def plot_pos_rad_ang(atoms, types, basis, dup=0):
Ntypes = len(set(types))
N = len(atoms)
cs = ["yellow", "green", "blue", "red", "purple", "orange", "black"]
#Periodic Atoms (duplicated, needed for distributions)
datoms, dtypes = duplicate26(atoms, types, basis)
#Neighbors needed for angular distribution
dneighbs = neighbors(datoms, 5.0, style="full")
#Radial Distribution
[rbins, rdist] = rdf(datoms, inloop=N, cutoff=12.0)
#Correlation of Angles
[abins, adist] = adf(datoms, dneighbs, inloop=N)
#Type sorted atoms lists
tatoms = [list() for i in range(Ntypes)]
if (dup == 1):
for i, j in enumerate(dtypes):
tatoms[j].append(datoms[i])
else:
for i, j in enumerate(types):
tatoms[j].append(atoms[i])
v1, v2, v3 = zip(*basis)
#findsymmetry([v1,v2,v3],types,zip(xs,ys,zs))
fig = pl.figure(figsize=(12, 6))
aa = fig.add_subplot(311, projection='3d')
aa.set_position([0, 0, 0.5, 1.0])
for i in range(Ntypes):
ax, ay, az = zip(*tatoms[i])
aa.scatter(ax, ay, az, c=cs.pop(0), marker="o")
aa.plot([0, v1[0]], [0, v1[1]], [0, v1[2]])
aa.plot([0, v2[0]], [0, v2[1]], [0, v2[2]])
aa.plot([0, v3[0]], [0, v3[1]], [0, v3[2]])
bb = fig.add_subplot(312)
bb.set_position([0.56, 0.55, 0.4, 0.4])
bb.plot(rbins, rdist)
pl.xlabel("Radius (A)")
pl.ylabel("Count")
cc = fig.add_subplot(313)
cc.set_position([0.56, 0.08, 0.4, 0.36])
cc.plot(abins, adist)
pl.xlabel("Angle (deg)")
pl.ylabel("Count")
pl.show()
def plot_pos_rad_ang(atoms,types,basis,dup=0):
Ntypes=len(set(types))
N=len(atoms)
cs=["yellow","green","blue","red","purple","orange","black"]
#Periodic Atoms (duplicated, needed for distributions)
datoms,dtypes=duplicate26(atoms,types,basis)
#Neighbors needed for angular distribution
dneighbs=neighbors(datoms,5.0,style="full")
#Radial Distribution
[rbins,rdist]=rdf(datoms,inloop=N,cutoff=12.0)
#Correlation of Angles
[abins,adist]=adf(datoms,dneighbs,inloop=N)
#Type sorted atoms lists
tatoms=[list() for i in range(Ntypes)]
if(dup==1):
for i,j in enumerate(dtypes):
tatoms[j].append(datoms[i])
else:
for i,j in enumerate(types):
tatoms[j].append(atoms[i])
v1,v2,v3=zip(*basis)
#findsymmetry([v1,v2,v3],types,zip(xs,ys,zs))
fig=pl.figure(figsize=(12,6))
aa = fig.add_subplot(311,projection='3d')
aa.set_position([0,0,0.5,1.0])
for i in range(Ntypes):
ax,ay,az=zip(*tatoms[i])
aa.scatter(ax,ay,az,c=cs.pop(0),marker="o")
aa.plot([0,v1[0]],[0,v1[1]],[0,v1[2]])
aa.plot([0,v2[0]],[0,v2[1]],[0,v2[2]])
aa.plot([0,v3[0]],[0,v3[1]],[0,v3[2]])
bb = fig.add_subplot(312)
bb.set_position([0.56,0.55,0.4,0.4])
bb.plot(rbins,rdist)
pl.xlabel("Radius (A)")
pl.ylabel("Count")
cc = fig.add_subplot(313)
cc.set_position([0.56,0.08,0.4,0.36])
cc.plot(abins,adist)
pl.xlabel("Angle (deg)")
pl.ylabel("Count")
pl.show()
print "Fitness= %s eV PerAtom Energy= %s eV\nkpoints= %sVolume= %sEnthalpy= %s"%(a,round(float(a)/N,3),kpoints.pop(0),volumes.pop(0),enthalpy.pop(0).strip())
if gencnt >= start:
#plot_pos_rad_ang(atoms,types,pdup=pdup)
#Periodic Atoms (duplicated)
datoms,dtypes,dbasis=duplicate26(atoms,types,basis)
#Neighbors needed for angular distribution
dneighbs=neighbors(datoms,5.0,style="full")
#Radial Distribution
[rbins,rdist]=rdf(datoms,inloop=N,cutoff=12.0)
#Correlation of Angles
[abins,adist]=adf(datoms,dneighbs,inloop=N)
#Type sorted atoms lists
tatoms=[list() for i in range(Ntypes)]
if(pdup==1):
for i,j in enumerate(dtypes):
tatoms[j].append(datoms[i])
else:
for i,j in enumerate(types):
tatoms[j].append(atoms[i])
fig=pl.figure(figsize=(12,6))
aa = fig.add_subplot(311,projection='3d')
aa.set_position([0,0,0.5,1.0])
for i in range(Ntypes):
ax,ay,az=zip(*tatoms[i])
3), kpoints.pop(0), volumes.pop(0), enthalpy.pop(0).strip())
if gencnt >= start:
#plot_pos_rad_ang(atoms,types,pdup=pdup)
#Periodic Atoms (duplicated)
datoms, dtypes, dbasis = duplicate26(atoms, types, basis)
#Neighbors needed for angular distribution
dneighbs = neighbors(datoms, 5.0, style="full")
#Radial Distribution
[rbins, rdist] = rdf(datoms, inloop=N, cutoff=12.0)
#Correlation of Angles
[abins, adist] = adf(datoms, dneighbs, inloop=N)
#Type sorted atoms lists
tatoms = [list() for i in range(Ntypes)]
if (pdup == 1):
for i, j in enumerate(dtypes):
tatoms[j].append(datoms[i])
else:
for i, j in enumerate(types):
tatoms[j].append(atoms[i])
fig = pl.figure(figsize=(12, 6))
aa = fig.add_subplot(311, projection='3d')
aa.set_position([0, 0, 0.5, 1.0])
for i in range(Ntypes):
ax, ay, az = zip(*tatoms[i])
def outcarADF(outcarfile,nbins,bl=-1.0,bw=-1.0):
outcar=open(outcarfile,"r")
tbinvals=list()
#Grab ion types
while True:
line=outcar.readline()
if "ions per type" in line:
break
atypes=map(int,line.split("=")[1].split())
#Grab basis vectors
while True:
line=outcar.readline()
if "direct lattice vectors" in line:
break
basis=array([map(float,outcar.readline().split()[:3]) for i in range(3)])
lengths=array([basis[0][0],basis[1][1],basis[2][2]])
#Grab atom positions and perform adf calculation
count=0
posit=False
for line in outcar:
if posit:
if "--" in line:
if len(atoms)==0:
continue
else:
#Analysis
if max(zip(*atoms)[0])<1.01:
atoms=dot(array(atoms),basis)
else:
atoms=array(atoms)
neighbs=voronoiNeighbors(atoms,basis,atypes,style='full')
if bl!=-1 and bw!=-1:
specbonds=[list() for i in range(len(atoms))]
for i in range(len(atoms)):
ai=atoms[i]#dot(atoms[i],basis)
for j in neighbs[i]:
aj=atoms[j]#dot(atoms[j],basis)
d=dist_periodic(ai,aj,lengths)
if fabs(d-bl)<bw:
if d<1.0:
print d
print dist_periodic(ai,aj,lengths)
print ai
print aj
exit(0)
specbonds[i].append(j)
else:
specbonds=neighbs
[angs,abins]=adf(atoms,specbonds,basis,nbins=nbins)
tbinvals.append(abins)
print count
posit=False
else:
atoms.append(map(float,line.split()[:3]))
elif "POSITION" in line:
atoms=list()
posit=True
count+=1
return angs,tbinvals
def outcarADF(outcarfile, nbins, bl=-1.0, bw=-1.0):
outcar = open(outcarfile, "r")
tbinvals = list()
#Grab ion types
while True:
line = outcar.readline()
if "ions per type" in line:
break
atypes = map(int, line.split("=")[1].split())
#Grab basis vectors
while True:
line = outcar.readline()
if "direct lattice vectors" in line:
break
basis = array(
[map(float,
outcar.readline().split()[:3]) for i in range(3)])
lengths = array([basis[0][0], basis[1][1], basis[2][2]])
#Grab atom positions and perform adf calculation
count = 0
posit = False
for line in outcar:
if posit:
if "--" in line:
if len(atoms) == 0:
continue
else:
#Analysis
if max(zip(*atoms)[0]) < 1.01:
atoms = dot(array(atoms), basis)
else:
atoms = array(atoms)
neighbs = voronoiNeighbors(atoms,
basis,
atypes,
style='full')
if bl != -1 and bw != -1:
specbonds = [list() for i in range(len(atoms))]
for i in range(len(atoms)):
ai = atoms[i] #dot(atoms[i],basis)
for j in neighbs[i]:
aj = atoms[j] #dot(atoms[j],basis)
d = dist_periodic(ai, aj, lengths)
if fabs(d - bl) < bw:
if d < 1.0:
print d
print dist_periodic(ai, aj, lengths)
print ai
print aj
exit(0)
specbonds[i].append(j)
else:
specbonds = neighbs
[angs, abins] = adf(atoms, specbonds, basis, nbins=nbins)
tbinvals.append(abins)
print count
posit = False
else:
atoms.append(map(float, line.split()[:3]))
elif "POSITION" in line:
atoms = list()
posit = True
count += 1
return angs, tbinvals
