exciting input file to VASP poscar file

xml2vasp.py

#!/usr/bin/env python

from lxml import etree
import xml.etree.ElementTree as xml
from math import *
import sys, getopt, os
from sys import stdout
from array import *
import numpy as np

from collections import Counter
from termcolor import colored

#*******************************DOCUMENTATION***********************************
#
#AUTHOR 	 : ASIF IQBAL BHATTI
#CREATED ON	 : 18/10/2015
#USAGE	   	 : To parse an EXCITING xml input file to VASP format.
#Output file has already been defined in the code (POSCAR.vasp).
#CAUTION: Use at your own risk (NOTEVEN IMPLIED GUARANTEED, WHATSOEVER),
#the code has been tested but the user in the end will have to verify the ouput 
#geometry and be vary of the order of atoms in list.
#
#************************END OF DOCUMENTATION***********************************

Bohr2angstrom = 0.529177249
yellow        = '\033[01;33m'
red           = '\033[01;31m'
blue          = '\x1b[01;34m'
cyan          = '\x1b[01;36m'
green         = yellow

#*********************DEFINITION FOR INPUTFILE**********************************

if len(sys.argv) < 2:
	sys.exit('Usage: %s <Exciting xml inputfile>' % sys.argv[0])
    
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... ", 'blue')
print '-'*80
print colored(" | Title is:  ", 'blue'), root.findtext('title')
f.write(root.findtext('title'))

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

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

#***************************SCALING DEFINITION********************************

for sca in struct.findall('crystal'):
	for key in sca.attrib:
		if key == 'scale': # SCALING HAS TO BE CHANGED
			sc = sca.get('scale')
			print colored(" | Scaling factor is:  ", 'blue'), float(sc)
		else:
			sc = float(1.00)
			print colored(" | Scaling factor is:  ", 'blue'), float(sc)		


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

#***********************LATTICE VECTORS SECTION************************

lv = []
for vect in struct.findall('crystal'):
	lat = vect.find('basevect')
	for k in vect.findall('basevect'):
		lv.append(k.text.split())	
for list in lv:
	for lv1 in list:
		a = float(lv1)*float(sc)*Bohr2angstrom
		sys.stdout.write(green + "\t%16.10f" % (a))
		f.write("%16.10f" % a)
    	stdout.write("\n")
    	f.write("\n")
    	
#******************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):
	sys.stdout.write(green + "\t%s" % lab[x])
	f.write("\t%s" % lab[x])
	for s in struct[x+1].iter('atom'):
		sp.append(lab[x])
stdout.write("\n")
f.write("\n")

for h in range(i-1):
	sys.stdout.write(green + "\t%d" % sp.count(lab[h]))
	f.write("\t%d" % sp.count(lab[h]))
stdout.write("\n")
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:
			for at in list:
				a = float(at)* Bohr2angstrom
				sys.stdout.write(green + "\t%16.10f" % (a))
				f.write("%16.10f" % (a))
    			stdout.write("\n")
    			f.write("\n")
    			
#**************************DIRECT COORDINATE*********************
			
	else:
		print "Direct"
		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])
		for list in ccl:
			for at in list:
				a = float(at)
				sys.stdout.write(green + "\t%16.10f" % (a))
				f.write("%16.10f" % (a))
    			stdout.write("\n")
    			f.write("\n")
    			
print "\n"				
print colored("File generated ... ", 'red')

f.close()