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)
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:
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:
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)
#!/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])
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)