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base repository: Asif-Iqbal-Bhatti/Script-to-extract-various-properties-from-VASP-OUTCAR-file
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head repository: Asif-Iqbal-Bhatti/Script-to-extract-various-properties-from-VASP-OUTCAR-file
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compare: sourcery/master
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  • 1 commit
  • 13 files changed
  • 1 contributor

Commits on Jul 17, 2022

  1. 'Refactored by Sourcery'

    Sourcery AI committed Jul 17, 2022
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    37b60c0 View commit details
212 changes: 99 additions & 113 deletions Exciting_Xml2Vasp.py
View file
Original file line number Diff line number Diff line change
@@ -33,131 +33,117 @@
#*********************DEFINITION FOR INPUTFILE**********************************

if len(sys.argv) < 2:
sys.exit('Usage: %s <Exciting xml inputfile>' % sys.argv[0])
sys.exit(f'Usage: {sys.argv[0]} <Exciting xml inputfile>')

tree = xml.parse(sys.argv[1])
root = tree.getroot()

struct = root.getchildren()[1] # pivot for controling element
lattice = struct.getchildren()


#*********************CONTROL SECTION FOR INPUT FILE***************************

f = open('POSCAR.vasp', 'w+')

print (colored("\nExtracting information from input file... ", 'yellow'))
print ('-'*80)
print (colored(" | Title is: ", 'yellow'), root.findtext('title'))
f.write(root.findtext('title'))
with open('POSCAR.vasp', 'w+') as f:
print (colored("\nExtracting information from input file... ", 'yellow'))
print ('-'*80)
print (colored(" | Title is: ", 'yellow'), root.findtext('title'))
f.write(root.findtext('title'))

#*************************DETECTING # OF SPECIES******************************
#*************************DETECTING # OF SPECIES******************************

i = 0
for child in struct:
i = i+1
print (colored(" | Species detected: ", 'yellow'), i-1 )
f.write(" |\t Number of species detected: {:d}\n".format(i-1))
i = 0
for _ in struct:
i = i+1
print (colored(" | Species detected: ", 'yellow'), i-1 )
f.write(" |\t Number of species detected: {:d}\n".format(i-1))

#***************************SCALING DEFINITION********************************
#reading from a file
for sca in struct.findall('crystal'):
for key in sca.attrib:
if key == 'scale': # SCALING HAS TO BE CHANGED
sc = sca.get('scale')
#***************************SCALING DEFINITION********************************
#reading from a file
for sca in struct.findall('crystal'):
for key in sca.attrib:
sc = sca.get('scale') if key == 'scale' else 1.0
print (colored(" | Scaling factor is: ", 'yellow'), float(sc))
else:
sc = float(1.00)
print (colored(" | Scaling factor is: ", 'yellow'), float(sc))


print (colored(" | Converting bohr to angstrom ... ", 'yellow'))
print (colored(" | Writing to a File in VASP format ... ", 'yellow'))
f.write("%f\n" % 1.0)
print ('-'*80)

#***********************LATTICE VECTORS SECTION************************
#reading from a file
lv = []
for vect in struct.findall('crystal'):
#lat = vect.find('basevect')
for k in vect.findall('basevect'):
lv.append(k.text.split())
###

convertion = Bohr2angstrom*float(sc)
for list in lv:
print ("\t{:10.8f} {:10.8f} {:10.8f}".format(float(list[0])*convertion,
float(list[1])*convertion, float(list[2])*convertion ) )
f.write ("\t{:10.8f} {:10.8f} {:10.8f}\n".format(float(list[0])*convertion,
float(list[1])*convertion, float(list[2])*convertion ) )

#******************SPECIES CONTROL SECTION*********************************

lab = []
for coord in struct.findall('species'):
spe = coord.get('speciesfile')
jj = os.path.splitext(spe)
lab.append(jj[0])

sp = []
for x in range(i-1):
print("{:s}".format(lab[x]))
f.write("\t%s" % lab[x])
for s in struct[x+1].iter('atom'):
sp.append(lab[x])
f.write("\n")

for h in range(i-1):
print("\t{:d}".format(sp.count(lab[h])) )
f.write("\t%d" % sp.count(lab[h]))
f.write("\n")

#*******************CONTROL SECTION FOR CARTESIAN COORDINATE***************

lll = []
ccl = []
checker = False
for cart in root.findall('structure'):
ca = cart.get('cartesian')
for key in cart.attrib:
if key == 'cartesian':
checker = True
if ca == "true":
print ("Cartesian")
f.write("Cartesian\n")
for i in range(i-1):
for s in struct[i+1].iter('atom'):
atom = s.get('coord')
ccl.append(atom.split())
lll.append(lab[i])
print (colored(" | Converting bohr to angstrom ... ", 'yellow'))
print (colored(" | Writing to a File in VASP format ... ", 'yellow'))
f.write("%f\n" % 1.0)
print ('-'*80)

#***********************LATTICE VECTORS SECTION************************
#reading from a file
lv = []
for vect in struct.findall('crystal'):
#lat = vect.find('basevect')
lv.extend(k.text.split() for k in vect.findall('basevect'))
###

convertion = Bohr2angstrom*float(sc)
for list in lv:
print ("\t{:10.8f} {:10.8f} {:10.8f}".format(float(list[0])*convertion,
float(list[1])*convertion, float(list[2])*convertion ) )
f.write ("\t{:10.8f} {:10.8f} {:10.8f}\n".format(float(list[0])*convertion,
float(list[1])*convertion, float(list[2])*convertion ) )

#******************SPECIES CONTROL SECTION*********************************

lab = []
for coord in struct.findall('species'):
spe = coord.get('speciesfile')
jj = os.path.splitext(spe)
lab.append(jj[0])

sp = []
for x in range(i-1):
print("{:s}".format(lab[x]))
f.write("\t%s" % lab[x])
sp.extend(lab[x] for _ in struct[x+1].iter('atom'))
f.write("\n")

for h in range(i-1):
print("\t{:d}".format(sp.count(lab[h])) )
f.write("\t%d" % sp.count(lab[h]))
f.write("\n")

#*******************CONTROL SECTION FOR CARTESIAN COORDINATE***************

lll = []
ccl = []
checker = False
for cart in root.findall('structure'):
ca = cart.get('cartesian')
for key in cart.attrib:
if key == 'cartesian':
checker = True
if ca == "true":
print ("Cartesian")
f.write("Cartesian\n")
for i in range(i-1):
for s in struct[i+1].iter('atom'):
atom = s.get('coord')
ccl.append(atom.split())
lll.append(lab[i])
# print (atom, lab[i])

for list in ccl:
print ("{:5.8f} {:5.8f} {:5.8f}".format(float(list[0])* Bohr2angstrom,
float(list[1])* Bohr2angstrom, float(list[2])* Bohr2angstrom ) )
f.write ("{:5.8f} {:5.8f} {:5.8f}\n".format(float(list[0])* Bohr2angstrom,
float(list[1])* Bohr2angstrom, float(list[2])* Bohr2angstrom ) )


for list in ccl:
print ("{:5.8f} {:5.8f} {:5.8f}".format(float(list[0])* Bohr2angstrom,
float(list[1])* Bohr2angstrom, float(list[2])* Bohr2angstrom ) )
f.write ("{:5.8f} {:5.8f} {:5.8f}\n".format(float(list[0])* Bohr2angstrom,
float(list[1])* Bohr2angstrom, float(list[2])* Bohr2angstrom ) )
#**************************DIRECT COORDINATE*********************
else:
print ("Direct")
f.write ("Direct\n")
for i in range(i-1):
for s in struct[i+1].iter('atom'):
atom = s.get('coord')
ccl.append(atom.split())
lll.append(lab[i])

else:
print ("Direct")
f.write ("Direct\n")
for i in range(i-1):
for s in struct[i+1].iter('atom'):
atom = s.get('coord')
ccl.append(atom.split())
lll.append(lab[i])
# print (atom, lab[i])
# print (ccl)

for list in ccl:
print ("{:5.8f} {:5.8f} {:5.8f}".format(float(list[0]),
float(list[1]), float(list[2]) ) )
f.write ("{:5.8f} {:5.8f} {:5.8f}\n".format(float(list[0]),
float(list[1]), float(list[2]) ) )

print (colored("File generated ... ", 'green'))

f.close()

for list in ccl:
print ("{:5.8f} {:5.8f} {:5.8f}".format(float(list[0]),
float(list[1]), float(list[2]) ) )
f.write ("{:5.8f} {:5.8f} {:5.8f}\n".format(float(list[0]),
float(list[1]), float(list[2]) ) )

print (colored("File generated ... ", 'green'))
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