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search_neg_freqsis a program for computational chemistry and physics that will print out the negative frequencies at each volume calculated with CRYSTAL. -
The information obtained from the scripts on this repository is used to run the scripts on the EOS_2_phonons repository.
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The EOS_2_phonons repository contains the scripts necessary to automate the runs for frequency calculations, and breaking symmetry over different volumes. The programs on EOS_2_phonons repository allow to obtain the needed outputs in order to further perform a quasi-harmonic approximation analyisis with the
QHA_2Dprogram
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.
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Get the code:
git clone https://github.com/DavidCdeB/search_neg_freqs.git -
Copy to the folder
search_neg_freqscreated, all the freqcuency outputs, one per volume. These outputs have to end in*.out. -
Run the program
bash extract_neg_freqs_v3.sh. -
The output is the following:
You can now open the 'neg_freqs_grabbing_more_decimals.txt' file, with the summary for all the negative freqs
Counting the number of negative freqs...
./P3221_1143.965721.out
./P3221_1114.515627.out
./P3221_1071.300672.out
./P3221_1085.572503.out
len(negatives) = 1
./P3221_1099.984555.out
len(negatives) = 1
./P3221_1043.035120.out
len(negatives) = 25
./P3221_1167.320319.out
len(negatives) = 1
./P3221_1129.183195.out
./P3221_1057.078411.out
len(negatives) = 2
./P3221_1029.133371.out
len(negatives) = 27
./P3221_1015.402996.out
len(negatives) = 27
This output is showing the number of negative frequencies each volume has.
- Open the file:
neg_freqs_grabbing_more_decimals.txt. This file shows in which dispersion k-point the negative frecuency has been found, and the value of this frequency. The following is an extract of that file. We can easily see that the volumes 1143.965721 and 1114.515627 do not contain negative frequencies. On the contrary, 1043.035120 and 1029.133371 contain lots of negative frequencies at finite k-points. The value of the frequencies is shown in square brackets.
./P3221_1143.965721.out
* WITH SHRINKING FACTORS: IS1 = 3 IS2 = 3 IS3 = 1 *
DISPERSION K POINT NUMBER 1 COORD: R( 0 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 2 COORD: C( 0 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 3 COORD: C( 0 2 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 4 COORD: C( 1 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 5 COORD: C( 1 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 6 COORD: C( 1 2 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 7 COORD: C( 2 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 8 COORD: C( 2 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 9 COORD: C( 2 2 0 ) WEIGHT: 1.
./P3221_1114.515627.out
* WITH SHRINKING FACTORS: IS1 = 3 IS2 = 3 IS3 = 1 *
DISPERSION K POINT NUMBER 1 COORD: R( 0 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 2 COORD: C( 0 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 3 COORD: C( 0 2 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 4 COORD: C( 1 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 5 COORD: C( 1 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 6 COORD: C( 1 2 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 7 COORD: C( 2 0 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 8 COORD: C( 2 1 0 ) WEIGHT: 1.
DISPERSION K POINT NUMBER 9 COORD: C( 2 2 0 ) WEIGHT: 1.
./P3221_1043.035120.out
* WITH SHRINKING FACTORS: IS1 = 3 IS2 = 3 IS3 = 1 *
DISPERSION K POINT NUMBER 1 COORD: R( 0 0 0 ) WEIGHT: 1.
['-27.4323']
DISPERSION K POINT NUMBER 2 COORD: C( 0 1 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 3 COORD: C( 0 2 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 4 COORD: C( 1 0 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 5 COORD: C( 1 1 0 ) WEIGHT: 1.
['-40.3447']
['-28.9624', '-28.9624']
DISPERSION K POINT NUMBER 6 COORD: C( 1 2 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 7 COORD: C( 2 0 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 8 COORD: C( 2 1 0 ) WEIGHT: 1.
['-33.7374']
['-20.3996']
['-13.8545']
DISPERSION K POINT NUMBER 9 COORD: C( 2 2 0 ) WEIGHT: 1.
['-40.3447']
['-28.9624', '-28.9624']
./P3221_1029.133371.out
* WITH SHRINKING FACTORS: IS1 = 3 IS2 = 3 IS3 = 1 *
DISPERSION K POINT NUMBER 1 COORD: R( 0 0 0 ) WEIGHT: 1.
['-46.4928']
['-37.8698', '-37.8698']
DISPERSION K POINT NUMBER 2 COORD: C( 0 1 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 3 COORD: C( 0 2 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 4 COORD: C( 1 0 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 5 COORD: C( 1 1 0 ) WEIGHT: 1.
['-53.6360']
['-47.1959', '-47.1959']
DISPERSION K POINT NUMBER 6 COORD: C( 1 2 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 7 COORD: C( 2 0 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 8 COORD: C( 2 1 0 ) WEIGHT: 1.
['-52.2115']
['-44.6610']
['-39.7488']
DISPERSION K POINT NUMBER 9 COORD: C( 2 2 0 ) WEIGHT: 1.
['-53.6360']
['-47.1959', '-47.1959']
Under the TEST folder, you will find all the programs
needed, together with a *out folder
with the frequency output.
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}
}
QHA is free software released under the Gnu Public Licence version 3.
All contributions to improve this code are more than welcome.
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Have a look at GitHub's "How to contribute".
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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.