"\n**WARNING: A file called CHGDIFF already exists in this directory."
)
if float(sys.version.split()[0][:3]) < 3.0:
yesno = raw_input(
"Type y to continue and overwrite it, any other key to stop\n"
)
else:
yesno = input(
"Type y to continue and overwrite it, any other key to stop\n"
)
if yesno != "y":
sys.exit(0)
# Writing data ...
print("Writing density difference data to file ...", end='')
sys.stdout.flush()
chg_total.write(filename="SPINCAR_total.vasp", format="chgcar")
chg_x.write(filename="SPINCAR_x.vasp", format="chgcar")
chg_y.write(filename="SPINCAR_y.vasp", format="chgcar")
chg_z.write(filename="SPINCAR_z.vasp", format="chgcar")
# adding atomic species
fin = [atoms.get_chemical_symbols()[0]]
for i in range(len(atoms.get_chemical_symbols())):
if i == len(atoms.get_chemical_symbols()) - 1: break
if atoms.get_chemical_symbols()[i] != atoms.get_chemical_symbols()[i +
1]:
fin.append(atoms.get_chemical_symbols()[i + 1])
for chgfiles in [
'SPINCAR_total.vasp', 'SPINCAR_x.vasp', 'SPINCAR_y.vasp',
'SPINCAR_z.vasp'
]:
sys.stdout.flush()
# Take difference
# -----------------
chgdiff = chgdiff - chg2
print "done."
vasp_charge_diff = VaspChargeDensity(filename=None)
vasp_charge_diff.atoms = [atoms1]
vasp_charge_diff.chg = [chgdiff]
# Print out charge density
# --------------------------
# Check whether CHGDIFF exists
if os.path.isfile("./CHGDIFF"):
print "\n**WARNING: A file called CHGDIFF already exists in this directory."
yesno = raw_input("Type y to continue and overwrite it, any other key to stop\n")
if yesno != "y":
sys.exit(0)
print "Writing density difference data to file CHGDIFF ...",
sys.stdout.flush()
vasp_charge_diff.write(filename="CHGDIFF", format="chgcar")
print "done."
endtime = time.clock()
runtime = endtime - starttime
print "\nEnd of calculation."
print "Program was running for %.2f seconds." % runtime
if chg1.is_spin_polarized():
print 'Spin polarized'
for i, cd in enumerate(chg1.chgdiff):
cd2 = chg2.chgdiff[i]
if op == '+':
nd = cd + cd2
elif op == '-':
nd = cd - cd2
elif op == '*':
nd = cd * cd2
elif op == '/':
nd = cd / cd2
elif op == 'avg':
nd = (cd + cd2) / 2
newchg.chgdiff.append(nd)
# Screw doing anything fancy with the augmentation charges
# Just take them from the same file as the embedded atoms object.
newchg.aug = chga.aug
newchg.augdiff = chga.augdiff
if options.outfile:
fname = options.outfile
else:
from os.path import basename
fname = basename(chgf1) + oplong + basename(chgf2)
newchg.write(fname)
zero = raw_input(
"Set negative values of the added charge density to zero (Yes/No): ")
vasp_charge_add = VaspChargeDensity(filename=None)
vasp_charge_add.atoms = [
atoms1,
]
vasp_charge_add.chg = [
chgadd,
]
# Print out charge density
#--------------------------
# Check whether CHGADD exists
if os.path.isfile("./CHGADD"):
print "\n**WARNING: A file called CHGADD already exists in this directory."
yesno = raw_input(
"Type y to continue and overwrite it, any other key to stop\n")
if yesno != "y":
sys.exit(0)
print "Writing added density data to file CHGADD ...",
sys.stdout.flush()
vasp_charge_add.write(filename="CHGADD", format="chgcar")
print "done."
endtime = time.clock()
runtime = endtime - starttime
print "\nEnd of calculation."
print "Program was running for %.2f seconds." % runtime
#---------------------------------------- parchg_up = (parchg_sum+parchg_diff)/2. # Calculate down spin density (sum-diff)/2 #---------------------------------------- parchg_down = (parchg_sum-parchg_diff)/2. # Write out parchg files #------------------------ parchgfile = PARCHGfile + ".UP" print "Writing up spin data to file %s..." % parchgfile, sys.stdout.flush() output_charge_data = VaspChargeDensity(filename=None) output_charge_data.atoms=[geomdata,] output_charge_data.chg=[parchg_up,] output_charge_data.write(filename=parchgfile,format="chgcar") print "done." parchgfile = PARCHGfile + ".DOWN" print "Writing down spin data to file %s..." % parchgfile, sys.stdout.flush() output_charge_data = VaspChargeDensity(filename=None) output_charge_data.atoms=[geomdata,] output_charge_data.chg=[parchg_down,] output_charge_data.write(filename=parchgfile,format="chgcar") print "done." parchgfile = PARCHGfile + ".DIFF" print "Writing up-down spin data to file %s..." % parchgfile, sys.stdout.flush() output_charge_data = VaspChargeDensity(filename=None)
def chgarith(chgf1, chgf2, op, filename, wcell):
# chgf1 = args[0]
# chgf2 = args[2]
# op = args[1]
chg1 = VaspChargeDensity(chgf1)
chg2 = VaspChargeDensity(chgf2)
# if options.wcell:
# wcell = int(options.wcell)
if wcell == 0:
chga = chg1
elif wcell == 1:
chga = chg2
# else:
# print ('Error, invalid argument to -w option')
# sys.exit(1)
# else:
# chga = chg1
if len(chg1.chg) != len(chg2.chg):
print(
'Number of images in charge density files not equal. Using just the final images in both files.'
)
print('len(chg.chg)', len(chg1.chg), len(chg2.chg))
chg1.chg = [chg1.chg[-1]]
chg1.atoms = [chg1.atoms[-1]]
if chg1.is_spin_polarized():
chg1.chgdiff = [chg1.chgdiff[-1]]
chg2.chgdiff = [chg2.chgdiff[-1]]
chg2.chg = [chg2.chg[-1]]
chg2.atoms = [chg2.atoms[-1]]
newchg = VaspChargeDensity(None)
print('Start charge manipul')
for i, atchg in enumerate(chg1.chg):
c1 = atchg
c2 = chg2.chg[i]
newchg.atoms.append(chga.atoms[i].copy())
if op == '+':
nc = c1 + c2
oplong = '_add_'
elif op == '-':
nc = c1 - c2
oplong = '_sub_'
elif op == '*':
nc = c1 * c2
oplong = '_mult_'
elif op == '/':
nc = c1 / c2
oplong = '_div_'
elif op == 'avg':
nc = (c1 + c2) / 2
oplong = '_avg_'
newchg.chg.append(nc)
if chg1.is_spin_polarized():
print('Spin polarized')
for i, cd in enumerate(chg1.chgdiff):
cd2 = chg2.chgdiff[i]
if op == '+':
nd = cd + cd2
elif op == '-':
nd = cd - cd2
elif op == '*':
nd = cd * cd2
elif op == '/':
nd = cd / cd2
elif op == 'avg':
nd = (cd + cd2) / 2
newchg.chgdiff.append(nd)
# Screw doing anything fancy with the augmentation charges
# Just take them from the same file as the embedded atoms object.
newchg.aug = chga.aug
newchg.augdiff = chga.augdiff
# if options.outfile:
# fname = options.outfile
# else:
# from os.path import basename
# fname = basename(chgf1) + oplong + basename(chgf2)
newchg.write(filename)
return filename
chgdiff = chgdiff - chg2
print "done."
vasp_charge_diff = VaspChargeDensity(filename=None)
vasp_charge_diff.atoms = [
atoms1,
]
vasp_charge_diff.chg = [
chgdiff,
]
# Print out charge density
#--------------------------
# Check whether CHGDIFF exists
if os.path.isfile("./CHGDIFF"):
print "\n**WARNING: A file called CHGDIFF already exists in this directory."
yesno = raw_input(
"Type y to continue and overwrite it, any other key to stop\n")
if yesno != "y":
sys.exit(0)
print "Writing density difference data to file CHGDIFF ...",
sys.stdout.flush()
vasp_charge_diff.write(filename="CHGDIFF", format="chgcar")
print "done."
endtime = time.clock()
runtime = endtime - starttime
print "\nEnd of calculation."
print "Program was running for %.2f seconds." % runtime
# Add charge density
#-----------------
chgadd += chg2
print "done."
zero = raw_input("Set negative values of the added charge density to zero (Yes/No): ")
vasp_charge_add = VaspChargeDensity(filename=None)
vasp_charge_add.atoms=[atoms1,]
vasp_charge_add.chg=[chgadd,]
# Print out charge density
#--------------------------
# Check whether CHGADD exists
if os.path.isfile("./CHGADD"):
print "\n**WARNING: A file called CHGADD already exists in this directory."
yesno=raw_input("Type y to continue and overwrite it, any other key to stop\n")
if yesno!="y":
sys.exit(0)
print "Writing added density data to file CHGADD ...",
sys.stdout.flush()
vasp_charge_add.write(filename="CHGADD",format="chgcar")
print "done."
endtime = time.clock()
runtime = endtime-starttime
print "\nEnd of calculation."
print "Program was running for %.2f seconds." % runtime
field *= x
if (options.plus != None):
plus = options.plus
field += plus
print plus, min(field), max(field)
# for i,x in enumerate(field):
# for j,y in enumerate(x):
# for k,z in enumerate(y):
# field[i][j][k] += plus
# print field.shape
# field = field +
####### WRITEING THE FILE #############
if (oformat == "xsf"):
# write_xsf(sys.stdout,field[1],field[0])
write_xsf(sys.stdout, atoms, field)
elif (oformat == "cube"):
# print "Warrning: Third line should contain number of atoms together with position of the origin of the volumetric data."
# print "Warrning: Make sure it contain corrrect data."
write_cube(sys.stdout, atoms, field)
elif (oformat == "locpot"):
locpot_out = VaspChargeDensity(filename=None)
locpot_out.atoms = [
atoms,
]
locpot_out.chg = [
field,
]
locpot_out.write(filename=sys.argv[num - 1] + ".out", format="chgcar")