qe_parse.py

#!/usr/bin/python

#===========================================================================#
#                                                                           #
#  File:       qe_parse.py                                                  #
#  Dependence: util.py                                                      #
#  Usage:      parse files generated by Quantum ESPRESSO                    #      
#  Author:     Shunhong Zhang <zhangshunhong@tsinghua.edu.cn>               #
#  Date:       Apr 22, 2017                                                 #
#                                                                           #
#===========================================================================#


import numpy as np
from math import *
import os


def parse_qe_eigenval(filename,nspin=1):
    print "Parsing {0} ...".format(filename)
    f=open(filename,'r')
    line = f.readline().split()
    nband = int(line[2].split(",")[0])
    nkpt = int(line[4])
    print "number of bands = ",nband,"\nnumber of q points = ",nkpt

    kpt = np.zeros((nkpt,3),float)
    eigenval = np.zeros((nkpt,nband,nspin),float)
    for ikpt in range(nkpt):
        line = f.readline().split()
        kpt[ikpt] = [float(line[i]) for i in range(3)]
        data = np.fromfile(f,sep=' ',count=nband*nspin).reshape((nspin,nband))
        for ispin in range(nspin):
            eigenval[ikpt,:,ispin]=[float(data[ispin,iband]) for iband in range(nband)]
            eigenval[ikpt,:,ispin].sort()
    f.close()
    print "Done"
    return kpt,eigenval

# Extract the final lattice and atom coordinates of a relaxation calculation by qe
def parse_qe_rx(filename):
    ibrav=int(os.popen('grep "bravais-lattice index" '+filename).readline().split('=')[1])
    get_cell=os.popen('grep -A 6 "Begin final " '+filename).readlines()
    alat=float(get_cell[3].split('=')[1].split(')')[0])
    cell = np.zeros((3,3),float)
    for i in range(3):
        for j in range(3):
            cell[i,j]=float(get_cell[i+4].split()[j])
    cell=cell*alat
    celldm = find_celldm(ibrav,cell)
    for i in range(1,7):
       if celldm[i]!=0:
          print "celldm("+str(i)+") =",celldm[i]
    natom = int(os.popen('grep "number of atoms" '+filename).readline().split('=')[1])
    pos = os.popen('grep -B '+str(natom)+' "End final coordinates" '+filename).readlines()[:-1]
    for i in range(len(pos)):
        print pos[i],

def get_rec_vec_qe():
    try:
       line=os.popen("grep 'lattice parameter (alat)' nscf.out").readline()
       alat=float(line.split()[4])*0.529
       print "alat=",alat,"angstrom"
    except:
       print "unable to extract the lattice parameter"
       exit()
    rec_vec=np.zeros((3,3),float)
    try:
       lines=os.popen("grep -A 3 'reciprocal axes' nscf.out").readlines()
       for i in range(3):
           for j in range(3):
               rec_vec[i,j] = float(lines[i+1].split()[j+3])/2/np.pi*alat
    except:
       print "unable to extract the reciprocal axes"
       exit()
    return rec_vec


def parse_abinit_eigenval(filename,nspin=1):
    print "Parsing {0} ...".format(filename)
    f=open(filename,'r')
    line = f.readline().split()
    nkpt = int(line[6])
    print "number of k points = ",nkpt

    kpt = np.zeros((nkpt,3),float)
    kweight=np.zeros(nkpt,float)
    eigenval=[]
    for ikpt in range(nkpt):
        line = f.readline().split()
        nband=int(line[3].rstrip(','))
        kweight[ikpt]=float(line[5].rstrip(','))
        kpt[ikpt] = [float(line[i]) for i in range(7,10)]
        data = np.fromfile(f,sep=' ',count=nband)
        eigenval.append(data)
    f.close()
    eigenval=np.array(eigenval)
    print "Done"
    return kpt,kweight,eigenval