Table of Contents

1. What is the EOS_2_phonons program ?
2. Data flow
3. Test
4. How to cite
5. Contributing
6. References

What is the EOS_2_phonons program ?

EOS_2_phonons is a program for computational chemistry and physics that allows to automate the runs for frequency calculations, and breaking symmetry over different volumes. The programs on this repository allow to obtain the needed outputs in order to further perform a quasi-harmonic approximation analyisis with the QHA_2D program

The program was developed as part of David Carrasco de Busturia PhD project at Prof. Nicholas Harrison's Computational Materials Science Group, Imperial College London. The program was used to investigate the phase diagram and phase transitions mechanisms on the calcium carbonate system.

Data flow

• Get the code: git clone https://github.com/DavidCdeB/EOS_2_phonons

• Copy to the folder EOS_2_phonons created, the *.out output from the EOS calulation:

EOS
[Optional sub-keywords]
END 

which contains the constant-volume optimization for several geometries.

• Run the program Eos_2_Phonons.py. This will prepare a frequency calculation input for each geometry. Before running this program, you should edit it and substitute [supercell expansion matrix here], [basis set here] and [functional here] by, respectively, the adequate supercell for the phonon calculation, the proper basis set and the DFT functional.

• Run ONE.sh. This will create the directories corresponding to each volume, and will send the jobs to run.

• At this point, we need to detect negative phonons found at certain volumes. These can be detected by running the programs inside the repository search_neg_freqs. Read the instructions in this repository, so that then you can identify which volumes contain a imaginary (negative) frequency.

• The next step is to distort the atomic coordinates along the eigenvectors. It is first necessary to bring these phonons back to the Gamma point. In order words, perform FREQCALC + SUPERCELL type of calculations. Edit the Eos_2_Phonons.py so that it contains the following:

SCELPHONO
[supercell expansion matrix here]
FREQCALC

• Edit TWO.sh, providing the list of volumes under the variable VOLUMES. This will run the frequency calculation bringing the phonons to Gamma.

• Edit Eos_2_Phonons.py so that it contains the following:

SUPERCELL
[supercell expansion matrix here]
FREQCALC
RESTART
SCANMODE
1 -10 10 0.4
1
END
END

Edit also the name of the files, i.e., change this line:

    with open(VOLUMES[vol_i] + '_FREQCALC.d12', 'w') as f:

by this line:

    with open(VOLUMES[vol_i] + '_SCANMODE_1.d12', 'w') as f:

or additionally by this line, if there is a second negative phonon mode:

    with open(VOLUMES[vol_i] + '_SCANMODE_2.d12', 'w') as f:

This will prepare the input files for the SCANMODE runs.

• Run THREE.sh. This will run the scanmodes. Provide the list of volumes under the variable SCANMODE_1_FILES or SCANMODE_2_FILES.

• Run FOUR.sh. This will extract the geometry of the minimum energy displacement of the scanmode. In addition, it will prepare a "findsym" input file for CRYSTAL. This will allow you to obtain a .FINDSYM file, ready to be read by the findsym program [1].

• Run FIVE.sh. This will modify the tolerances of the .FINDSYM file, creating a set of different files corresponding to different tolerances:

0_1.FINDSYM -> 0.1 tolerance
0_01.FINDSYM -> 0.01 tolerance
0_001.FINDSYM -> 0.001 tolerance
0_0001.FINDSYM -> 0.0001 tolerance
0_00001.FINDSYM -> 0.00001 tolerance
0_000001.FINDSYM -> 0.000001 tolerance
0.FINDSYM -> 0 tolerance

Once done this, the findsym program will run, and will generate a cif file for each tolerance.

• Run SIX.sh. This will run the cif2cell program [2] over each of these cif files previously generated. An input file for a constant volume optimization run will be created for the most common tolerance used, 0.1. You would have to change the CVOLOPT_fragment, which is the tail for the input file, specifying the basis set you are using.

• Run SEVEN.sh. This will run the constant volume optimization.

• At this point, if the space group of the broken symmetry structure starts with P, then the primitve cell is equivalent to the crystalographic. In this case, you should run EIGHT.sh. If the broken symmetry structure contains a crystallographic cell different from a primitve, you should run EIGHT.sh by changing every instance of Eos_2_Phonons_when_threre_is_no_crystallographic_cell.py by Eos_2_Phonons.py.

Test

Under the TEST folder, you will find all the programs needed, together with a *out folder with the frequency output.

How to cite

Please cite the following reference when using this code:

D. Carrasco-Busturia, "The temperature - pressure phase diagram of the calcite I - calcite II phase transition: A first-principles investigation", Journal of Physics and Chemistry of Solids, vol. 154, p. 110 045, 2021. DOI: https://doi.org/10.1016/j.jpcs.2021.110045.

Here the bibtex:

@article{CARRASCOBUSTURIA2021110045,                                                                        
title = {The temperature - pressure phase diagram of the calcite {I} - calcite {II} phase transition: A first-principles investigation},
journal = {Journal of Physics and Chemistry of Solids},
volume = {154},
pages = {110045},
year = {2021},
issn = {0022-3697},
doi = {https://doi.org/10.1016/j.jpcs.2021.110045},
url = {https://www.sciencedirect.com/science/article/pii/S0022369721001116},
author = {David Carrasco-Busturia}
}

Contributing

QHA is free software released under the Gnu Public Licence version 3. All contributions to improve this code are more than welcome.

• Have a look at GitHub's "How to contribute".

• If you are familiar with git: fork this repository and submit a pull request.

• If you are not familiar with git:

  • If something should be improved, open an issue here on GitHub
  • If you think a new feature would be interesting, open an issue
  • If you need a particular feature for your project contact me directly.

References

[1] Stokes, Harold T. and Hatch, Dorian M., Journal of Applied Crystallography 2005, 38, 237-238

[2] Björkman, T., Computer Physics Communications 182, 1183–1186 (2011)