def cube_generator_dftbplus(project_name, time_step, min_band, max_band,
waveplot_exe, isUKS):
"""
This function generates the cube files by first forming the 'fchk' file from 'chk' file.
Then it will generate the cube files from min_band to max_band the same as CP2K naming.
This will helps us to use the read_cube and integrate_cube functions easier.
Args:
project_name (string): The project_name.
time_step (integer): The time step.
min_band (integer): The minimum state number.
max_band (integer): The maximum state number.
waveplot_exe (str): Location of the executable for the waveplot program of the dftb+ software package
isUKS (integer): The unrestricted spin calculation flag. 1 is for spin unrestricted calculations.
Other numbers are for spin restricted calculations
Returns:
None
"""
# Make the cubefiles. For dftb+, this simply means executing the waveplot program
# The min and max band are already defind in the waveplot template. So, we just use
# them here for renaming the cubefiles
os.system(waveplot_exe)
# For now, only spin-restricted
for state in range(min_band, max_band + 1):
# Use cp2k names because the rest of the code expects this format
state_name = CP2K_methods.state_num_cp2k(state)
cube_name = '%s-%d-WFN_%s_1-1_0.cube' % (project_name, time_step,
state_name)
print('Renaming cube for state %d' % state)
# Now, rename the cubefile from what waveplots calls it to the standard format
os.system("mv *" + str(state) + "-real.cube " + cube_name)
def cube_generator_gaussian( project_name, time_step, min_band, max_band, nprocs, sample_cube_file, isUKS ):
"""
This function generates the cube files by first forming the 'fchk' file from 'chk' file.
Then it will generate the cube files from min_band to max_band the same as CP2K naming.
This will helps us to use the read_cube and integrate_cube functions easier.
Args:
project_name (string): The project_name.
time_step (integer): The time step.
min_band (integer): The minimum state number.
max_band (integer): The maximum state number.
nprocs (integer): The number of processors used to generate the cubes using 'cubegen'.
sample_cube_file (str): The path to a sample cube file. This file is used to generate the cube
files according the mesh of this file. Therefore the integration will be plausible.
isUKS (integer): The unrestricted spin calculation flag. 1 is for spin unrestricted calculations.
Other numbers are for spin restricted calculations
Returns:
None
"""
# Form the fchk file from the chk file
os.system('formchk %s-%d.chk %s-%d.fchk'%(project_name, time_step, project_name, time_step))
# Print the commands...
print('formchk %s-%d.chk %s-%d.fchk'%(project_name, time_step, project_name, time_step))
# Generate the sample cube file, if it exists it will not create it again
if not os.path.isfile(sample_cube_file):
# Generate the sample cube file with the maximum fineness ---> 100 as in Gaussian website
os.system('cubegen %d MO=H**o %s-%d.fchk %s 100 h'%(nprocs, project_name, time_step, sample_cube_file))
# For spin unrestricted
if isUKS == 1:
# Generate the names and cube files for each state. Here we use the cube names by CP2K. This will increase the speed of our work.
for state in range(min_band,max_band+1):
# State name in CP2K format
state_name = CP2K_methods.state_num_cp2k(state)
# Cube file name
cube_name = '%s-%d-WFN_%s_1-1_0.cube'%(project_name, time_step, state_name)
print('Generating cube for state %d'%state)
# Generate cube files for alpha spin using the 'cubegen'
os.system('cubegen %d AMO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))
print('cubegen %d AMO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))
cube_name = '%s-%d-WFN_%s_2-1_0.cube'%(project_name, time_step, state_name)
print('Generating cube for state %d'%state)
# Generate cube files for beta spin using the 'cubegen'
os.system('cubegen %d BMO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))
print('cubegen %d BMO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))
# Spin restricted case
else:
for state in range(min_band,max_band+1):
# Use cp2k names because the rest of the code expects this format
state_name = CP2K_methods.state_num_cp2k(state)
cube_name = '%s-%d-WFN_%s_1-1_0.cube'%(project_name, time_step, state_name)
print('Generating cube for state %d'%state)
# Generate the cubes for alpha spin only
os.system('cubegen %d MO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))
print('cubegen %d MO=%d %s-%d.fchk %s -1 h %s'%(nprocs, state, project_name, time_step, cube_name, sample_cube_file))