Source code for EPWpy.utilities.epw_pp
#!/usr/bin/env python3
#
# Post-processing script from of PH data in format used by EPW
# 14/07/2015 - Creation of the script - Samuel Ponce
# 14/03/2018 - Automatically reads the number of q-points - Michael Waters
# 14/03/2018 - Detect if SOC is included in the calculation - Samuel Ponce
# 05/06/2019 - Removed SOC for xml detection instead - Felix Goudreault
#
from __future__ import print_function
try:
from builtins import input
except ImportError:
print('Install future. e.g. "pip install --user future"')
# import numpy as np
import os
import re
from xml.dom import minidom
import argparse
# Return the number of q-points in the IBZ
[docs]
def get_nqpt(prefix):
fname = '_ph0/' + prefix + '.phsave/control_ph.xml'
fid = open(fname, 'r')
lines = fid.readlines()
# these files are relatively small so reading the whole thing shouldn't
# be an issue
fid.close()
line_number_of_nqpt = 0
while 'NUMBER_OF_Q_POINTS' not in lines[line_number_of_nqpt]:
# increment to line of interest
line_number_of_nqpt += 1
line_number_of_nqpt += 1 # its on the next line after that text
nqpt = int(lines[line_number_of_nqpt])
return nqpt
# Check if the calculation include SOC
[docs]
def hasSOC(prefix):
fname = prefix+'.save/data-file-schema.xml'
xmldoc = minidom.parse(fname)
item = xmldoc.getElementsByTagName('spinorbit')[0]
lSOC = item.childNodes[0].data
return lSOC
# Check if the calculation includes PAW
[docs]
def hasPAW(prefix):
fname = prefix+'.save/data-file-schema.xml'
#nprint(os.getcwd())
try:
xmldoc = minidom.parse(fname)
item = xmldoc.getElementsByTagName('paw')[0]
lPAW = (item.childNodes[0].data == 'true')
return lPAW
except FileNotFoundError:
return(False)
# check if the calculation include Hubbard correction
[docs]
def hasdftU(prefix):
fname = prefix+'.save/data-file-schema.xml'
xmldoc = minidom.parse(fname)
if (xmldoc.getElementsByTagName('lda_plus_u_kind')) == [] :
ldftU = False
else :
ldftU = True
return ldftU
# Check if the calculation used .fc or .fc.xml files
[docs]
def hasfc(prefix):
fname = str(prefix)+'.fc.xml'
if (os.path.isfile(fname)):
lfc = True
else:
fname_no_xml = re.sub('\.xml$', '', fname)
if (os.path.isfile(fname_no_xml)):
lfc = True
else:
lfc = False
return lfc
# check if calculation used xml files (irrelevant of presence of SOC)
[docs]
def hasXML(prefix):
# check for a file named prefix.dyn1.xml
# if it exists => return True else return False
fname = os.path.join(prefix + ".dyn1.xml")
if os.path.isfile(fname):
return True
# check if the other without .xml extension exists
# if not raise an error
fname_no_xml = re.sub('\.xml$', '', fname)
class FileNotFoundError(Exception):
pass
if not os.path.isfile(fname_no_xml):
raise FileNotFoundError
return False
# Check if the calculation was done in sequential
[docs]
def isSEQ(prefix):
fname = '_ph0/'+str(prefix)+'.dvscf'
if (os.path.isfile(fname)):
lseq = True
else:
lseq = False
return lseq
[docs]
def run_pp(user_input):
#print(os.getcwd())
prefix = str(user_input)
XML = hasXML(prefix)
# Test if PAW
PAW = hasPAW(prefix)
# Test if dftU
dftU = hasdftU(prefix)
# Test if fc
fc = hasfc(prefix)
# Test if seq. or parallel run
SEQ = isSEQ(prefix)
if True: # this gets the nqpt from the outputfiles
nqpt = get_nqpt(prefix)
else:
# Enter the number of irr. q-points
user_input = input(
'Enter the number of irreducible q-points\n')
nqpt = user_input
try:
nqpt = int(user_input)
except ValueError:
raise Exception('The value you enter is not an integer!')
os.system('mkdir save 2>/dev/null')
for iqpt in range(1, nqpt+1):
label = str(iqpt)
# Case calculation in seq.
if SEQ:
# Case with XML files
if XML:
os.system('cp '+prefix+'.dyn0 '+prefix+'.dyn0.xml')
os.system('cp '+prefix+'.dyn'+str(iqpt)+'.xml save/'+prefix
+ '.dyn_q'+label+'.xml')
if (iqpt == 1):
os.system('cp _ph0/'+prefix+'.dvscf* save/'+prefix+'.dvscf_q'
+ label)
os.system('cp -r _ph0/'+prefix+'.phsave save/')
if fc:
os.system('cp '+prefix+'.fc.xml save/ifc.q2r.xml')
if PAW:
os.system('cp _ph0/'+prefix+'.dvscf_paw* save/'+prefix +
'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.dnsscf* save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.dnsbare* save/'+prefix+'.dnsbare_q'+label)
os.system('cp '+prefix+'.save/occup.txt save/'+prefix+'.occup')
else:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf* save/'+prefix+'.dvscf_q'+label)
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
if PAW:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf_paw* save/'+prefix+'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsscf* save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsbare* save/'+prefix+'.dnsbare_q'+label)
# Case without XML files
else:
os.system('cp '+prefix+'.dyn'+str(iqpt)+' save/'+prefix+'.dyn_q' +
label)
if (iqpt == 1):
os.system('cp _ph0/'+prefix+'.dvscf save/'+prefix+'.dvscf_q' +
label)
os.system('cp -r _ph0/'+prefix+'.phsave save/')
if fc:
os.system('cp '+prefix+'.fc save/ifc.q2r')
if PAW:
os.system('cp _ph0/'+prefix+'.dvscf_paw save/'+prefix +
'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.dnsbare save/'+prefix+'.dnsbare_q'+label)
os.system('cp '+prefix+'.save/occup.txt save/'+prefix+'.occup')
else:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf save/'+prefix+'.dvscf_q'+label)
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
if PAW:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf_paw save/'+prefix+'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsbare save/'+prefix+'.dnsbare_q'+label)
else:
# Case with XML format
if XML:
os.system('cp '+prefix+'.dyn0 '+prefix+'.dyn0.xml')
os.system('cp '+prefix+'.dyn'+str(iqpt)+'.xml save/'+prefix +
'.dyn_q'+label+'.xml')
if (iqpt == 1):
os.system('cp _ph0/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q' +
label)
os.system('cp -r _ph0/'+prefix+'.phsave save/')
if fc:
os.system('cp '+prefix+'.fc.xml save/ifc.q2r.xml')
if PAW:
os.system('cp _ph0/'+prefix+'.dvscf_paw1 save/'+prefix +
'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.dnsbare save/'+prefix+'.dnsbare_q'+label)
os.system('cp '+prefix+'.save/occup.txt save/'+prefix+'.occup')
else:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf1 save/'+prefix+'.dvscf_q'+label)
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
if PAW:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf_paw1 save/'+prefix+'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsbare save/'+prefix+'.dnsbare_q'+label)
# Case without XML format
else:
os.system('cp '+prefix+'.dyn'+str(iqpt)+' save/'+prefix+'.dyn_q' +
label)
if (iqpt == 1):
os.system('cp _ph0/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q' +
label)
os.system('cp -r _ph0/'+prefix+'.phsave save/')
if fc:
os.system('cp '+prefix+'.fc save/ifc.q2r')
if PAW:
os.system('cp _ph0/'+prefix+'.dvscf_paw1 save/'+prefix +
'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.dnsbare save/'+prefix+'.dnsbare_q'+label)
os.system('cp '+prefix+'.save/occup.txt save/'+prefix+'.occup')
else:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf1 save/'+prefix+'.dvscf_q'+label)
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
if PAW:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dvscf_paw1 save/'+prefix+'.dvscf_paw_q'+label)
if dftU:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsscf save/'+prefix+'.dnsscf_q'+label)
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix +
'.dnsbare save/'+prefix+'.dnsbare_q'+label)
