cp2k-output-tools
Modular CP2K output file parsers, mostly in the form of regular expressions plus other tools to mangle various CP2K output:
cp2kparse... parse CP2K output (for restart & input files look at the cp2k-input-tools project) and allow easy selection of common values.xyz_restart_parser... when restarts occur during an MD you may end up with duplicated frames in the trajectory, this tool filters them (and can easily handle huge files)cp2k_bs2csv... convert a CP2K band structure file to multiple (one-per-set) CSV files for easier plotting. There is also an API available if you need to import bandstructure data into your application.cp2k_pdos... apply a convolution with Gaussians on a regular grid on the CP2K PDOS output and generate a CSV file for further processing or plotting. The same grid is used for all input files with the min/max of the grid automatically determined, but no summation of the different projections is done.
Requirements
- Python 3.9+
- regex 2021+
- click 8+
- numpy 1.19+
- optional: ruamel.yaml
For development: https://poetry.eustace.io/ https://pytest.org/
Usage: cp2kparse
There is a simple command-line interface cp2kparse:
$ cp2kparse --help
Usage: cp2kparse [OPTIONS] [FILE|-]
Parse the CP2K output FILE and return a structured output
Options:
-f, --format [json|yaml|highlight]
Output format (json or yaml are structure
formats, highlight shows which lines of the
output have been matched)
--color [auto|always] When to colorize output
-s, --safe-keys generate 'safe' key names (e.g. without
spaces, dashes, ..)
-S, --statistics print some statistics to stderr
-k, --key <PATH> Path, ex.: 'energies/total force_eval'
--help Show this message and exit.
$ cp2kparse calc.out
{
"cp2k": {
"cp2kflags: libint fftw3 libxc xsmm spglib": " ",
"data directory path": "/data/tiziano/cp2k/data",
"input file name": "Si-supercell-001.inp",
"is freely available from": "https://www.cp2k.org/",
"program compiled at": "Mon Sep 16 14:42:43 CEST 2019",
"program compiled for": "local",
"program compiled on": "tcpc18",
"source code revision number": "git:43f50e2",
"version string": "CP2K version 7.0 (Development Version)"
},
"dbcsr": {
"cpu multiplication driver": "XSMM",
"maximum elements for images": "UNLIMITED",
"multiplication size stacks": 3,
"multiplication stack size": 1000,
"multiplicative factor virtual images": 1,
"multrec recursion limit": 512,
"use multiplication densification": true
},
"energies": {
"total force_eval": -251.6873903110507
},
"global": {
"all-to-all communication in single precision": false,
"basis set file name": "BASIS_MOLOPT",
"coordinate file name": "__STD_INPUT__",
"cpu model name": "Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz",
"cpuid": 1002,
"ffts using library dependent lengths": false,
"force environment number": 1,
"global print level": "MEDIUM",
"method name": "CP2K",
"mm potential file name": "MM_POTENTIAL",
"mpi i/o enabled": true,
"number of threads for this process": 1,
"potential file name": "POTENTIAL",
"preferred diagonalization lib.": "SL",
"preferred fft library": "FFTW3",
"project name": "Si-supercell-001",
"run type": "ENERGY_FORCE",
"this output is from process": 0,
"total number of message passing processes": 1
},
"mulliken population analysis": {
"per atom": [
{
"charge": 7e-06,
"element": "Si",
"kind": 1,
"population": 3.999993
},
{
"charge": 0.0,
"element": "Si",
"kind": 1,
"population": 4.0
},
{
"charge": -0.0,
"element": "Si",
"kind": 1,
"population": 4.0
},
{
"charge": -1e-06,
"element": "Si",
"kind": 1,
"population": 4.000001
},
{
"charge": -0.0,
"element": "Si",
"kind": 1,
"population": 4.0
},
{
"charge": -1e-06,
"element": "Si",
"kind": 1,
"population": 4.000001
},
{
"charge": -1e-06,
"element": "Si",
"kind": 1,
"population": 4.000001
},
{
"charge": -0.0,
"element": "Si",
"kind": 1,
"population": 4.0
},
{
"charge": 0.000137,
"element": "Si",
"kind": 1,
"population": 3.999863
},
{
"charge": -2e-05,
"element": "Si",
"kind": 1,
"population": 4.00002
},
{
"charge": -0.000133,
"element": "Si",
"kind": 1,
"population": 4.000133
},
{
"charge": 2.1e-05,
"element": "Si",
"kind": 1,
"population": 3.999979
},
{
"charge": -0.000133,
"element": "Si",
"kind": 1,
"population": 4.000133
},
{
"charge": 2.1e-05,
"element": "Si",
"kind": 1,
"population": 3.999979
},
{
"charge": 0.000137,
"element": "Si",
"kind": 1,
"population": 3.999863
},
{
"charge": -2e-05,
"element": "Si",
"kind": 1,
"population": 4.00002
},
{
"charge": -3.9e-05,
"element": "Si",
"kind": 1,
"population": 4.000039
},
{
"charge": 3.6e-05,
"element": "Si",
"kind": 1,
"population": 3.999964
},
{
"charge": -1e-05,
"element": "Si",
"kind": 1,
"population": 4.00001
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": -3.9e-05,
"element": "Si",
"kind": 1,
"population": 4.000039
},
{
"charge": 3.6e-05,
"element": "Si",
"kind": 1,
"population": 3.999964
},
{
"charge": -1e-05,
"element": "Si",
"kind": 1,
"population": 4.00001
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": -3.9e-05,
"element": "Si",
"kind": 1,
"population": 4.000039
},
{
"charge": 3.6e-05,
"element": "Si",
"kind": 1,
"population": 3.999964
},
{
"charge": -3.9e-05,
"element": "Si",
"kind": 1,
"population": 4.000039
},
{
"charge": 3.6e-05,
"element": "Si",
"kind": 1,
"population": 3.999964
},
{
"charge": -1e-05,
"element": "Si",
"kind": 1,
"population": 4.00001
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": -1e-05,
"element": "Si",
"kind": 1,
"population": 4.00001
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": 6e-06,
"element": "Si",
"kind": 1,
"population": 3.999994
},
{
"charge": 3.5e-05,
"element": "Si",
"kind": 1,
"population": 3.999965
},
{
"charge": 3.3e-05,
"element": "Si",
"kind": 1,
"population": 3.999967
},
{
"charge": 9e-06,
"element": "Si",
"kind": 1,
"population": 3.999991
},
{
"charge": 3.3e-05,
"element": "Si",
"kind": 1,
"population": 3.999967
},
{
"charge": 9e-06,
"element": "Si",
"kind": 1,
"population": 3.999991
},
{
"charge": 3e-06,
"element": "Si",
"kind": 1,
"population": 3.999997
},
{
"charge": -0.000312,
"element": "Si",
"kind": 1,
"population": 4.000312
},
{
"charge": 3e-06,
"element": "Si",
"kind": 1,
"population": 3.999997
},
{
"charge": -0.000311,
"element": "Si",
"kind": 1,
"population": 4.000311
},
{
"charge": 3.4e-05,
"element": "Si",
"kind": 1,
"population": 3.999966
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": 3.4e-05,
"element": "Si",
"kind": 1,
"population": 3.999966
},
{
"charge": 1e-05,
"element": "Si",
"kind": 1,
"population": 3.99999
},
{
"charge": 6e-06,
"element": "Si",
"kind": 1,
"population": 3.999994
},
{
"charge": 3.5e-05,
"element": "Si",
"kind": 1,
"population": 3.999965
},
{
"charge": -9e-06,
"element": "Si",
"kind": 1,
"population": 4.000009
},
{
"charge": -3.3e-05,
"element": "Si",
"kind": 1,
"population": 4.000033
},
{
"charge": 0.000308,
"element": "Si",
"kind": 1,
"population": 3.999692
},
{
"charge": -4e-06,
"element": "Si",
"kind": 1,
"population": 4.000004
},
{
"charge": -3.6e-05,
"element": "Si",
"kind": 1,
"population": 4.000036
},
{
"charge": -7e-06,
"element": "Si",
"kind": 1,
"population": 4.000007
},
{
"charge": -9e-06,
"element": "Si",
"kind": 1,
"population": 4.000009
},
{
"charge": -3.3e-05,
"element": "Si",
"kind": 1,
"population": 4.000033
},
{
"charge": -8e-06,
"element": "Si",
"kind": 1,
"population": 4.000008
},
{
"charge": -3.3e-05,
"element": "Si",
"kind": 1,
"population": 4.000033
},
{
"charge": -3.5e-05,
"element": "Si",
"kind": 1,
"population": 4.000035
},
{
"charge": -6e-06,
"element": "Si",
"kind": 1,
"population": 4.000006
},
{
"charge": 0.000308,
"element": "Si",
"kind": 1,
"population": 3.999692
},
{
"charge": -4e-06,
"element": "Si",
"kind": 1,
"population": 4.000004
},
{
"charge": -8e-06,
"element": "Si",
"kind": 1,
"population": 4.000008
},
{
"charge": -3.3e-05,
"element": "Si",
"kind": 1,
"population": 4.000033
}
],
"total": {
"charge": 0.0,
"population": 256.0
}
},
"program info": {
"ended at": "2019-09-17 17:02:35.738",
"process id": "23773",
"ran by": "tiziano",
"ran on": "tcpc18",
"started at": "2019-09-17 17:01:19.273",
"started by": "tiziano",
"started in": "/users/tiziano/work/phonopy/example/Si-CP2K",
"started on": "tcpc18",
"stopped in": "/users/tiziano/work/phonopy/example/Si-CP2K"
}
}and an API:
from cp2k_output_tools import parse_iter
with open("calc.out", "r") as fhandle:
for match in parse_iter(fhandle.read()):
print(match.values)Usage: xyz_restart_cleaner
$ xyz_restart_cleaner orig_trajectory.xyz new_trajectory.xyz
found restart point @1, dropping 1 frames, flushing 1
flushing remaining 2 framesUsage: cp2k_bs2csv
Given a .bs file as written by CP2K the script will generate CSV files with the same name and suffixes .set-X.csv in the same directory as the source file:
$ cp2k_bs2csv WO3.bs
writing point set WO3.bs.set-1.csv (total number of k-points: 11)
with the following special points:
GAMMA: 0.00000000 / 0.00000000 / 0.00000000
X: 0.00000000 / 0.50000000 / 0.00000000
writing point set WO3.bs.set-2.csv (total number of k-points: 11)
with the following special points:
X: 0.00000000 / 0.50000000 / 0.00000000
M: 0.50000000 / 0.50000000 / 0.00000000
writing point set WO3.bsset-3.csv (total number of k-points: 11)
with the following special points:
M: 0.50000000 / 0.50000000 / 0.00000000
GAMMA: 0.00000000 / 0.00000000 / 0.00000000
writing point set WO3.bs.set-4.csv (total number of k-points: 11)
with the following special points:
GAMMA: 0.00000000 / 0.00000000 / 0.00000000
R: 0.50000000 / 0.50000000 / 0.50000000
writing point set WO3.bs.set-5.csv (total number of k-points: 11)
with the following special points:
R: 0.50000000 / 0.50000000 / 0.50000000
X: 0.00000000 / 0.50000000 / 0.00000000
writing point set WO3.bs.set-6.csv (total number of k-points: 11)
with the following special points:
R: 0.50000000 / 0.50000000 / 0.50000000
M: 0.50000000 / 0.50000000 / 0.00000000
$ ls
WO3.cp2k-8.bs WO3.cp2k-8.bs.set-2.csv WO3.cp2k-8.bs.set-4.csv WO3.cp2k-8.bs.set-6.csv
WO3.cp2k-8.bs.set-1.csv WO3.cp2k-8.bs.set-3.csv WO3.cp2k-8.bs.set-5.csvDevelopment
$ poetry install
$ poetry run pytest -v