funcflExtractor

#!@Python3_EXECUTABLE@
"""Funcfl Extractor
 
Opens an DYNAMO86 EAM funcfl file, parses the data and writes out
separate files for F[rho], rho(r), and Z(r)
 
Usage: funcflExtractor
 
Options:
  -h,  --help              show this help
  -f,  --funcfl=...        use specified funcfl file for the data
  -o,  --output-base=...   use specified name for the base of the output files
 
Example:
   funcflExtractor -f Au.u3.funcfl -o Au_u3
 
"""
 
__author__ = "Dan Gezelter (gezelter@nd.edu)"
__copyright__ = "Copyright (c) 2004-present The University of Notre Dame. All Rights Reserved."
__license__ = "OpenMD"
 
import sys
import getopt
import string
 
z = []
rho = []
fRho = []
 
def usage():
    print(__doc__)
 
def readFuncflFile(funcflFileName):
 
    eamFile = open(funcflFileName, 'r')
    lines = eamFile.readlines()
    eamFile.close()
 
    lineNo = 0
    tokensFound = 0
 
    for l in lines:
        lineNo = lineNo +1
        if (lineNo == 3):
            L = string.split(l)
            nrho = int(L[0])
            drho = float(L[1])
            nR = int(L[2])
            dR = float(L[3])
            rcut = float(L[4])
        if (lineNo > 3):
            L = string.split(l)
            for i in range(0, 5):
                tokensFound = tokensFound + 1
                if (tokensFound <= nrho):
                    fRho.append(float(L[i]))
                elif (tokensFound <= nrho+nR):
                    z.append(float(L[i]))
                else:
                    rho.append(float(L[i]))
 
    eamFile.close()
    return (nrho, drho, nR, dR, rcut)
 
def writeFiles(outputBaseName, nrho, drho, nR, dR, rcut):
 
    fFile = open(outputBaseName + ".F.dat", 'w')
    zFile = open(outputBaseName + ".Z.dat", 'w')
    rhoFile = open(outputBaseName + ".rho.dat", 'w')
                
    for i in range(0, nR):
        r = i*dR
        zFile.write( "%f\t%f\n" % (r, z[i]))
        rhoFile.write( "%f\t%f\n" % (r, rho[i]))
 
 
    for i in range(0, nrho):
        rhoVal = i * drho
        fFile.write("%f\t%f\n" % (rhoVal, fRho[i]))
 
    fFile.close()
    zFile.close()
    rhoFile.close()
 
    
def main(argv):
    global haveFuncflFileName
    global haveOutputBaseName
 
    haveFuncflFileName = False
    haveOutputBaseName = False
 
    try:                                
        opts, args = getopt.getopt(argv, "hf:o:", ["help",  "funcfl=", "output-base="]) 
    except getopt.GetoptError:           
        usage()                          
        sys.exit(2)                     
    for opt, arg in opts:                
        if opt in ("-h", "--help"):      
            usage()                     
            sys.exit()
        elif opt in ("-f", "--funcfl"): 
            funcflFileName = arg
            haveFuncflFileName = True
        elif opt in ("-o", "--output-base"): 
            outputBaseName = arg
            haveOutputBaseName = True
    if (not haveFuncflFileName):
        usage() 
        print("No funcfl file was specified")
        sys.exit()
    if (not haveOutputBaseName):
        usage()
        print("No output base name was specified")
        sys.exit()
 
    (nrho, drho, nR, dR, rcut) = readFuncflFile(funcflFileName)
    writeFiles(outputBaseName, nrho, drho, nR, dR, rcut)
 
if __name__ == "__main__":
    if len(sys.argv) == 1:
        usage()
        sys.exit()
    main(sys.argv[1:])