usage()
print "Error parsing rcut args"
exit(0)
outcarFile=sys.argv[1]
try:
num=sys.argv[1].split("_")[1]
except IndexError:
num=None
refStructure=None
if len(sys.argv)==3:
refStructure=int(sys.argv[2])
#First and last configurations
dummy,dummy,basisFirst,atomsFirst,dummy,typesFirst = outcarIO.outcarReadConfig(outcarFile,wantconfig=0)
dummy,dummy,basisLast,atomsLast,dummy,typesLast = outcarIO.outcarReadConfig(outcarFile,wantconfig=-1)
#MSD
delT,msdAtom=outcarMeanSquareDisplaceAtom(outcarFile,refStructure)
#TET
tetsFirst,rcutFirst=tetrahedral(atomsFirst,basisFirst,rcut=rcut)
print "First Tetra/rcut",sum(tetsFirst)/len(tetsFirst),rcutFirst
tetsLast,rcutLast=tetrahedral(atomsLast,basisLast,rcut=rcut)
print "Last Tetra/rcut",sum(tetsLast)/len(tetsLast),rcutLast
#CN
cnFirst,rcutFirst=coordinationNumber(atomsFirst,basisFirst,rcut=rcut)
print "First CN/rcut",float(sum(cnFirst))/len(cnFirst),rcutFirst
cnLast,rcutLast=coordinationNumber(atomsLast,basisLast,rcut=rcut)
else:
usage()
exit(0)
#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:
#======================================================
# Gather the order parameters
#======================================================
orderVals=list()
for pn in fileNames:
if "POSCAR" in pn or "CONTCAR" in pn:#fileNames[0]:
poscar=open(pn,"r").readlines()
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar)
orderVals.append(orderParams[op]( \
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)
#grep to check for PREC = high command, if not present spit out error and quit.
precResults = subprocess.check_output("grep PREC %s"%ocfile,shell=True).split("=")[1].split()[0]
if precResults not in ["high","High"]:
print "Error: VASP Simulation not performed with \'high\' precision."
exit(0)
#get the force configuration number (the total number of configs in the forcefil)
dbcnfgcnt=0 #Force Data Base Configuration Counter
for line in fordb:
if "#N" in line[0:2]:
dbcnfgcnt+=1
fordb.close()
fordb = open(forcefil,"a")
TE,stress,basis,atoms,forces,types=outcarReadConfig(ocfile,grabconfig)
stress=[i/160.2 for i in stress]
#Change atoms to be in cartesian coords instead of fractional
#bT=basis.T
#atoms=[bT.dot(atom) for atom in atoms]
natom=len(atoms)
#Number of atoms, use force, header
if scaleEnable:
line="#N\t%d 1 ifconf=%d Taken From:%s Config:#%d\n"%\
(natom,dbcnfgcnt,os.getcwd()+"/"+ocfile,grabconfig)
else:
line="#N\t%d 1 ifconf=%d Taken From:%s Config:#%d scaleEnable0\n"%\
(natom,dbcnfgcnt,os.getcwd()+"/"+ocfile,grabconfig)
try:
num = sys.argv[1].split("_")[1]
except IndexError:
num = None
refStructure = None
if len(sys.argv) == 3:
refStructure = int(sys.argv[2])
delT, msdAtom = outcarMeanSquareDisplaceAtom(outcarFile, refStructure)
pl.figure()
for atom in range(msdAtom.shape[0]):
pl.plot(delT, msdAtom[atom])
dummy, dummy, basis, atoms, forces, types = outcarIO.outcarReadConfig(
outcarFile, -1)
from mayavi import mlab
ax, ay, az = atoms.T
ops = msdAtom.T[-1]
v1, v2, v3 = basis
#Box... bleh I hate this code.
mlab.plot3d([0, v1[0], v1[0] + v2[0], v2[0], 0, v3[0]],
[0, v1[1], v1[1] + v2[1], v2[1], 0, v3[1]],
[0, v1[2], v1[2] + v2[2], v2[2], 0, v3[2]],
color=(0, 0, 0),
line_width=0.5)
mlab.plot3d(
[v3[0], v3[0] + v1[0], v3[0] + v2[0] + v1[0], v3[0] + v2[0], v3[0]],
[v3[1], v3[1] + v1[1], v3[1] + v2[1] + v1[1], v3[1] + v2[1], v3[1]],
usage()
exit(0)
#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
#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.
usage()
print "Error parsing rcut args"
exit(0)
outcarFile = sys.argv[1]
try:
num = sys.argv[1].split("_")[1]
except IndexError:
num = None
refStructure = None
if len(sys.argv) == 3:
refStructure = int(sys.argv[2])
#First and last configurations
dummy, dummy, basisFirst, atomsFirst, dummy, typesFirst = outcarIO.outcarReadConfig(
outcarFile, wantconfig=0)
dummy, dummy, basisLast, atomsLast, dummy, typesLast = outcarIO.outcarReadConfig(
outcarFile, wantconfig=-1)
#MSD
delT, msdAtom = outcarMeanSquareDisplaceAtom(outcarFile, refStructure)
#TET
tetsFirst, rcutFirst = tetrahedral(atomsFirst, basisFirst, rcut=rcut)
print "First Tetra/rcut", sum(tetsFirst) / len(tetsFirst), rcutFirst
tetsLast, rcutLast = tetrahedral(atomsLast, basisLast, rcut=rcut)
print "Last Tetra/rcut", sum(tetsLast) / len(tetsLast), rcutLast
#CN
cnFirst, rcutFirst = coordinationNumber(atomsFirst, basisFirst, rcut=rcut)
print "First CN/rcut", float(sum(cnFirst)) / len(cnFirst), rcutFirst
#======================================================
# Gather the order parameters
#======================================================
orderVals = list()
for pn in fileNames:
if "POSCAR" in pn or "CONTCAR" in pn: #fileNames[0]:
poscar = open(pn, "r").readlines()
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
orderVals.append(orderParams[op]( \
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:
num=sys.argv[1].split("_")[1]
except IndexError:
num=None
refStructure=None
if len(sys.argv)==3:
refStructure=int(sys.argv[2])
delT,msdAtom=outcarMeanSquareDisplaceAtom(outcarFile,refStructure)
pl.figure()
for atom in range(msdAtom.shape[0]):
pl.plot(delT,msdAtom[atom])
dummy,dummy,basis,atoms,forces,types=outcarIO.outcarReadConfig(outcarFile,-1)
from mayavi import mlab
ax,ay,az=atoms.T
ops=msdAtom.T[-1]
v1,v2,v3=basis
#Box... bleh I hate this code.
mlab.plot3d([0,v1[0],v1[0]+v2[0],v2[0],0,v3[0]],[0,v1[1],v1[1]+v2[1],v2[1],0,v3[1]],[0,v1[2],v1[2]+v2[2],v2[2],0,v3[2]],color=(0,0,0),line_width=0.5)
mlab.plot3d([v3[0],v3[0]+v1[0],v3[0]+v2[0]+v1[0],v3[0]+v2[0],v3[0]],[v3[1],v3[1]+v1[1],v3[1]+v2[1]+v1[1],v3[1]+v2[1],v3[1]],[v3[2],v3[2]+v1[2],v3[2]+v2[2]+v1[2],v3[2]+v2[2],v3[2]],color=(0,0,0),line_width=0.5)
mlab.plot3d([v1[0],v1[0]+v3[0]],[v1[1],v1[1]+v3[1]],[v1[2],v1[2]+v3[2]],color=(0,0,0),line_width=0.5)
mlab.plot3d([v2[0],v2[0]+v3[0]],[v2[1],v2[1]+v3[1]],[v2[2],v2[2]+v3[2]],color=(0,0,0),line_width=0.5)
mlab.plot3d([v1[0]+v2[0],v1[0]+v2[0]+v3[0]],[v1[1]+v2[1],v1[1]+v2[1]+v3[1]],[v1[2]+v2[2],v1[2]+v2[2]+v3[2]],color=(0,0,0),line_width=0.5)
#Atoms
mp3d = mlab.points3d(ax,ay,az,ops,colormap='gist_earth',scale_factor=1.9,scale_mode='none',resolution=25)