# Brief introduction of the input files¶

## Input¶

The `Input`

file describes the basic information about the system and the parameters required to calculate the function. For a complete list of the input parameters, please consult this input list.

The following is an example of a `Input`

file:

```
INPUT_PARAMETERS
{
nspin 4
package ABACUS
fermi_energy 9.481194886038594
fermi_energy_unit eV
HR_route data-HR-sparse_SPIN0.csr
SR_route data-SR-sparse_SPIN0.csr
rR_route new-data-rR-tr_SPIN4
HR_unit Ry
rR_unit Bohr
max_kpoint_num 8000
}
LATTICE
{
lattice_constant 1.8897162
lattice_constant_unit Bohr
lattice_vector
-2.069 -3.583614 0.000000
2.069 -3.583614 0.000000
0.000 2.389075 9.546667
}
BAND_STRUCTURE
{
wf_collect 0
kpoint_mode line
kpoint_num 5
high_symmetry_kpoint
0.00000 0.00000 0.0000 100 # G
0.00000 0.00000 0.5000 100 # Z
0.50000 0.50000 0.0000 100 # F
0.00000 0.00000 0.0000 100 # G
0.50000 0.00000 0.0000 1 # L
}
```

The `Input`

file consists of three main sections (**INPUT_PARAMETERS**, **LATTICE**, **FUNCTION**), each of which is represented by the `keyword + {}`

, namely:

```
KEYWORD
{
parameter xx
}
```

The **INPUT_PARAMETERS** section is utilized to specify public parameters and indicate the HR, SR, and rR files required for the calculation.

The **LATTICE** section outlines lattice information and includes three parameters: lattice_constant, lattice_constant_unit, and lattice_vector.

The **FUNCTION** section lists the parameters necessary for each calculation function. These parameters differ depending on the specific function being used.

**NOTE**:

The keyword of the section must be capitalized, and the parameters in the section must be lowercase.

Each parameter value is provided by specifying the name of the input variable and then putting the value after the name, separated by one or more blank characters(space or tab).

Any line starting with

`#`

or`//`

will be ignored. To ignore a function section, add`#`

in front of the section name. This will cause all parameters within that function section to be ignored.Proper case is required to avoid reading errors. For example,

`eV`

must not be written as`ev`

, and`Bohr`

must not be written as`bohr`

.

## HR, SR, rR¶

HR, SR, and rR are important input files for PYATB and contain information about the tight binding model, which can be generated by ABACUS.

In the PYATB program, if only the *Bands module* is used, it is enough to provide HR and SR, and specifying rR is not required. However, when the functions of the calculations are related to the *Geometric module* or *Optical module*, the rR file must be specified.

### How to generate HR, SR, rR files using ABACUS¶

Run the **scf** calculation of ABACUS normally, specifies the parameters `out_mat_hs2`

and `out_mat_r`

in the `INPUT`

file, and three files of sparse format `data-HR-sparse_SPIN0.csr`

, `data-SR-sparse_ SPIN0.csr`

, `data-rR-sparse.csr`

(and `data-HR-sparse_SPIN1.csr`

when `nspin`

is 2), will be generated in OUT* folder.

**NOTE**:

nspin=4 and nspin=1, nspin=2 output different files. nspin=4 files contain imaginary numbers, so the correct nspin parameter needs to be strictly specified when executing pyatb programs.

### Format description of HR, SR, rR¶

We use the file `data-HR-sparse_SPIN0.csr`

as an example to explain the format of HR. This file contains a series of \(H(R)\) matrices, where each R corresponds to an \(H(R)\) matrix. The specific format of the file is as follows:

The dimension of the \(H(R)\) matrix is recorded on the first line, for example,

`Matrix Dimension of H(R): 270`

, indicating that each \(H(R)\) matrix is a 270*270 matrix.The number of R is recorded on the second line, for example,

`Matrix number of H(R): 97`

, indicating that there are a total of 97 \(H(R)\) matrices.Starting from the third line, every 4 lines form a group, recording the sparse matrix of \(H(R)\). Following the example above, the file still has 4*97 lines left, divided into 97 groups.

The first line of each group contains 4 integers. The first three numbers represent the

`(x, y, z)`

fractional coordinates of R, and the last number represents the number of non-zero elements in the sparse matrix.The second to fourth lines of each group record the

`data`

,`indices`

, and`indptr`

information of the sparse matrix in`csr`

format.

The sparse matrix `csr`

format is explained below, with reference to `Wikipedia`

. Please refer to Sparse matrix.

We will use the following matrix as an example:

The sparse matrix in `csr`

format has three sets of data, corresponding to three lines in the output file. The first line contains the non-zero element `data`

, the second line contains the column indices of the non-zero elements `indices`

, and the third line contains the row offset `indptr`

.

Note that our counting starts from 0.

First, the first row of the matrix is `4 2 0 0`

, which has 2 non-zero elements `4 2`

, with corresponding column indices `0 1`

. The second row of the matrix is `0 3 0 0`

, which has 1 non-zero element `3`

, with corresponding column index `1`

. The third row of the matrix has 2 non-zero elements `4 5`

, with corresponding column indices `1 2`

. The fourth row is all zeros and has no non-zero elements.

Therefore, we have:

```
data = [4, 2, 3, 4, 5] # non-zero elements
indices = [0, 1, 1, 1, 2] # column indices of each non-zero element
'''
The number of non-zero elements in each row from the first to
the fourth row is 2, 1, 2, 0, respectively;
the corresponding offset values are 0, 2, 3, 5, 5.
These values are used to record the starting offset of each
row's first element in the data array, and can also be used
for the indices array. The number of non-zero elements in
each row can be obtained by subtracting the previous offset value
from the current offset value, i.e., 2-0=2, 3-2=1, 5-3=2, 5-5=0.
'''
# the dimension of this array must be the number of rows of the matrix plus 1.
indptr = [0, 2, 3, 5, 5]
```

**NOTE**:

When the

`npsin`

parameter in the PYATB`Input`

file is set to`1`

or`2`

, the HR matrix read is purely real. When`nspin`

is set to`4`

, the HR matrix read is complex, with matrix elements in the format of`(real part, imaginary part)`

.

The file format for the SR matrix is identical to that of the HR matrix. The rR matrix format is slightly different because it includes the \(r_x\), \(r_y\), and \(r_z\) directions. We use `data-rR-sparse.csr`

as an example to illustrate the rR file format.

The first line is

`Matrix Dimension of r(R): 270`

.The second line is

`Matrix number of r(R): 97`

.The third line consists of three numbers, representing the fractional coordinates

`(x, y, z)`

of R.Starting from the fourth line, every 4 lines form a group, with a total of three groups, recording the \(r_x(R)\), \(r_y(R)\), and \(r_z(R)\) matrices respectively. After that, the loop is performed for different R.

The first line of each group is an integer, recording the number of non-zero elements in the sparse matrix.

The second to fourth lines of each group are in the

`csr`

format of the sparse matrix, recording the`data`

,`indices`

, and`indptr`

information respectively.

## Other file¶

For the calculation of some functions, structure files and NAOs (numerical atomic orbital bases) files are also required.

The structure file

This file describes the structural information about the system, e.g., lattice constant, lattice vectors, and positions of the atoms within a unit cell. The structure file format of ABACUS is currently used.

The NAOs files

This file describes the numerical atomic orbitals used to expand the Hamiltonian. The NAOs file format of ABACUS is currently used.