tcal Documentation¶

Requirements¶

Python 3.9 or newer
NumPy
Gaussian 09 or 16

Important

The path of the Gaussian must be set.

Installation¶

pip install yu-tcal

Verify Installation¶

After installation, you can verify by running:

tcal --help

Options¶

Short	Long	Explanation
`-a`	`--apta`	Perform atomic pair transfer analysis.
`-c`	`--cube`	Generate cube files.
`-g`	`--g09`	Use Gaussian 09. (default is Gaussian 16)
`-h`	`--help`	Show options description.
`-l`	`--lumo`	Perform atomic pair transfer analysis of LUMO.
`-m`	`--matrix`	Print MO coefficients, overlap matrix and Fock matrix.
`-o`	`--output`	Output csv file on the result of apta.
`-r`	`--read`	Read log files without executing Gaussian.
`-x`	`--xyz`	Convert xyz file to gjf file.
	`--napta N1 N2`	Perform atomic pair transfer analysis between different levels. N1 is the number of level in the first monomer. N2 is the number of level in the second monomer.
	`--hetero N`	Calculate the transfer integral of heterodimer. N is the number of atoms in the first monomer.
	`--nlevel N`	Calculate transfer integrals between different levels. N is the number of levels from HOMO-LUMO. N=0 gives all levels.
	`--skip N...`	Skip specified Gaussian calculation. If N is 1, skip 1st monomer calculation. If N is 2, skip 2nd monomer calculation. If N is 3, skip dimer calculation.

How to Use¶

1. Create gjf file¶

First of all, create a gaussian input file as follows:

Example: xxx.gjf

The xxx part is an arbitrary string.

Description of link commands¶

pop=full: Required to output coefficients of basis functions, overlap matrix, and Fock matrix.
iop(3/33=4,5/33=3): Required to output coefficients of basis functions, overlap matrix, and Fock matrix.

How to create a gjf using Mercury¶

Open cif file in Mercury.
Display the dimer you want to calculate.
Save in mol file or mol2 file.
Open a mol file or mol2 file in GaussView and save it in gjf format.

2. Execute tcal¶

Suppose the directory structure is as follows:

yyy
└── xxx.gjf

Open a terminal.
Go to the directory where the files is located.
```
cd yyy
```
Execute the following command.
```
tcal -a xxx.gjf
```

3. Visualization of molecular orbitals¶

Execute the following command.
```
tcal -cr xxx.gjf
```
Open xxx.fchk in GaussView.
[Results] → [Surfaces/Contours…]
[Cube Actions] → [Load Cube]
Open xxx_m1_HOMO.cube and xxx_m2_HOMO.cube.
Visualize by operating [Surface Actions] → [New Surface].

Interatomic Transfer Integral¶

For calculating the transfer integral between molecule A and molecule B, DFT calculations were performed for monomer A, monomer B, and the dimer AB. The monomer molecular orbitals \(\ket{A}\) and \(\ket{B}\) were obtained from the monomer calculations. Fock matrix F was calculated in the dimer system. Finally the intermolecular transfer integral \(t^{[1]}\) was calculated by using the following equation:

\[t = \frac{\braket{A|F|B} - \frac{1}{2} (\epsilon_{A}+\epsilon_{B})\braket{A|B}}{1 - \braket{A|B}^2},\]

where \(\epsilon_A \equiv \braket{A|F|A}\) and \(\epsilon_B \equiv \braket{B|F|B}\).

In addition to the intermolecular transfer integral in general use, we developed an interatomic transfer integral for further analysis \(^{[2]}\). By grouping the basis functions \(\ket{i}\) and \(\ket{j}\) for each atom, the molecular orbitals can be expressed as

\[\ket{A} = \sum^A_{\alpha} \sum^{\alpha}_i a_i \ket{i},\]

\[\ket{B} = \sum^B_{\beta} \sum^{\beta}_j b_j \ket{j},\]

where \(\alpha\) and \(\beta\) are the indices of atoms, \(i\) and \(j\) are indices of basis functions, and \(a_i\) and \(b_j\) are the coefficients of basis functions. Substituting this formula into aforementioned equation gives

\[t = \sum^A_{\alpha} \sum^B_{\beta} \sum^{\alpha}_i \sum^{\beta}_j a^*_i b_j \frac{\braket{i|F|j} - \frac{1}{2} (\epsilon_A + \epsilon_B) \braket{i|j}}{1 - \braket{A|B}^2}\]

Here we define the interatomic transfer integral \(u_{\alpha\beta}\) as:

\[u_{\alpha \beta} \equiv \sum^{\alpha}_i \sum^{\beta}_j a^*_i b_j \frac{\braket{i|F|j} - \frac{1}{2} (\epsilon_A + \epsilon_B) \braket{i|j}}{1 - \braket{A|B}^2}\]

References¶

[1] Veaceslav Coropceanu et al., Charge Transport in Organic Semiconductors, Chem. Rev. 2007, 107, 926-952.

[2] Koki Ozawa et al., Statistical analysis of interatomic transfer integrals for exploring high-mobility organic semiconductors, Sci. Technol. Adv. Mater. 2024, 25, 2354652.

Citation¶

When publishing works that benefited from tcal, please cite the following article:

Koki Ozawa, Tomoharu Okada, Hiroyuki Matsui, Statistical analysis of interatomic transfer integrals for exploring high-mobility organic semiconductors, Sci. Technol. Adv. Mater., 2024, 25, 2354652.

DOI: 10.1080/14686996.2024.2354652

Example of using tcal¶

API Reference¶

API Reference

src
- tcal package

Indices and Tables¶

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 @)

Acknowledgements¶

This work was supported by JST, CREST, Grand Number JPMJCR18J2.

License¶

This project is released under the MIT License.

For more details, see the LICENSE file on GitHub.