Beispiel #1
0
        sh2Enable = True
        sys.argv.pop(i)

    #Parse Args
    inputFile = sys.argv[1]

    isfType = "total"
    if sys.argv[2][0] in ['s','S']:
        isfType = "self"
    else:
        isfType = "total"

    criteria = sys.argv[3]
    criteFile = sys.argv[4]

    configIterator = parserGens.parseEnsemble(criteFile)
    crTime = array([cr for cr in configIterator][-1])

    criteriaTxt = criteria.replace("gt",">")
    criteriaTxt = criteria.replace("lt","<")

    if scale == None:
        if "OUTCAR" in inputFile:
            scale = 5E-15 #5fs (potim=5)
        else:
            scale = 0.001E-12 #0.001ps (default for units = metal)

    if logtEnable:
        header = "#Generated by %s using file %s\n log(t) ISF \n"%(sys.argv[0].split("/")[-1],inputFile)
    else:
        header = "#Generated by %s using file %s\n t(ps) ISF \n"%(sys.argv[0].split("/")[-1],inputFile)
Beispiel #2
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        sys.argv.remove("-logt")
        logtEnable = True
    if "-scale" in sys.argv:
        i = sys.argv.index("-scale")
        scale = float(sys.argv[i+1])
        sys.argv.pop(i)
        sys.argv.pop(i)
    if "-nStep" in sys.argv:
        i = sys.argv.index("-nStep")
        nStep = int(sys.argv[i+1])
        sys.argv.pop(i)
        sys.argv.pop(i)

    inputFile = sys.argv[1]
    criteria = sys.argv[3]
    configIterator = parserGens.parseEnsemble(inputFile+".rmsd")
    rmsdTime = array([rmsd for rmsd in configIterator][-1])

    isfType = "total"
    if sys.argv[2][0] in ['s','S']:
        isfType = "self"
    else:
        isfType = "total"

    if scale == None:
        if "OUTCAR" in inputFile:
            scale = 5E-15 #5fs (potim=5)
        else:
            scale = 0.001E-12 #0.001ps (default for units = metal)

    if "OUTCAR" in inputFile:
Beispiel #3
0
import lammpsIO
import parserGens
import utils

possibleSuffix = [".rmsd",".cn",".tetra",".rmsd50",".rmsd100",".rmsd1000",".rmsd5000",".rmsd10000",".2shelltetra",".2shellcn",".2shellrmsd100",".tetra.avg1000",".tetra.avg5000",".tetra.avg100",".tetra.avg500"]

utils.usage(["<outcar,lamps dump>"],1,1,"Note: Automatically looks for <OUTCAR/dump.suffix> for per atom ensembles. to include in the dump")

fname = sys.argv[1]
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:
Beispiel #4
0
utils.usage(["<.ensembleFile>","<window size (int or all)>"],2,2)

inputFile = sys.argv[1]
possibleSuffixes = [".tetra",".rmsd",".cn"]
if not any([suffix for suffix in possibleSuffixes if suffix in inputFile]):
    print "wrong input file dummy."
    exit(0)

windowSize = sys.argv[2]
outputFile = inputFile+".avg"+windowSize

#assume first line is a header
head = open(inputFile,"r").readline()

configIterator = parserGens.parseEnsemble(inputFile,keepAvg=True)
ops = zip(*[a for a in configIterator])

if windowSize == "all":
    opAvg = [sum(op)/len(op) for op in ops]
    opLines = [" ".join(map(str,opAvg))+"\n"]
else:
    windowSize = int(windowSize)

    opAvg = zip(*[datatools.wsmooth(atet,windowSize) for atet in ops])
    opLines = [" ".join(map(str,line))+"\n" for line in opAvg]

out = open(outputFile,"w")
out.write(head)
out.writelines(opLines)
Beispiel #5
0
#!/usr/bin/python

import sys
import itertools
#mine
import utils,parserGens,datatools

utils.usage(["<file.neighbs>","<ensemble file (tetra, cn, rmsd, w/e)>"],2,2)

neighbFile = sys.argv[1]
ensembFile = sys.argv[2]

neighbGen = parserGens.parseNeighbor(neighbFile)
ensembGen = parserGens.parseEnsemble(ensembFile)

#secondShellEnsemb=list()
efp = ensembFile.split(".")
outfile = ".".join(efp[0:-1]) + ".2shell" + efp[-1]
out = open(outfile,"w")
out.write("2ndShellAvg%s 2ndShellPerAtom%s\n"%(efp[1],efp[1]))
stopFlag=False
for ensembG,neighbG in itertools.izip(ensembGen,neighbGen):

    secondShellEnsemb = list()
    for a,firstNeighbs in enumerate(neighbG):

        secondNeighbs = [neighbG[i] for i in firstNeighbs]
        totalNeighb = set(datatools.flatten([firstNeighbs]+secondNeighbs))
        N = len(totalNeighb)        
        if N==0:
            secondShellEnsemb.append(ensembG[a])
Beispiel #6
0
if __name__ == "__main__":
    utils.usage(["<dump.dat or OUTCAR>", "<'s'-self 'd'-distinct or 't'-total'>, default total"], 1, 3)

    RMAX = 10.0

    plotEnable = True
    logtEnable = False
    if "-noPlot" in sys.argv:
        sys.argv.remove("-noPlot")
        plotEnable = False
    if "-logt" in sys.argv:
        sys.argv.remove("-logt")
        logtEnable = True

    inputFile = sys.argv[1]
    configIterator = parserGens.parseEnsemble(inputFile + ".tetra")
    tetraTime = array([tetra for tetra in configIterator])

    # steps = map(int,sys.argv[2].split(","))
    isfType = "total"
    if sys.argv[2][0] in ["s", "S"]:
        isfType = "self"
    else:
        isfType = "total"

    if "OUTCAR" in inputFile:
        ocarFile = inputFile
        atomByteNums = outcarIO.atomBytes(ocarFile)
        nAtom = outcarIO.nAtoms(ocarFile)
        basis = outcarIO.basis(ocarFile)