Cp2kData 0.4.1

Small Package to Postprocessing Cp2k Output

CP2KDATA

Python Package to postprocess cp2k data.

including cube file, pdos file, output file

• CP2KDATA
• Idea List
• TO DO
• Installation
• Generate Standard Test Inputs
• Plot Standard Test Output
• Processing Output File
  • Basick Usage
  • Parse ENERGY_FORCE Outputs
  • Parse GEO_OPT Outputs
  • Parse MD outputs
• Plug-in for dpdata
• Processing Cube File
• Processing PDOS File
  • Processing Single PDOS File
  • Quickplot of PDOS Files in Single Point Energy Calculation

Idea List

1. manipulate cube, pdos data
2. modify step information on cube files
3. extract information from output
4. generate standard test input and directory
5. generate nice figures

TO DO

cli interface

Installation

pip install .

Generate Standard Test Inputs

One can use command line tools to generate standard test input with provided template input.inp and other files.

# generate cutoff test files
cp2kdata gen cutoff <template input> <a list of other neccessary files> -crange <cutoff range: min, max, step> --scf_converge <whether scf converge>

# example
cp2kdata gen cutoff input.inp coord.xyz cp2k.lsf -crange 100 800 100 --scf_converge True

# generate basis test files
cp2kdata gen basis <template input> <a list of other neccessary files> -e <test element> -sr <whether test short range basis>

# example
cp2kdata gen basis input.inp coord.xyz cp2k.lsf -e Fe -sr True

# generate Hubbard U test files
cp2kdata gen hubbardu <template input> <a list of other neccessary files> -ur u <test value: min, max, step> -e <test element> -orb <test orbital>  
# example
cp2kdata gen hubbardu input.inp coord.xyz cp2k.lsf -ur 0 8.1 1 -e Fe -orb d  

Plot Standard Test Output

After you finished the above tests, you readily plot the result using command cp2kdata plot cutoff, cp2kdata plot basis, cp2kdata plot hubbardu

Processing Output File

Basick Usage

One can use Cp2kOutput class to parse cp2k output file, which is the standard output from cp2k code. Depending on run types, required files may be more than a standard output. For example, if you parse md outputs, you may ask to provide additional Project-1.ener, Project-pos-1.xyz, and Project-frc-1.xyz files to obtain energies, position, and forces information. Detail usages are provided in the following subsections.

from cp2kdata import Cp2kOutput
cp2k_output_file = "cp2k_output"
cp2koutput = Cp2kOutput(cp2k_output_file, path_prefix=".")
# path_prefix is the directory where the cp2k_output is
# show the brief summary on stdout
print(cp2koutput)

Cp2k Output Summary

--------------------------------------

Cp2k Version       : 6.1

Run Type           : ENERGY_FORCE

Atom Numbers       : 30

Frame Numbers      : 1

Force in Output    : Yes

Stress in Output   : Yes

Element List       : Fe1  Fe2  O    

Element Numb       : 6    6    18   
--------------------------------------

Parse ENERGY_FORCE Outputs

from cp2kdata import Cp2kOutput
cp2k_output_file = "output_energy_force"
cp2koutput=Cp2kOutput(cp2k_output_file)
# get the version of cp2k
print(cp2koutput.get_version_string())
# get the run type
print(cp2koutput.get_run_type())
# symbols with true element
print(cp2koutput.get_chemical_symbols())
# symbols with your set in input
print(cp2koutput.get_chemical_symbols_fake())

Parse GEO_OPT Outputs

from cp2kdata import Cp2kOutput
cp2k_output_file = "output_geo_opt"
cp2koutput=Cp2kOutput(cp2k_output_file)
# get the version of cp2k
print(cp2koutput.get_version_string())
# get the run type
print(cp2koutput.get_run_type())
# get potential energy
print(cp2koutput.get_energies_list())
# get initial coordinates
print(cp2koutput.get_init_atomic_coordinates())
# symbols with true element
print(cp2koutput.get_chemical_symbols())
# symbols with your set in input
print(cp2koutput.get_chemical_symbols_fake())
# get the geometry optimization information
print(cp2koutput.get_geo_opt_info())
# quick plot of geometry optimization information 
cp2koutput.get_geo_opt_info_plot()

Parse MD outputs

On parsing MD outputs, you can choose parse with or without standard outputs. Three additional files, Project-1.ener, Project-pos-1.xyz, and Project-frc-1.xyz files, are required to obtain energies, position, and forces information.

If you parse with standard outputs, Cp2kOutput can collect full information from outputs. In specific, cell information and kind symbols can be obtained.

from cp2kdata import Cp2kOutput
cp2k_output_file = "output_md"
cp2koutput=Cp2kOutput(cp2k_output_file)

Alternatively, you may parse without standard outputs. Consequently, you will loss the cell and atomic kind infromations. When parsing without standard outputs, you must manually set the optional argument run_type as md, otherwise it will raise error.

from cp2kdata import Cp2kOutput
cp2k_output_file = "output_md"
cp2koutput=Cp2kOutput(run_type="md")

Plug-in for dpdata

Cp2kData support plug in for dpdata. When installed with pip, Cp2kData automatically installs plug in for dpdata.

For usages of dpdata, we refer to https://github.com/deepmodeling/dpdata.

Currently, we only support two flavors of format for dpdata. One is cp2kdata/e_f for parsing ENERGY_FORCE outputs, the other is cp2kdata/md for parsing MD outputs.

An Example for parsing ENERGY_FORCE outputs:

import dpdata

dp = dpdata.LabeledSystem("cp2k_e_f_output", fmt="cp2kdata/e_f")
print(dp)

An Example for parsing MD outputs:

import dpdata
cp2kmd_dir = "."
cp2kmd_output_name = "output"
dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
print(dp)

Processing Cube File

from cp2kdata.cube import Cp2kCube
cube_file = "xxx.cube"
mycube = Cp2kCube(cube_file)

# structure is include in cube file
# you can obtain ASE atoms from cube
stc = mycube.get_stc()
print(stc)

# get Planar average data without interpolation.
pav_x, pav = mycube.get_pav(axis="z", interpolate=False)
# get Planar average data  with interpolation. the number of interpolation point is 4096
pav_x, pav = mycube.get_pav(axis="z", interpolate=True)

l1 = 4.8 # length for first periodicity
l2 = 4.8 # length for second periodicity
ncov = 1 # set 1 if the system is slab-vacuum system.
ncov = 2 # set 2 if the system is interface.
# get Macro average data without interpolation of the original data.
mav_x, mav = mycube.get_mav(l1=l1, l2=l2, ncov=ncov, interpolate=False)
# get Macro average data with interpolation of the original data.
mav_x, mav = mycube.get_mav(l1=l1, l2=l2, ncov=ncov, interpolate=True)

# quick plot
mycube.quick_plot(axis="z", interpolate=False, output_dir="./")

The Planar Average and Macro Average results are benchmarked from MACROAVE used in Siesta and Abinit and shown in the following figures

Processing PDOS File

Processing Single PDOS File

from cp2kdata.pdos import Pdos
dosfile = "Universality-ALPHA_k2-1_50.pdos"
mypdos = Pdos(dosfile)
dos, ener = mypdos.get_dos()

Quickplot of PDOS Files in Single Point Energy Calculation

from cp2kdata.pdos import quick_plot_uks, quick_plot_rks
Calculation_dir = "./"
# if uks calculation use this
quick_plot_uks(Calculation_dir)
# if rks calculation use this 
quick_plot_rks(Calculation_dir)