mcal Documentation¶

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, PySCF, or ORCA
Calculation of transfer integrals
Calculation of reorganization energy
Computation of mobility tensors and eigenvalues

Requirements¶

Python 3.11 or newer
NumPy
Pandas
Matplotlib
yu-tcal==5.0.1

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))
ORCA 6.1.0 or newer

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)¶

pip install yu-mcal

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

pip install "yu-mcal[pyscf]"

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

Check your installed CUDA Toolkit version:

nvcc --version

Install mcal with GPU acceleration:

If your CUDA Toolkit version is 13.x:

pip install "yu-mcal[gpu4pyscf-cuda13]"

If your CUDA Toolkit version is 12.x:

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

If your CUDA Toolkit version is 11.x:

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

Using ORCA 6.1.0 or newer¶

pip install "yu-mcal[orca]"

Verify Installation¶

After installation, you can verify by running:

mcal --help

mcal Usage Manual¶

Basic Usage¶

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¶

# 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

`--bse`¶

Use Basis Set Exchange for basis-set definitions (PySCF only).

Example: mcal xxx.cif p --pyscf --bse -M "B3LYP/def2-SVP"

ORCA Settings¶

`--orca`¶

Use ORCA instead of Gaussian for all calculations. Requires yu-mcal[orca].

Example: mcal xxx.cif p --orca

`--mpi <path>`¶

Specify the path to the OpenMPI installation directory for ORCA parallel execution. This sets the OPI_MPI environment variable used by the ORCA Python Interface (OPI). Only valid with --orca.

Example: mcal xxx.cif p --orca --mpi /usr/lib/x86_64-linux-gnu/openmpi

Parallel Execution¶

To use multiple CPU cores (--cpu N), OpenMPI must be installed. First, confirm that mpirun is available:

which mpirun

If OpenMPI is already in $PATH and $LD_LIBRARY_PATH (common on Linux/WSL after apt install), no further configuration is needed.

If parallel execution does not work, find the OpenMPI base directory (the directory that contains bin/ and lib/) and pass it via OPI_MPI or --mpi.

Linux / WSL¶

Note

ORCA requires a specific version of OpenMPI. The version available via apt may not match. If parallel execution fails, it is recommended to build OpenMPI from source using the version specified in the ORCA documentation.

When mpirun is installed under a dedicated directory (e.g., built from source or via a module system):

which mpirun
# e.g., /opt/openmpi/bin/mpirun  →  base: /opt/openmpi
export OPI_MPI=$(dirname $(dirname $(which mpirun)))

When installed system-wide via apt (Ubuntu/Debian), mpirun is typically at /usr/bin/mpirun but the OpenMPI libraries live under /usr/lib/. Check with:

which mpirun
# /usr/bin/mpirun  →  base is usually /usr/lib/x86_64-linux-gnu/openmpi
export OPI_MPI=/usr/lib/x86_64-linux-gnu/openmpi

macOS (Homebrew)¶

which mpirun
# e.g., /opt/homebrew/bin/mpirun
export OPI_MPI=$(brew --prefix open-mpi)

Passing the path with `--mpi`¶

Instead of setting the environment variable, you can pass the path directly:

mcal xxx.cif p --orca -c 8 --mpi /path/to/openmpi

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; with ORCA, reads from output (.out) 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; with ORCA, checks .out file termination.

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:

Pair screening: pairs are normally skipped based on moment of inertia and center-of-mass distance; --fullcal disables this screening.
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, 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

`-j, --json`¶

Save calculation results to a JSON file (<input>_result.json). Contains reorganization energy (with intermediate energies), transfer integrals, diffusion coefficient tensor, mobility tensor, eigenvalues, and eigenvectors, along with metadata (mcal version, method, backend). Can be combined with -p.

Example: mcal xxx.cif p -j

`--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¶

# 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¶

# 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¶

# 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

# Use Basis Set Exchange with --method in PySCF mode
mcal xxx.cif p --pyscf --bse -M "B3LYP/def2-SVP"

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

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

ORCA Calculations¶

# Calculate using ORCA
mcal xxx.cif p --orca

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

# Specify OpenMPI path for ORCA parallel execution
mcal xxx.cif p --orca --mpi /usr/lib/x86_64-linux-gnu/openmpi

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

# Read from existing ORCA output files
mcal xxx.cif p --orca -r

Reusing Results¶

# 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

ORCA:

xxx_opt_n_input.xyz / xxx_opt_n.out / xxx_opt_n.xyz — geometry optimization of neutral molecule
xxx_c_input.xyz / xxx_c.out (or xxx_a) — SP energy of ion at neutral geometry
xxx_opt_c_input.xyz / xxx_opt_c.out / xxx_opt_c.xyz (or xxx_opt_a) — geometry optimization of ion
xxx_n_input.xyz / xxx_n.out — SP energy of neutral at ion geometry

Transfer Integral Files¶

mcal generates calculation files named using the (s_t_i_j_k) notation (Gaussian and PySCF). For ORCA, the @s_t_i_j_k notation is used instead because ORCA cannot handle parentheses in filenames.

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 (Gaussian / PySCF): 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.

Example (ORCA): xxx@0_0_1_0_0 represents the same pair as above.

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

ORCA:

xxx@s_t_i_j_k.xyz / xxx@s_t_i_j_k.out — dimer
xxx@s_t_i_j_k_m1.out — monomer 1
xxx@s_t_i_j_k_m2.out — monomer 2

Notes¶

Note

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.
Memory Usage: Ensure sufficient memory for large systems
Gaussian Installation: Gaussian 09 or Gaussian 16 is required
Dependencies: Make sure all required Python libraries are installed

Troubleshooting¶

If calculation stops midway¶

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

Memory shortage error¶

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

To reduce calculation time¶

# 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:

Convert the CIF format using another software: Use software such as Mercury to open the CIF file and re-export it, which may resolve the issue.
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

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.

Acknowledgements¶

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

References¶

[1] Qiming Sun et al., Recent developments in the PySCF program package, J. Chem. Phys. 2020, 153, 024109.
[2] Lee-Ping Wang, Chenchen Song, Geometry optimization made simple with translation and rotation coordinates, J. Chem. Phys. 2016, 144, 214108.
[3] Benjamin P. Pritchard et al., New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community, J. Chem. Inf. Model. 2019, 59, 4814-4820.
[4] Frank Neese, The ORCA program system, Wiley Interdiscip. Rev. Comput. Mol. Sci., 2012, 2, 73-78.

API Reference¶

API Reference

mcal
- mcal package

mcal Documentation¶

Overview¶

Features¶

Requirements¶

Quantum Chemistry Calculation Tools¶

Installation¶

Using Gaussian 09 or 16 (without PySCF)¶

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

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

Using ORCA 6.1.0 or newer¶

Verify Installation¶

mcal Usage Manual¶

Basic Usage¶

Required Arguments¶

Basic Examples¶

Options¶

Calculation Settings¶

-M, --method <method>¶

-c, --cpu <number>¶

-m, --mem <memory>¶

-g, --g09¶

PySCF Settings¶

--pyscf¶

--gpu4pyscf¶

--cart¶

--bse¶

ORCA Settings¶

--orca¶

--mpi <path>¶

Parallel Execution¶

Linux / WSL¶

macOS (Homebrew)¶

Passing the path with --mpi¶

Calculation Control¶

-r, --read¶

-rp, --read_pickle¶

--resume¶

--fullcal¶

--no-monomer-cache¶

--cellsize <number>¶

Output Settings¶

-p, --pickle¶

-j, --json¶

--plot-plane <plane>¶

Practical Usage Examples¶

Basic Calculations¶

High-Precision Calculations¶

PySCF Calculations¶

ORCA Calculations¶

Reusing Results¶

Output¶

Standard Output¶

Generated Files¶

Reorganization Energy Files¶

Transfer Integral Files¶

Notes¶

Troubleshooting¶

If calculation stops midway¶

Memory shortage error¶

To reduce calculation time¶

If a CIF file cannot be read¶

Authors¶

License¶

Acknowledgements¶

References¶

API Reference¶

Indices and Tables¶

`-M, --method <method>`¶

`-c, --cpu <number>`¶

`-m, --mem <memory>`¶

`-g, --g09`¶

`--pyscf`¶

`--gpu4pyscf`¶

`--cart`¶

`--bse`¶

`--orca`¶

`--mpi <path>`¶

Passing the path with `--mpi`¶

`-r, --read`¶

`-rp, --read_pickle`¶

`--resume`¶

`--fullcal`¶

`--no-monomer-cache`¶

`--cellsize <number>`¶

`-p, --pickle`¶

`-j, --json`¶

`--plot-plane <plane>`¶