xxx_opt_c.gjf`` / ``xxx_opt_c.log`` (or ``xxx_opt_a``) — geometry optimization of ion
* ``xxx_n.gjf`` / ``xxx_n.log`` — SP energy of neutral at ion geometry

**PySCF:**

* ``xxx_opt_n.xyz`` / ``xxx_opt_n.chk`` — geometry optimization of neutral molecule
* ``xxx_c.chk`` (or ``xxx_a.chk``) — SP energy of ion at neutral geometry
* ``xxx_opt_c.xyz`` / ``xxx_opt_c.chk`` (or ``xxx_opt_a``) — geometry optimization of ion
* ``xxx_n.chk`` — SP energy of neutral at ion geometry

Transfer Integral Files
^^^^^^^^^^^^^^^^^^^^^^^

mcal generates calculation files named using the ``(s_t_i_j_k)`` notation:

.. list-table::
   :header-rows: 1

   * - Symbol
     - Meaning
   * - ``s``
     - Molecule index in the reference unit cell (0,0,0)
   * - ``t``
     - Molecule index in the neighboring unit cell
   * - ``i``
     - Translation index along the **a**-axis
   * - ``j``
     - Translation index along the **b**-axis
   * - ``k``
     - Translation index along the **c**-axis

**Example:** ``xxx-(0_0_1_0_0)`` represents the transfer integral between the 0th molecule
in the (0,0,0) cell and the 0th molecule in the (1,0,0) cell.

**Gaussian:**

* ``xxx-(s_t_i_j_k).gjf`` / ``xxx-(s_t_i_j_k).log`` — dimer
* ``xxx-(s_t_i_j_k)_m1.gjf`` / ``xxx-(s_t_i_j_k)_m1.log`` — monomer 1
* ``xxx-(s_t_i_j_k)_m2.gjf`` / ``xxx-(s_t_i_j_k)_m2.log`` — monomer 2

**PySCF:**

* ``xxx-(s_t_i_j_k).xyz`` / ``xxx-(s_t_i_j_k).chk`` — dimer
* ``xxx-(s_t_i_j_k)_m1.chk`` — monomer 1
* ``xxx-(s_t_i_j_k)_m2.chk`` — monomer 2

Notes
-----

.. note::

   1. **Calculation Time**: Calculation time varies significantly depending on the number of
      molecules and cell size. By default, two speedup mechanisms are enabled: pair pre-screening
      (skipping pairs unlikely to have significant transfer integrals) and monomer caching
      (reusing the isolated-molecule SCF result for molecule types already computed).
      Use ``--fullcal`` to disable both.
   2. **Memory Usage**: Ensure sufficient memory for large systems
   3. **Gaussian Installation**: Gaussian 09 or Gaussian 16 is required
   4. **Dependencies**: Make sure all required Python libraries are installed

Troubleshooting
---------------

If calculation stops midway
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Resume with --resume option
   mcal xxx.cif p --resume

Memory shortage error
~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Increase memory amount
   mcal xxx.cif p -m 32

To reduce calculation time
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Enable speedup processing (default)
   mcal xxx.cif p

   # Use smaller supercell for faster calculation
   mcal xxx.cif p --cellsize 1

   # Increase number of CPUs
   mcal xxx.cif p -c 16

If a CIF file cannot be read
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CIF files come in various formats, and some may not be readable by mcal. Please try the following:

1. **Convert the CIF format using another software**: Use software such as
   `Mercury <https://www.ccdc.cam.ac.uk/solutions/software/mercury/>`_ to open the CIF file
   and re-export it, which may resolve the issue.
2. **Contact us**: If you send the unreadable CIF file to us by email, we will work on adding
   support for it. Please contact us at the email address listed in the Authors section below.

Authors
=======

`Matsui Laboratory, Research Center for Organic Electronics (ROEL), Yamagata University <https://matsui-lab.yz.yamagata-u.ac.jp/index-e.html>`_

* Hiroyuki Matsui
* Koki Ozawa

Email: h-matsui[at]yz.yamagata-u.ac.jp (Please replace ``[at]`` with ``@``)

License
=======

This project is released under the MIT License.

For more details, see the `LICENSE file on GitHub <https://github.com/matsui-lab-yamagata/mcal/blob/main/LICENSE>`_.

Acknowledgements
================

This work was supported by JSPS Grant-in-Aid for JSPS Fellows Grant Number JP25KJ0647.

API Reference
=============

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   modules

Indices and Tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
