xsd2vasp.py

#!/usr/bin/env python3

from sys import argv
import xml.dom.minidom
import numpy as np
from ase.data import chemical_symbols

prefix = "/home/zeyitu/.local/opt/Parameters/vasp-pseudopotential"

cellformat = "   1.00000000000000\n" \
			 "  {0[0][0]:21.16f} {0[0][1]:21.16f} {0[0][2]:21.16f}\n" \
			 "  {0[1][0]:21.16f} {0[1][1]:21.16f} {0[1][2]:21.16f}\n" \
			 "  {0[2][0]:21.16f} {0[2][1]:21.16f} {0[2][2]:21.16f}".format
vecformat = " {0[0]:19.16f} {0[1]:19.16f} {0[2]:19.16f}".format

fxsd = argv[1]
xsd = xml.dom.minidom.parse(fxsd)
aimdoms = xsd.getElementsByTagName("IdentityMapping")
for aimdom in aimdoms:
	sxyzlist = aimdom.getElementsByTagName("Atom3d")
	if len(sxyzlist) > 0: break

symbols = [sxyz.getAttribute("Components") for sxyz in sxyzlist]
positions = np.array([sxyz.getAttribute("XYZ").split(',') for sxyz in sxyzlist], dtype=np.double)

for aimdom in aimdoms:
	vectors = aimdom.getElementsByTagName("SpaceGroup")
	if len(vectors) > 0: break

cell = np.array([vectors[0].getAttribute(axis).split(',') for axis in ("AVector", "BVector", "CVector")], dtype=np.double)

atomNums = np.array([chemical_symbols.index(symbol) for symbol in symbols])
atomOrder = np.argsort(atomNums, kind="mergesort")
atomNums = atomNums[atomOrder]
positions = positions[atomOrder]

nums, syms, history = [], [], []
for n in atomNums:
	if n not in history:
		history.append(n)
		nums.append(1)
		syms.append(chemical_symbols[n])
	else:
		nums[-1] += 1

txt_list = ['xsd', cellformat(cell)]
txt_list.append(' '.join(['{:>3s}'.format(sym) for sym in syms]))
txt_list.append(' '.join(['{:5d}'.format(num) for num in nums]))
txt_list.append("Direct")
txt_list.append('\n'.join([vecformat(vec) for vec in positions]))
with open("POSCAR", 'w') as f:
	f.write('\n'.join(txt_list))

pot_list = []
for sym in syms:
	with open('/'.join([prefix, sym, "POTCAR"]), 'r') as f:
		pot_list.append(f.read())
with open("POTCAR", 'w') as f:
	f.write(''.join(pot_list))