Understanding Symmetry Inequivalent Atoms

Oct 13, 2025 by wbrum.org 24 views

Introduction

When performing a vc-relax calculation on a supercell of a material, it is often necessary to extract the positions of only the symmetry inequivalent atoms. This can be particularly useful when analyzing the results of the calculation, as it allows you to focus on the unique atoms that contribute to the material's properties. In this article, we will discuss how to extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms after a vc-relax calculation.

Understanding Symmetry Inequivalent Atoms

Symmetry inequivalent atoms are atoms that are not equivalent under the symmetry operations of the crystal lattice. In other words, they are atoms that have unique positions and cannot be transformed into each other by applying the symmetry operations of the lattice. In the context of a vc-relax calculation, symmetry inequivalent atoms are those that have unique positions in the supercell and are not equivalent to each other.

Using the `space_group` Option

To extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms, you need to use the space_group option in your vc-relax input file. The space_group option specifies the space group of the material, which is used to determine the symmetry operations of the lattice. In your case, you have specified space_group = 221, which corresponds to the cubic space group.

Extracting Symmetry Inequivalent Atoms

To extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms, you can use the following steps:

Run the vc-relax calculation: First, you need to run the vc-relax calculation on your supercell of CsPbI3 with a Pb vacancy.
Extract the ATOMIC_POSITIONS: After the calculation is complete, you can extract the ATOMIC_POSITIONS from the vc-relax output file.
Use the space_group option: To extract only the symmetry inequivalent atoms, you need to use the space_group option in your input file.
Use the symmetry option: You also need to use the symmetry option to specify the symmetry operations of the lattice.
Extract the unique atoms: Finally, you can extract the unique atoms from the output file using the symmetry option.

Example Input File

Here is an example input file that you can use to extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms:

&system
 ibrav = 2
 celldm(1) = 10.0
 celldm(2) = 10.0
 celldm(3) = 10.0
 nat = 16
 ntyp = 2
 typat = 1 2
 znucl = 82 53
 &
&electrons
 encut = 500
 ediff = 1e-6
 ediffg = -1e-4
 &
&ions
 ion_dynamics = 'verlet'
 &
&symmetry
 space_group = 221
 &
&atomic_positions
 ATOMIC_POSITIONS {alat}
  Pb  0.0000000000000000  0.0000000000000000  0.0000000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.750000000000<br/>
# How to extract ATOMIC_POSITIONS of only symmetry inequivalent atoms after vc-relax calculation?
Introduction
When performing a vc-relax calculation on a supercell of a material, it is often necessary to extract the positions of only the symmetry inequivalent atoms. This can be particularly useful when analyzing the results of the calculation, as it allows you to focus on the unique atoms that contribute to the material's properties. In this article, we will discuss how to extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms after a vc-relax calculation.
Understanding Symmetry Inequivalent Atoms
Symmetry inequivalent atoms are atoms that are not equivalent under the symmetry operations of the crystal lattice. In other words, they are atoms that have unique positions and cannot be transformed into each other by applying the symmetry operations of the lattice. In the context of a vc-relax calculation, symmetry inequivalent atoms are those that have unique positions in the supercell and are not equivalent to each other.
Using the space_group Option
To extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms, you need to use the space_group option in your vc-relax input file. The space_group option specifies the space group of the material, which is used to determine the symmetry operations of the lattice. In your case, you have specified space_group = 221, which corresponds to the cubic space group.
Extracting Symmetry Inequivalent Atoms
To extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms, you can use the following steps:

Run the vc-relax calculation: First, you need to run the vc-relax calculation on your supercell of CsPbI3 with a Pb vacancy.
Extract the ATOMIC_POSITIONS: After the calculation is complete, you can extract the ATOMIC_POSITIONS from the vc-relax output file.
Use the space_group option: To extract only the symmetry inequivalent atoms, you need to use the space_group option in your input file.
Use the symmetry option: You also need to use the symmetry option to specify the symmetry operations of the lattice.
Extract the unique atoms: Finally, you can extract the unique atoms from the output file using the symmetry option.

Example Input File
Here is an example input file that you can use to extract the ATOMIC_POSITIONS of only symmetry inequivalent atoms:
&amp;system
 ibrav = 2
 celldm(1) = 10.0
 celldm(2) = 10.0
 celldm(3) = 10.0
 nat = 16
 ntyp = 2
 typat = 1 2
 znucl = 82 53
 &amp;
&amp;electrons
 encut = 500
 ediff = 1e-6
 ediffg = -1e-4
 &amp;
&amp;ions
 ion_dynamics = &#39;verlet&#39;
 &amp;
&amp;symmetry
 space_group = 221
 &amp;
&amp;atomic_positions
 ATOMIC_POSITIONS {alat}
  Pb  0.0000000000000000  0.0000000000000000  0.0000000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.7500000000000000
  I  0.7500000000000000  0.7500000000000000  0.7500000000000000
  I  0.2500000000000000  0.7500000000000000  0.7500000000000000
  I  0.7500000000000000  0.2500000000000000  0.7500000000000000
  I  0.2500000000000000  0.2500000000000000  0.2500000000000000
  I  0.7500000000000000  0.7500000000000000  0.2500000000000000
  I  0.2500000000000000  0.7500000000000000  0.2500000000000000
  I  0.7500000000000000  0.2500000000000000  0.2500000000000000
  I  0.2500000000000000  0.2500000000000000  0.750000000000</code></pre>


                
                    
                        

                    
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