Esempio n. 1
0
        header = "#Generated by %s using file %s\n t(ps) ISF \n"%(sys.argv[0].split("/")[-1],inputFile)

    if "OUTCAR" in inputFile:
        ocarFile = inputFile
        atomByteNums = outcarIO.atomBytes(ocarFile)
        nAtom = outcarIO.nAtoms(ocarFile)
        basis = outcarIO.basis(ocarFile)
        
        configIterator = parserGens.parseOutcarAtoms(atomByteNums,ocarFile,nAtom)
        atomsTime = [array(atoms) for atoms in configIterator]
        atomsTime = unwrap(atomsTime,basis)
    else:
        lmpFile = inputFile
        atomByteNums = lammpsIO.atomsBytes(lmpFile)
        nAtom = lammpsIO.nAtoms(lmpFile)
        basis = lammpsIO.basis(lmpFile)
        bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]

        configIterator = parserGens.parseLammpsAtoms(atomByteNums,lmpFile,nAtom)
        atomsTime = [array(atoms) for atoms in configIterator]
    bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
    
    if len(crTime)+1 == nAtom:
        crTime=crTime[1:] #chop off the average if necessary

    if sh2Enable:
        rcut = 3.1
        neighbs = secondShell( neighbors(array(atomsTime[-1]),bounds,rcut) )
        ns = map(len,neighbs)
        crTime = [sum([crTime[j] for j in neighbs[i]])/ns[i] if ns[i]>0 else crTime[i] for i in range(len(neighbs))]
Esempio n. 2
0
dumpFilename = fname+"lmp.dump"
possibleSuffix = [i for i in possibleSuffix if os.path.isfile(fname+i)]
print possibleSuffix
ensembleHead   = " ".join([i.strip(".") for i in possibleSuffix])
ensembles = None
if len(possibleSuffix)>0:
    ensembles  = [parserGens.parseEnsemble(fname+i) for i in possibleSuffix]

if "OUTCAR" in fname:
    nAtoms = outcarIO.nAtoms(fname)
    basis = array(map(array,outcarIO.basis(fname)))
    bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
    types = outcarIO.types(fname)

    #Find the starting locations of atomic data in outcarfile
    grepResults = subprocess.check_output("grep -b POSITION %s"%fname,shell=True).split("\n")
    bytenums=[int(i.split(":")[0]) for i in grepResults if len(i)>2]
    outcarParsed = parserGens.parseOutcarAtoms(bytenums,fname,nAtoms)

    lammpsIO.writeDump(dumpFilename,basis,types,outcarParsed,ensembles,ensembleHead)

else:
    nAtoms = lammpsIO.nAtoms(fname)
    basis = lammpsIO.basis(fname)
    bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
    b = lammpsIO.atomsBytes(fname)
    dummy,types = lammpsIO.parseAtoms(fname,b[0],nAtoms,basis)
    dumpParsed = parserGens.parseLammpsAtoms(b,fname,nAtoms)

    lammpsIO.writeDump(dumpFilename,basis,types,dumpParsed,ensembles,ensembleHead)