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Manual Pseudopotentials and orbitals Examples

 

3.1.2 The STRU file

 

The STRU file contains the information about the name(s) and/or location(s) of the pseudopotential and numerical orbital files, as well as the structural information about the system. Take the diamond as an example, there are only two atoms in the primitive cell, and its STRU file looks as follows:

 

ATOMIC_SPECIES
Si 1.000 Si.pz-vbc.UPF // label; mass; pseudo_file
NUMERICAL_ORBITAL
Si_lda_8.0au_50Ry_2s2p1d //numerical_orbital_file
LATTICE_CONSTANT
10.2 // lattice scaling factor (Bohr)
LATTICE_VECTORS
0.5 0.5 0.0 // latvec1
0.5 0.0 0.5 // latvec2
0.0 0.5 0.5 // latvec3
ATOMIC_POSITIONS
Direct //Cartesian or Direct coordinate.
Si // Element type
0.0 // magnetism
2 // number of atoms
0.00 0.00 0.00 0 0 0
0.25 0.25 0.25 1 1 1

 


The STRU file contains several sections, and each section must start with a keyword like ATOMIC_SPECIES, NUMERICAL_ORBITAL, or LATTICE_ CONSTANT, etc. to signify what type of information that comes below.
In this example, only the names of the pseudopotential and numerical orbital files are given, but not the location. This simply means these files are located in the work directory.



1. ATOMIC_SPECIES

This section provides information about the type of chemical elements contained the unit cell. Each line defines one type of element. The user should specify the name, the mass, and the pseudopotential file used for each element. The mass of the elment is only used in molecular dynamics simulations. For electronic-structure calculations, the actual mass value isn’t important, and it is set to 1.000 here. ‘Si.pz-vbc.UPF’ is the pseudopotential file. Here, no explicit path is specified, and this simply means that the file is located in work directory. If this is not the case, please explicitly specify the precise location of the pseudopotential file.



2. NUMERICAL_ORBITAL

Numerical atomic orbitals are only needed for LCAO calculations. Thus this section will be neglected in PW calcultions. ‘Si_50Ry_8.0au_dzp’ is name of the numerical orbital file. Again here the path is not specified, which means that this file is located in the work directory.



3. LATTICE_CONSTANT

The lattice constant of the system in unit of Bohr.



4. LATTICE_VECTORS

The lattice vectors of the unit cell. It is a 3×3 matrix written in 3 lines. Please note that the lattice vectors here are scaled by the lattice constant.



5. ATOMIC_POSITIONS

This section specifies the positions and other information of individual atoms. The first line signifies whether atom positions are given in Cartesian or Direct coordinates.

The following three lines tells the elemental type (Si), the initial magnetic moment (0.0), and the number of atoms for this particular element (2) repsectively.
The last two lines in this example are the coordinates of atomic positions. There are six numbers in each line: the first three specifies the atomic positions and the last three control how the atom move in geometry relaxation calculations. The numbers “0 0 0” following the coordinates of the first atom means this atom are not allowed to move in all three directions, and the numbers “1 1 1” following the coordinates of the second atommeans this atom can move in all three directions.

 

 

 

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