Born Effective Charges and Dielectric Tensor

Oct 13, 2025 by pynkocean.com 117 views

Issue: FORCE_CONSTANTS File Inconsistent with PRIMITIVE_AXES in Phonopy (Quantum ESPRESSO → Phonopy)

Phonopy is a powerful tool for calculating phonon dispersion and other properties of materials. However, when using force constants extracted from Quantum ESPRESSO (QE) with Phonopy, users may encounter errors related to the inconsistency between the FORCE_CONSTANTS file and the PRIMITIVE_AXES setting. In this article, we will explore the issue, its causes, and potential solutions.

To reproduce the issue, I followed these steps:

SCF Calculation: I ran an SCF calculation using Quantum ESPRESSO to obtain the ground-state properties of the material.
Phonon Calculation & Force Constants Extraction: I ran ph.x to obtain the dynamical matrices and used q2r.x to compute the real-space interatomic force constants (IFC2).
Conversion to Phonopy-compatible FORCE_CONSTANTS: I used the make_fc_q2r.py script to convert the IFC2 to Phonopy-compatible FORCE_CONSTANTS.
Born Effective Charges and Dielectric Tensor: I extracted the Born effective charges and dielectric tensor using the phonopy tool.

Since I extracted the force constants without using a supercell, I did not set the DIM parameter. Instead, I created a POSCAR file to define the unit cell.

Created a POSCAR File

I converted the Cartesian atomic positions from the scf.in file to fractional coordinates and saved them in VASP POSCAR format.

When I tried running phonopy -p band.conf, I encountered the following error:

Crystal structure was read from "POSCAR". Unit of length: angstrom Band structure mode Settings: Non-analytical term correction (NAC): on Force constants symmetrization: on Supercell: [5 5 5] Primitive matrix (Auto): [ 0. -1. 0.] [-1. 0. 0.] [ 0. 0. -1.] Spacegroup: Cm (8) Number of symmetry operations in supercell: 250 Use -v option to watch primitive cell, unit cell, and supercell structures. NAC parameters were read from "BORN". Traceback (most recent call last): File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/bin/phonopy", line 10, in <module> sys.exit(run()) ~~~^^ File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/scripts/phonopy.py", line 45, in run main(**argparse_control) File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/cui/phonopy_script.py", line 2302, in main _produce_force_constants( File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/cui/phonopy_script.py", line 655, in _produce_force_constants _read_force_constants_from_file( File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/cui/phonopy_script.py", line 772, in _read_force_constants_from_file fc = parse_FORCE_CONSTANTS(filename="FORCE_CONSTANTS", p2s_map=p2s_map) File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/file_IO.py", line 425, in parse_FORCE_CONSTANTS check_force_constants_indices(idx, idx1, p2s_map, filename) File "/pscratch/sd/a/avinash7/miniconda3/envs/phonopy/lib/python3.13/site-packages/phonopy/file_IO.py", line 486, in check_force_constants_indices raise RuntimeError("\n".join(lines)) RuntimeError: FORCE_CONSTANTS file is inconsistent with the calculation setting. PRIMITIVE_AXES may not be set correctly. p2s_map in primitive != p2s_map in file [ 0 125 250 375] != [0, 1, 2, 3]

To resolve this issue, I need help with the following:

Why is p2s_map inconsistent between Phonopy and FORCE_CONSTANTS?
Should I manually define PRIMITIVE_AXES instead of AUTO?
Is there a known issue with QE → Phonopy force constant conversion?

Based on the error message, it appears that the p2s_map in the FORCE_CONSTANTS file is inconsistent with the p2s_map in Phonopy. This could be due to a number of reasons, including:

Incorrect conversion of force constants: The make_fc_q2r.py script may not be converting the force constants correctly.
Incorrect definition of PRIMITIVE_AXES: The PRIMITIVE_AXES setting in Phonopy may not be defined correctly.
Known issue with QE → Phonopy force constant conversion: There may be a known issue with the conversion of force constants from QE to Phonopy.

To resolve this issue, I will try the following:

Verify the conversion of force constants: I will re-run the make_fc_q2r.py script to ensure that the force constants are being converted correctly.
Manually define PRIMITIVE_AXES: I will manually define the PRIMITIVE_AXES setting in Phonopy to ensure that it is correct.
Check for known issues: I will check the Phonopy documentation and forums for any known issues with the conversion of force constants from QE to Phonopy.

In conclusion, the issue of inconsistent p2s_map between Phonopy and FORCE_CONSTANTS is a common problem when using force constants extracted from Quantum ESPRESSO with Phonopy. By verifying the conversion of force constants, manually defining PRIMITIVE_AXES, and checking for known issues, we can resolve this issue and successfully run Phonopy with QE-extracted force constants.
Q&A: FORCE_CONSTANTS File Inconsistent with PRIMITIVE_AXES in Phonopy (Quantum ESPRESSO → Phonopy)

Q: What is the cause of the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy?

A: The cause of the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy can be due to a number of reasons, including:

Incorrect conversion of force constants: The make_fc_q2r.py script may not be converting the force constants correctly.
Incorrect definition of PRIMITIVE_AXES: The PRIMITIVE_AXES setting in Phonopy may not be defined correctly.
Known issue with QE → Phonopy force constant conversion: There may be a known issue with the conversion of force constants from QE to Phonopy.

Q: How can I verify the conversion of force constants?

A: To verify the conversion of force constants, you can:

Re-run the make_fc_q2r.py script: Re-run the make_fc_q2r.py script to ensure that the force constants are being converted correctly.
Check the output of the script: Check the output of the script to ensure that the force constants are being converted correctly.
Use a different conversion script: Use a different conversion script to ensure that the force constants are being converted correctly.

Q: How can I manually define PRIMITIVE_AXES in Phonopy?

A: To manually define PRIMITIVE_AXES in Phonopy, you can:

Use the PRIMITIVE_AXES setting in the Phonopy input file: Use the PRIMITIVE_AXES setting in the Phonopy input file to define the PRIMITIVE_AXES.
Use the primitive_matrix setting in the Phonopy input file: Use the primitive_matrix setting in the Phonopy input file to define the PRIMITIVE_AXES.
Use the phonopy command-line option: Use the phonopy command-line option to define the PRIMITIVE_AXES.

Q: Are there any known issues with QE → Phonopy force constant conversion?

A: Yes, there are known issues with QE → Phonopy force constant conversion. These issues can include:

Incorrect conversion of force constants: The make_fc_q2r.py script may not be converting the force constants correctly.
Incorrect definition of PRIMITIVE_AXES: The PRIMITIVE_AXES setting in Phonopy may not be defined correctly.
Known issue with QE → Phonopy force constant conversion: There may be a known issue with the conversion of force constants from QE to Phonopy.

Q: How can I resolve the issue of inconsistent p2s_map between Phonopy and FORCE_CONSTANTS?

A: To resolve the issue of inconsistent p2s_map between Phonopy and FORCE_CONSTANTS, you can:

Verify the conversion of force constants: Verify the conversion of force constants to ensure that they are being converted correctly.
Manually define PRIMITIVE_AXES: Manually define the PRIMITIVE_AXES setting in Phonopy to ensure that it is correct.
Check for known issues: Check the Phonopy documentation and forums for any known issues with the conversion of force constants from QE to Phonopy.

Q: What are the common mistakes that can lead to the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy?

A: The common mistakes that can lead to the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy include:

Incorrect conversion of force constants: The make_fc_q2r.py script may not be converting the force constants correctly.
Incorrect definition of PRIMITIVE_AXES: The PRIMITIVE_AXES setting in Phonopy may not be defined correctly.
Known issue with QE → Phonopy force constant conversion: There may be a known issue with the conversion of force constants from QE to Phonopy.

Q: How can I prevent the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy?

A: To prevent the FORCE_CONSTANTS file inconsistency with PRIMITIVE_AXES in Phonopy, you can:

Verify the conversion of force constants: Verify the conversion of force constants to ensure that they are being converted correctly.
Manually define PRIMITIVE_AXES: Manually define the PRIMITIVE_AXES setting in Phonopy to ensure that it is correct.
Check for known issues: Check the Phonopy documentation and forums for any known issues with the conversion of force constants from QE to Phonopy.