pythonLab/poscarToFEFF.py at master · tboland1/pythonLab · GitHub

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# This file will read any POSCAR / CONTCAR formatted file and create an
# atoms.inp file which can be turned into a feff.inp input file using the
# gfortran compile file atoms246.f
# You must have the atoms element tag line in the POSCAR/CONTCAR in order
# to tag the atoms properly.


## Enter the location of the POSCAR/CONTCAR
#file='/home/tara/POSCAR210'
#filename = str(input("What is the file name? "))
file= 'POSCAR1unit' #CONTCAR'

# title
title=[]
# what type of atoms are in the poscar
eleTag=[]
# number of each element in the poscar
eleCount=[]
# get all the coordinates unparsed by type
coordTot=[]
# add the line counter
linecounter=0

## Enter the target atom
target=input("What is the Target atom? ")        # get the target

# open the file & get system info: # of atoms, type of atoms, lattice params, pull atom coords into coordTot
fileopen=open(file)
for line in fileopen:
    linecounter+=1
    line=line.strip()

    # get the system tag name
    if linecounter == 1:
        line=line.replace(" ","")
        title.append(line.strip())
    # get the a,b,c lattice vectors has to be cubic
    elif linecounter > 2 and linecounter < 6:
        if linecounter == 3:
            varA=line.split()
            a=float(varA[0])
        elif linecounter == 4:
            varB=line.split()
            b=float(varB[1])
            #print(b)
        elif linecounter == 5:
            varC=line.split()
            c=float(varC[2])
    # get the elements tags
    elif linecounter == 6:
        eleTag=line.split()
    elif linecounter == 7:
        eleCount=[int(x) for x in line.split()]
        #print(eleCount)
    elif linecounter >= 9:
        coordTot.append(line)
        #print(coordTot)
fileopen.close()

## Now construct the extra data types
# count the number of atom types
countType=len(eleCount)
# element type tag
eleType=[]
# element type number
eleNum=[]
# count total number of atoms
countAtoms=sum(eleCount)

for element in eleCount:
    linecounter=0
    for i in range(1:eleCount):
        linecounter+=1

    # now count through all the elements and fill coordArray
    if linecounter >= 9 and linecounter <=  numO[0]+numCe[0]+9:
        if linecounter >=9 and linecounter <= 9+numO[0]-1:
            atomcountO+=1
            oTag.append('O'+str(atomcountO))
            oshell.append('O')
        elif linecounter > 9+numO[0]-1 and linecounter <= numO[0]+numCe[0]+9-1:
            atomcountCe+=1
            ceTag.append('Ce'+str(atomcountCe))
            ceshell.append('Ce')


##! Uncomment for cart coords
# linecounter=0
# fileopen=open(file)
# for line in fileopen:
#     linecounter+=1
#     if linecounter < 9:
#         cat=1
#     elif linecounter >= 9 and linecounter <=  numO[0]+numCe[0]+9:
#         # normalize the coordinates
#         if linecounter >=9 and linecounter <= 9+numO[0]-1:
#             coord=line.split()
#             x1=float(coord[0])/a
#             x2=float(coord[1])/b
#             x3=float(coord[2])/c
#             #disp goes here
#             ocoord.append([x1,x2,x3])
#         elif linecounter > 9+numO[0]-1 and linecounter <= numO[0]+numCe[0]+9-1:
#             coord=line.split()
#             x1=float(coord[0])/a
#             x2=float(coord[1])/b
#             x3=float(coord[2])/c
#             #total= ((x1-xtar[0])**2+(x2-xtar[1])**2+(x3-xtar[2])**2)**(1/2.0) #disp goes here
#             cecoord.append([x1,x2,x3])
# fileopen.close()

##! Uncomment for fractional coords
# linecounter=0
# fileopen=open(file)
# for line in fileopen:
#     linecounter+=1
#     if linecounter < 9:
#         cat=1
#     elif linecounter >= 9 and linecounter <=  numO[0]+numCe[0]+9:
#         # normalize the coordinates
#         if linecounter >=9 and linecounter <= 9+numO[0]-1:
#             coord=line.split()
#             x1=float(coord[0])
#             x2=float(coord[1])
#             x3=float(coord[2])
#             ocoord.append([x1,x2,x3])
#         elif linecounter > 9+numO[0]-1 and linecounter <= numO[0]+numCe[0]+9-1:
#             coord=line.split()
#             x1=float(coord[0])
#             x2=float(coord[1])
#             x3=float(coord[2])
#             cecoord.append([x1,x2,x3])
# fileopen.close()

# write the atoms.inp file
linecounter=0
countce=0
filenew=open('atoms.inp','w')
filenew.write('title'+' '+title[0]+'\n')
filenew.write('space P 1 \n')
filenew.write('a='+str(a)+' '+'b='+str(b)+' '+'c='+str(c)+'\n')
filenew.write('rmax=16'+' '+'core='+target+'\n')
filenew.write('index=t\n')
filenew.write('atom\n')
for line in range(1,numO[0]+1):
    filenew.write(oshell[linecounter]+'  '+str(ocoord[linecounter][0])+' '+str(ocoord[linecounter][1])+' '+str(ocoord[linecounter][2])+'    '+oTag[linecounter]+'\n')
    linecounter+=1

for line in range(1,numCe[0]+1):
    filenew.write(ceshell[countce]+' '+str(cecoord[countce][0])+' '+str(cecoord[countce][1])+' '+str(cecoord[countce][2])+'    '+ceTag[countce]+'\n')
    countce+=1
filenew.write('--------------------------------------')
filenew.close()


## use atomsToFeff on the file generated here then copy and paste this
# into the top of the feff.inp file

# CONTROL   1   1   1     1     1
# PRINT     0   0   0     0     0
#
# COREHOLE RPA
# SCF 7.0 0 30 0.2 1
# EXCHANGE 0 1.97 0 0
# COREECTIONS 0 0.03
# EDGE K
# S02 0.0
#
# ELNES 4 0.02 0
# 300 1 0 1
# 2.4 0
# 5 3
# 0 0