def findsymmetry(vs,ts,xyzpnts):
tfname="tmpsym.in"
tf=open(tfname,"w")
wrdata="Comment line\n"
wrdata+="0\taccuracy\n"
wrdata+="1\tlattice form: vectors\n"
wrdata+="%g %g %g\n"%(vs[0][0],vs[0][1],vs[0][2])
wrdata+="%g %g %g\n"%(vs[1][0],vs[1][1],vs[1][2])
wrdata+="%g %g %g\n"%(vs[2][0],vs[2][1],vs[2][2])
wrdata+="1\n"
wrdata+="1 0 0\n0 1 0\n0 0 1\n"
wrdata+="%d\n"%(sum(ts))
types=" ".join([str(k) for k in flatten([[i+1 for j in range(ts[i])] for i in range(len(ts))])])
wrdata+="%s\n"%types
for i,dat in enumerate(xyzpnts):
wrdata+="%g %g %g\n"%(dat[0],dat[1],dat[2])
tf.write(wrdata)
tf.close()
#Issue the findsym command and parse the data
os.system("findsym < %s > temp"%tfname)
os.system("rm %s"%tfname)
utpt=open("temp","r").readlines()
os.system("rm temp")
for line in utpt:
if "space_group_name" in line:
print "Symmetry Space Group= "+" ".join(line.split()[1:])
break
def cellNeighbs(celli):
#Uses Ncell and Ncells, these must be defined correctly as
#the total number of cells and cell dimensions respectively.
coordx=int(floor(celli/(Ncy*Ncz))) #Cell coordinates
coordy=int(floor(celli%(Ncy*Ncz)/Ncz))
coordz=int(celli%Ncz)
cxs=[(coordx-1)%Ncx, coordx, (coordx+1)%Ncx ] #Neighbor coordinates
cys=[(coordy-1)%Ncy, coordy, (coordy+1)%Ncy ]
czs=[(coordz-1)%Ncz, coordz, (coordz+1)%Ncz ]
cneighbs= [[[(cx,cy,cz) for cz in czs] for cy in cys] for cx in cxs]
cneighbs= flatten(flatten(cneighbs))
cneighbs= set([coord2ind(cn) for i,cn in enumerate(cneighbs)])
return cneighbs
def findsymmetry(vs, ts, xyzpnts):
tfname = "tmpsym.in"
tf = open(tfname, "w")
wrdata = "Comment line\n"
wrdata += "0\taccuracy\n"
wrdata += "1\tlattice form: vectors\n"
wrdata += "%g %g %g\n" % (vs[0][0], vs[0][1], vs[0][2])
wrdata += "%g %g %g\n" % (vs[1][0], vs[1][1], vs[1][2])
wrdata += "%g %g %g\n" % (vs[2][0], vs[2][1], vs[2][2])
wrdata += "1\n"
wrdata += "1 0 0\n0 1 0\n0 0 1\n"
wrdata += "%d\n" % (sum(ts))
types = " ".join([
str(k) for k in flatten([[i + 1 for j in range(ts[i])]
for i in range(len(ts))])
])
wrdata += "%s\n" % types
for i, dat in enumerate(xyzpnts):
wrdata += "%g %g %g\n" % (dat[0], dat[1], dat[2])
tf.write(wrdata)
tf.close()
#Issue the findsym command and parse the data
os.system("findsym < %s > temp" % tfname)
os.system("rm %s" % tfname)
utpt = open("temp", "r").readlines()
os.system("rm temp")
for line in utpt:
if "space_group_name" in line:
print "Symmetry Space Group= " + " ".join(line.split()[1:])
break
def cellNeighbs(celli):
#Uses Ncell and Ncells, these must be defined correctly as
#the total number of cells and cell dimensions respectively.
coordx = int(floor(celli / (Ncy * Ncz))) #Cell coordinates
coordy = int(floor(celli % (Ncy * Ncz) / Ncz))
coordz = int(celli % Ncz)
cxs = [(coordx - 1) % Ncx, coordx,
(coordx + 1) % Ncx] #Neighbor coordinates
cys = [(coordy - 1) % Ncy, coordy, (coordy + 1) % Ncy]
czs = [(coordz - 1) % Ncz, coordz, (coordz + 1) % Ncz]
cneighbs = [[[(cx, cy, cz) for cz in czs] for cy in cys] for cx in cxs]
cneighbs = flatten(flatten(cneighbs))
cneighbs = set([coord2ind(cn) for i, cn in enumerate(cneighbs)])
return cneighbs
def secondShell(neighbs):
shell2 = list()
#loop over each central atoms
for i, ineighbs in enumerate(neighbs):
#use set to get uniques
ashell = list(set(flatten([neighbs[j] for j in ineighbs] + ineighbs)))
shell2.append(ashell)
return shell2
def secondShell(neighbs):
shell2=list()
#loop over each central atoms
for i,ineighbs in enumerate(neighbs):
#use set to get uniques
ashell = list(set(flatten([neighbs[j] for j in ineighbs]+ineighbs)))
shell2.append(ashell)
return shell2
def secondShell(neighbs):
shell2 = list()
# loop over each central atoms
for i, ineighbs in enumerate(neighbs):
# use set to get uniques
ashell = list(set([z for z in flatten([neighbs[j] for j in ineighbs])] + ineighbs))
try:
ashell.remove(i) # remove central atom from neighbor list (atom can't be a neighbor to itself)
except ValueError:
pass
shell2.append(ashell)
return shell2
def rdf_by_adf(atoms,neighbs,basis,rcut=10.0,nADFbins=45,nRDFbins=100,angtype='deg'):
#atoms: list of atoms[N][3]
#neighbs: the *full* neighbor list for atoms
#angtype: 'deg' or 'rad'
#nbins: number of bins to store in radial distro
#The angular range is always 0-180 deg and angles are taken modulo 180
#This function bins bond length by the angles to which they belong.
bins = zeros(nADFbins*nRDFbins)
natoms=len(atoms)
atoms.shape=natoms*3
nneighbsf=array([len(i) for i in neighbs])
neighbsf=array([i for i in flatten(neighbs)])
cut=rcut
b=basis
b.shape=9
weave.inline(RDFBYADFcode,['atoms','natoms','neighbsf','nneighbsf','bins','nADFbins','nRDFbins','cut','b'])
atoms.shape=[len(atoms)/3,3]
adfVals = [(i+0.5)*180./nADFbins for i in range(nADFbins)]
rdfVals = [(i+0.5)*rcut/nRDFbins for i in range(nRDFbins)]
bins.shape=[nADFbins,nRDFbins]
dr=float(rcut)/nRDFbins
#Ndensity=N/volume(basis)
for i,r in enumerate(rdfVals):
m = sum(bins[:,i])
if i==0:
vol=4.0*pi*dr*dr*dr/3.0
else:
vol=4.0*pi*r*r*dr
for j in range(nADFbins):
if m==0:
m=1
bins[j,i]/=vol
return [(adfVals,rdfVals),bins]
def adf(atoms,neighbs,basis,cutoff,nbins=360,angtype='deg'):
#atoms: list of atoms[N][3]
#neighbs: the *full* neighbor list for atoms
#angtype: 'deg' or 'rad'
#nbins: number of bins to store in radial distro
#The angular range is always 0-180 deg and angles are taken modulo 180
bins = zeros(nbins)
cut=cutoff
natoms=len(atoms)
atoms.shape=natoms*3
b=basis
b.shape=9
nneighbsf=array([len(i) for i in neighbs])
neighbsf=array([i for i in flatten(neighbs)])
weave.inline(ADFcode,['atoms','natoms','neighbsf','nneighbsf','bins','nbins','b','cut'],compiler=('gcc'))
b.shape=[3,3]
atoms.shape=[len(atoms)/3,3]
abins = [(i+0.5)*180./nbins for i in range(nbins)]
bins /= nbins
return [abins,bins]
exit(0)
if path.isdir(sys.argv[1]):
outcar = open(sys.argv[1] + "/OUTCAR", "r")
poscar = open(sys.argv[1] + "/POSCAR",
"r") #need to use the poscar to fetch the atom types
elif path.isfile(sys.argv[1]):
outcar = False
poscar = open(sys.argv[1], "r")
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar.readlines())
[v1, v2, v3] = basis
atoms = zip(*atoms)
ax, ay, az = atoms[0], atoms[1], atoms[2]
afx, afy, afz = [0] * len(ax), [0] * len(ay), [0] * len(az)
types = [i for i in flatten([[i] * num for i, num in enumerate(atypes)])]
startconfig = 0
plotdisabled = False
if outcar:
if (len(sys.argv) >= 3):
startconfig = int(sys.argv[2])
if (len(sys.argv) >= 4):
if int(sys.argv[3]) == 0:
plotdisabled = True
if not (plotdisabled):
from mayavi import mlab
global thelock
thelock = threading.Event()
def usage():
print "Usage:"
print "%s <POSCAR> <XDATCAR> <optional: starting config #> <optional 0: disables plotting>"%(sys.argv[0].split("/")[-1])
#Reading in the options and preparing for file reading
if len(sys.argv)<3:
usage()
exit(0)
poscar = open(sys.argv[1],"r")
xdatcar = open(sys.argv[2],"r").readlines()[6:]
v1,v2,v3,atypes,ax,ay,az,head,poscar=readposcar(poscar.readlines())
afx,afy,afz=[0]*len(ax),[0]*len(ay),[0]*len(az)
types=[i for i in flatten([[i]*num for i,num in enumerate(atypes)])]
startconfig=0
plotdisabled=False
if (len(sys.argv)>=4):
startconfig=int(sys.argv[3])
if (len(sys.argv)>=5):
if int(sys.argv[4])==0:
plotdisabled=True
if not(plotdisabled):
from mayavi import mlab
global thelock
thelock=threading.Event()
count=0
lval=""
xylabels={"BO" :[r"BondOrder($Q_%s$)"%str(lval), r"$P(Q_%s)$"%str(lval)],
"CN" :[r"Coordination Number", r"P(CN)"],
"RDF":[r"R$(\AA)$", "#_Bonds"],
"ADF":[r"$\theta(deg)$", "#_Bond_Angles"],
"BA" :[r"R$(\AA)$", r"$G_{%s}(r)$"%str(lval)],
"SF" :[r"Q$(\AA^{-1})$", r"S(Q)"]}
if args.averageFlag:
if op not in ["BO","CN","TN","TET"]:
t = zip(*[orderVals[i][1] for i in range(len(orderVals))])
avgy = map(lambda x:sum(x)/len(x),t)
avgx = orderVals[0][0]
elif op=="CN":
hd,rcuts=zip(*orderVals)
hd = [i for i in flatten(list(hd))] #flatten for averaging
avgy,avgx,dummy=pl.hist(hd,bins=range(0,16),visible=False,normed=True)
avgx = avgx[:-1]
pl.xlabel(xylabels["CN"][0])
pl.ylabel(xylabels["CN"][1])
if args.saveFlag:
if op in ["TN","TET"]:
savetxt("AVERAGE."+op+str(lval),array([avgx,avgy]).T,delimiter=" ")
elif op in ["ADF"]:
savetxt("AVERAGE."+op+str(args.rcut),array([avgx,avgy]).T,delimiter=" ",header=" ".join(xylabels[op]),comments="")
else:
savetxt("AVERAGE."+op+str(lval),array([avgx,avgy]).T,delimiter=" ",header=" ".join(xylabels[op]),comments="")
exit(0)
else:
rcut=3.1
#Get the order parameter and convert to integer format (opsn) for coloring of atoms
if opFlag:
ops,rcut = orderParams[op](np.array(atoms),np.array(basis),l=lval,rcut=rcut)
elif ops==None:
ops = types
if shell2Flag:
bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
neighbs = neighbors(atoms,bounds,rcut)
secondShell = list()
for a,firstNeighbs in enumerate(neighbs):
secondNeighbs = [neighbs[i] for i in firstNeighbs]
totalNeighb = set(datatools.flatten([firstNeighbs]+secondNeighbs))
N = len(totalNeighb)
if N==0:
secondShell.append(ops[a])
else:
secondShell.append(sum([ops[i] for i in totalNeighb])/N)
ops = secondShell
n=None
mnop = min(ops)
mxop = max(ops)
if op in ["TET"]:
mnop, mxop, n = 0.0, 1.0, 11
r"$P(Q_%s)$" % str(lval)],
"CN": [r"Coordination Number", r"P(CN)"],
"RDF": [r"R$(\AA)$", "#_Bonds"],
"ADF": [r"$\theta(deg)$", "#_Bond_Angles"],
"BA": [r"R$(\AA)$", r"$G_{%s}(r)$" % str(lval)],
"SF": [r"Q$(\AA^{-1})$", r"S(Q)"]
}
if args.averageFlag:
if op not in ["BO", "CN", "TN", "TET"]:
t = zip(*[orderVals[i][1] for i in range(len(orderVals))])
avgy = map(lambda x: sum(x) / len(x), t)
avgx = orderVals[0][0]
elif op == "CN":
hd, rcuts = zip(*orderVals)
hd = [i for i in flatten(list(hd))] #flatten for averaging
avgy, avgx, dummy = pl.hist(hd,
bins=range(0, 16),
visible=False,
normed=True)
avgx = avgx[:-1]
pl.xlabel(xylabels["CN"][0])
pl.ylabel(xylabels["CN"][1])
if args.saveFlag:
if op in ["TN", "TET"]:
savetxt("AVERAGE." + op + str(lval),
array([avgx, avgy]).T,
delimiter=" ")
elif op in ["ADF"]:
def types(outcarFile):
nums = subprocess.check_output("head -n 1000 %s | grep ions\ per\ type "%outcarFile,shell=True).split("\n")[0].split("=")[1:]
nums=map(int,nums)
types = [j for j in flatten([[i]*nums[i] for i in range(len(nums))])]
return types
