Cp2kData 0.2.0

Small Package to Postprocessing Cp2k Output

CP2KDATA

Python Package to postprocess cp2k data.

including cube file, pdos file, output file

• CP2KDATA
  • Installation
  • Processing Output File
    • Basick Usage
    • Processing ENERGY and FORCE Calculation
    • Processing GEOMETRY OPTIMIZATION Calculation
    • Error Handing
  • Processing Cube File
  • Processing PDOS File
    • Processing Single PDOS File
    • Quickplot of PDOS Files in Single Point Energy Calculation

Installation

pip install .

Processing Output File

Basick Usage

from cp2kdata.output import Cp2kOutput
cp2k_output_file = "output_energy_force"
cp2koutput=Cp2kOutput(cp2k_output_file)
# 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   
--------------------------------------

Processing ENERGY and FORCE Calculation

from cp2kdata.output 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())

Processing GEOMETRY OPTIMIZATION Calculation

from cp2kdata.output 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()

Error Handing

if cp2k output contains exceed execution time, the Cp2kOutput class won't read it. Instead, to ignore the error, set 'ignore_error=True'

cp2k_output_file = "output_geo_opt"
cp2koutput=Cp2kOutput(cp2k_output_file, ignore_error=True)

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)