array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
elif "OUTCAR" in pn:
if len(cfgNums)==1:
TE,stress,basis,atoms,forces,types = outcarIO.outcarReadConfig(pn,cfgNums)
orderVals.append( orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else:
TEs,stresss,basiss,atomss,forcess,typess = outcarIO.outcarReadConfig(pn,cfgNums)
for basis,atoms in zip(basiss,atomss):
orderVals.append(orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else: #LAMMPS DUMP
if len(cfgNums)==1:
basis,types,atoms = lammpsIO.readConfig(pn,cfgNums)
orderVals.append( orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else:
basiss,types,atomss = lammpsIO.readConfig(pn,cfgNums)
for basis,atoms in zip(basiss,atomss):
orderVals.append(orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
#======================================================
# Plot!
#======================================================
labels=[]
if lval==None:
lval=""
xylabels={"BO" :[r"BondOrder($Q_%s$)"%str(lval), r"$P(Q_%s)$"%str(lval)],
#Parse POSCAR
j=0
if "POSCAR" in configFile or "CONTCAR" in configFile:
poscar=open(configFile,"r").readlines()
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
types=list()
for i in atypes:
types+=[j+1]*i
j+=1
elif "OUTCAR" in configFile:
TE,stress,basis,atoms,forces,types = outcarIO.outcarReadConfig(configFile,Nconfig)
#Parse LAMMPS DUMP
else:
basis,types,atoms = lammpsIO.readConfig(configFile,Nconfig)
ax,ay,az=map(np.array,zip(*atoms))
v1,v2,v3=basis
if rectifyFlag:
ax,ay,az = ax%v1[0], ay%v2[1], az%v3[2]
fig=mlab.figure(bgcolor=(0.8,0.8,0.8))
#Set default rcut value for tetrahedral ordering
if op=="TET" and rcut==None:
rcut=3.2
#Get the order parameter and convert to integer format (opsn) for
#coloring of atoms
print "%s <lammps dump> <config #> <POSCAR output>" % sys.argv[0].split("/")[-1]
print "If only the dump file is provided, the number of configurations will be reported"
print "Converts a lammps dump to POSCAR"
# If only the filename is provided, count the number of configurations and spit that out
if len(sys.argv) == 2:
dumpdata = open(sys.argv[1], "r").readlines()
usage()
print "\nNumber of configurations:", len([i for i in dumpdata if "ITEM: TIMESTEP" in i]), "\n"
exit(0)
if len(sys.argv) != 4:
usage()
exit(0)
dumpdata = sys.argv[1] # open(sys.argv[1],"r").readlines()
configN = int(sys.argv[2])
posname = sys.argv[3]
# Read in lammps data
basis, types, atoms = lammpsIO.readConfig(dumpdata, configN)
# atoms,types = zip(*[[[i[0],i[1],i[2]-basis[2][2]/2.0],t] for i,t in zip(atoms,types) if i[2]>basis[2][2]/2.0])
# basis[2][2]/=2.0
header = "POSCAR generated by %s on %s" % (sys.argv[0].split("/")[-1], time.asctime())
# Write out POSCAR data
atypes = [types.count(j) for j in sorted(list(set(types)))]
poscarIO.write(posname, basis, atoms, atypes, header, autoFrac=False, frac=False)
j=0
if "POSCAR" in configFile or "CONTCAR" in configFile:
poscar=open(configFile,"r").readlines()
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
types=list()
for i in atypes:
types+=[j+1]*i
j+=1
#Parse OUTCAR
elif "OUTCAR" in configFile:
TE,stress,basis,atoms,forces,types = outcarIO.outcarReadConfig(configFile,Nconfig)
#Parse LAMMPS
else:
basis,types,atoms = lammpsIO.readConfig(configFile,Nconfig)
ax,ay,az=map(np.array,zip(*atoms))
nAtom = len(ax)
v1,v2,v3=basis
if shiftFlag:
atoms = [[a[0]+v1[0]/2.,a[1]+v2[1]/2.,a[2]+v3[2]/2.55] for a in atoms]
rectifyFlag = True
if rectifyFlag:
atoms = np.array(atoms) #unrectified for orderParam calculations.
ax = np.mod(atoms[:,0],v1[0])
ay = np.mod(atoms[:,1],v2[1])
az = np.mod(atoms[:,2],v3[2])
elif "OUTCAR" in pn:
if len(cfgNums) == 1:
TE, stress, basis, atoms, forces, types = outcarIO.outcarReadConfig(
pn, cfgNums)
orderVals.append( orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else:
TEs, stresss, basiss, atomss, forcess, typess = outcarIO.outcarReadConfig(
pn, cfgNums)
for basis, atoms in zip(basiss, atomss):
orderVals.append(orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else: #LAMMPS DUMP
if len(cfgNums) == 1:
basis, types, atoms = lammpsIO.readConfig(pn, cfgNums)
orderVals.append( orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
else:
basiss, types, atomss = lammpsIO.readConfig(pn, cfgNums)
for basis, atoms in zip(basiss, atomss):
orderVals.append(orderParams[op]( \
array(atoms),array(basis),l=lval,neighbs=neighbs,rcut=args.rcut,debug=args.debug))
#======================================================
# Plot!
#======================================================
labels = []
if lval == None:
lval = ""
xylabels = {
#!/usr/bin/python
import sys
#mine
import lammpsIO
import utils
utils.usage(["<input dump file>","<configuration #>","<output config file>"],3,3,"LAMMPS dump file must have bounds, atom type and atomic locations.")
iDump=sys.argv[1]
cfg=int(sys.argv[2])
bounds,types,atoms=lammpsIO.readConfig(iDump,cfg)
oCnfg=open(sys.argv[3],"w")
lammpsIO.dumpWriteConfig(oCnfg,bounds,types,atoms,"config made by %s, from file %s config %d"%(sys.argv[0].split("/")[-1],iDump,cfg))
dumpdata = open(sys.argv[1], "r").readlines()
usage()
print "\nNumber of configurations:", len(
[i for i in dumpdata if "ITEM: TIMESTEP" in i]), "\n"
exit(0)
if len(sys.argv) != 4:
usage()
exit(0)
dumpdata = sys.argv[1] #open(sys.argv[1],"r").readlines()
configN = int(sys.argv[2])
posname = sys.argv[3]
#Read in lammps data
basis, types, atoms = lammpsIO.readConfig(dumpdata, configN)
#atoms,types = zip(*[[[i[0],i[1],i[2]-basis[2][2]/2.0],t] for i,t in zip(atoms,types) if i[2]>basis[2][2]/2.0])
#basis[2][2]/=2.0
header = "POSCAR generated by %s on %s" % (sys.argv[0].split("/")[-1],
time.asctime())
#Write out POSCAR data
atypes = [types.count(j) for j in sorted(list(set(types)))]
poscarIO.write(posname,
basis,
atoms,
atypes,
header,
autoFrac=False,
frac=False)
