def unFractional(posfile):
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
xs,ys,zs = zip(*atoms)
if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
print "Error: it appears these are already unfractional coordinates. %s"%posfile
exit(0)
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=False)
poscarIO.write(posfile,basis, atoms,atypes,head,frac=True,autoFrac=False)
def fractional(posfile):
[basis,atypes,atoms,head,poscar] = poscarIO.read(open(posfile,"r").readlines(),frac_coord=True)
fraced=False
xs,ys,zs = zip(*atoms)
if sum(xs)/len(xs)>1.0 or sum(ys)/len(ys)>1.0 or sum(zs)/len(zs)>1.0:
fraced=True
if not fraced:
print "Error: it appears these are already fractional coordiantes. %s"%posfile
exit(0)
poscarIO.write(posfile,basis,atoms,atypes,head,frac=True)
def fractional(posfile):
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=True)
fraced = False
xs, ys, zs = zip(*atoms)
if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
zs) > 1.0:
fraced = True
if not fraced:
print "Error: it appears these are already fractional coordiantes. %s" % posfile
exit(0)
poscarIO.write(posfile, basis, atoms, atypes, head, frac=True)
def unFractional(posfile):
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=True)
xs, ys, zs = zip(*atoms)
if sum(xs) / len(xs) > 1.0 or sum(ys) / len(ys) > 1.0 or sum(zs) / len(
zs) > 1.0:
print "Error: it appears these are already unfractional coordinates. %s" % posfile
exit(0)
[basis, atypes, atoms, head, poscar] = poscarIO.read(open(posfile,
"r").readlines(),
frac_coord=False)
poscarIO.write(posfile,
basis,
atoms,
atypes,
head,
frac=True,
autoFrac=False)
def outcar2poscar(outcar,outposcar,wantconfig):
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcar,wantconfig)
poscarIO.write(outposcar,basis,atoms,atypes,head)
def prompt_iface(md, count, stresskb, T, PE, KE, ax, ay, az, afx, afy, afz, v1,
v2, v3, types):
print "=" * 50
print "Step Number: %d" % (count)
print "Stress (in kB) XX YY ZZ XY YZ XZ:"
print stresskb
if md == True:
print "T=%g, PE=%g, TE=%g" % (T, PE, KE)
else:
print "PE=%g" % (PE)
print "=" * 50
print ""
if not (plotdisabled):
athread = threading.Thread(target=plot3,
args=(md, ax, ay, az, afx, afy, afz, v1, v2,
v3, types))
athread.start()
athread.join()
while True:
try:
val = raw_input(
"Input coords and radius of sphere (x y z r) or (Enter) to continue:\n"
)
[rx, ry, rz, rr] = [float(k) for k in val.split()]
N = len(ax)
atoms = [[ax[i], ay[i], az[i], types[i]] for i in range(N)
if sqrt((ax[i] - rx)**2 + (ay[i] - ry)**2 +
(az[i] - rz)**2) <= rr]
atoms.sort(key=lambda x: x[3])
d1, d2, d3, types = zip(*atoms)
cs = [types.count(i) for i in range(max(types) + 1)]
while True:
try:
val = float(
raw_input(
"Scale factor (increases vacuum around cluster): \n"
))
except ValueError:
print "Scaling factor should be a floating point value between 1.2 and 3.0."
else:
break
for atom in atoms:
print "% 5.5g % 5.5g % 5.5g" % (tuple(atom[:3]))
poscarIO.write("POSCAR.CLUSTER%d" % len(atoms),
array([v1, v2, v3]) * val,
[atom[:3] for atom in atoms], cs,
"Cluster genearted by grabcluster.py")
print "POSCAR.CLUSTER%d written to." % len(atoms)
exit(0)
except ValueError:
if len(val) == 0:
break
else:
if not (plotdisabled):
bthread = threading.Thread(target=plot3sphere,
args=(md, ax, ay, az, afx, afy, afz,
v1, v2, v3, rx, ry, rz, rr))
bthread.start()
bthread.join()
try:
val = raw_input("Good? (y/n):")
if val == "y" or val == "Y":
N = len(ax)
atoms = [[ax[i], ay[i], az[i], types[i]]
for i in range(N)
if sqrt((ax[i] - rx)**2 + (ay[i] - ry)**2 +
(az[i] - rz)**2) <= rr]
atoms.sort(key=lambda x: x[3])
d1, d2, d3, types = zip(*atoms)
cs = [types.count(i) for i in range(N)]
#cut off types list after last non-zero number
last = 0
for i, v in enumerate(cs):
if v > 0:
last = i
cs = cs[:last + 1]
print cs[:]
for atom in atoms:
print "% 5.5g % 5.5g % 5.5g" % (tuple(atom[:3]))
exit(0)
except ValueError:
pass
atype = [0] * natom
ax = [0.0] * natom
ay = [0.0] * natom
az = [0.0] * natom
afx = [0.0] * natom
afy = [0.0] * natom
afz = [0.0] * natom
for i in range(natom):
line = forcedb.readline().split()
atype[i] = int(line[0])
[ax[i], ay[i], az[i], afx[i], afy[i],
afz[i]] = [float(j) for j in line[1:7]]
if (count == confignum):
pcar = sys.argv[3]
poscarIO.write(pcar, array(basis), zip(ax, ay, az), atype, head)
"""
wrt=pcar+" "+msg+"\n"
wrt+="1.0\n"
wrt+=boundx+"\n"
wrt+=boundy+"\n"
wrt+=boundz+"\n"
types=[atype.count(u) for u in set(atype)]
wrt+=" ".join(map(str,types))+"\n"#type information
wrt+="Direct\n"
a=array([bndx,bndy,bndz])
for b in zip(ax,ay,az):
x=linalg.solve(a.transpose(),b)
wrt+="%9.9f %9.9f %9.9f\n"%(x[0],x[1],x[2])
def poscarGrow(poscarName,outputName,cx,cy,cz):
poscar=open(poscarName,"r").readlines()
nCopies=cx*cy*cz
[basis,atypes,atoms,head,poscar] = poscarIO.read(poscar,frac_coord=True)
natoms=len(atoms)
v1,v2,v3=map(array,basis)
ax,ay,az=map(array,zip(*atoms))
#duplicate and tile
ax=array(split(tile(ax,nCopies),nCopies))
ay=array(split(tile(ay,nCopies),nCopies))
az=array(split(tile(az,nCopies),nCopies))
#Shift tiles in x dirn
shift=array([1]*natoms)
shiftfull=array([shift*j for j in range(cx)])
for i in range(cy*cz):
ax[i*cx+array(range(cx))]+=shiftfull
#Shift tiles in y dirn
shift=array([1]*natoms)
shiftfull=array([shift*(j/cx) for j in range(cy*cx)])
for i in range(cz):
ay[i*cx*cy+array(range(cy*cx))]+=shiftfull
#Shift tiles in z dirn
shift=array([1]*natoms)
shiftfull=array([shift*(j/cx/cy) for j in range(cy*cx*cz)])
az+=shiftfull
ax=ax.reshape([nCopies*natoms])
ay=ay.reshape([nCopies*natoms])
az=az.reshape([nCopies*natoms])
#need to normalize with new positions with respect to duplicated lattice params
v1*=cx
v2*=cy
v3*=cz
basis=[v1,v2,v3]
A=matrix([[float(cx),0.0,0.0],[0.0,float(cy),0.0],[0.0,0.0,float(cz)]])
ax,ay,az=zip(*[linalg.solve(A,array(p).T)[:] for p in zip(ax,ay,az)])
# if max(ax)>1.0 or max(ay)>1.0 or max(az)>1.0:
# continue
# exit(0)
atoms=zip(ax,ay,az)
#Sort atoms by type, as required by POSCAR
types=list()
j=0
for i in atypes:
types+=[j+1]*i
j+=1
newtypes=types*cx*cy*cz
atoms,types=zip(*sorted(zip(atoms,newtypes),key=lambda x:x[1]))
atypes=[i*nCopies for i in atypes]
poscarIO.write(outputName,basis,atoms,atypes,head)
return len(atoms),basis
forcedb.readline() #The #F
atype=[0]*natom
ax=[0.0]*natom
ay=[0.0]*natom
az=[0.0]*natom
afx=[0.0]*natom
afy=[0.0]*natom
afz=[0.0]*natom
for i in range(natom):
line=forcedb.readline().split()
atype[i]=int(line[0])
[ax[i],ay[i],az[i],afx[i],afy[i],afz[i]]=[float(j) for j in line[1:7]]
if(count==confignum):
pcar=sys.argv[3]
poscarIO.write(pcar,array(basis),zip(ax,ay,az),atype,head)
"""
wrt=pcar+" "+msg+"\n"
wrt+="1.0\n"
wrt+=boundx+"\n"
wrt+=boundy+"\n"
wrt+=boundz+"\n"
types=[atype.count(u) for u in set(atype)]
wrt+=" ".join(map(str,types))+"\n"#type information
wrt+="Direct\n"
a=array([bndx,bndy,bndz])
for b in zip(ax,ay,az):
x=linalg.solve(a.transpose(),b)
exit(0)
#Gather poscar information for last set of atoms
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
outcarFile, configRequest)
#Convert from fractional units to cartesian
def u2a(u):
a = list()
a.append(u[0] * basis[0][0] + u[0] * basis[1][0] + u[0] * basis[2][0])
a.append(u[0] * basis[0][1] + u[1] * basis[1][1] + u[1] * basis[2][1])
a.append(u[0] * basis[0][2] + u[2] * basis[1][2] + u[2] * basis[2][2])
return a
stepb0 = map(u2a, atoms)
stepb1 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 1)[2])
stepb2 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 2)[2])
stepb3 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 3)[2])
stepb4 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 4)[2])
velo5 = list()
for b0, b1, b2, b3, b4 in zip(stepb0, stepb1, stepb2, stepb3, stepb4):
velo5.append([
(25 * b0[i] - 48 * b1[i] + 36 * b2[i] - 16 * b3[i] + 3 * b4[i]) /
(12.0 * timestep) for i in range(3)
])
poscarIO.write("VDATCAR", basis, atoms, atypes, head, velocities=velo5)
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)
def prompt_iface(md,count,stresskb,T,PE,KE,ax,ay,az,afx,afy,afz,v1,v2,v3,types):
print "="*50
print "Step Number: %d"%(count)
print "Stress (in kB) XX YY ZZ XY YZ XZ:"
print stresskb
if md==True:
print "T=%g, PE=%g, TE=%g" % (T,PE,KE)
else:
print "PE=%g" % (PE)
print "="*50
print ""
if not(plotdisabled):
athread=threading.Thread(target=plot3,args=(md,ax,ay,az,afx,afy,afz,v1,v2,v3,types))
athread.start()
athread.join()
while True:
try:
val=raw_input("Input coords and radius of sphere (x y z r) or (Enter) to continue:\n")
[rx,ry,rz,rr]=[float(k) for k in val.split()]
N=len(ax)
atoms=[[ax[i],ay[i],az[i],types[i]] for i in range(N) if sqrt((ax[i]-rx)**2+(ay[i]-ry)**2+(az[i]-rz)**2)<=rr]
atoms.sort(key=lambda x:x[3])
d1,d2,d3,types=zip(*atoms)
cs=[types.count(i) for i in range(max(types)+1)]
while True:
try:
val=float(raw_input("Scale factor (increases vacuum around cluster): \n"))
except ValueError:
print "Scaling factor should be a floating point value between 1.2 and 3.0."
else:
break
for atom in atoms:
print "% 5.5g % 5.5g % 5.5g" % (tuple(atom[:3]))
poscarIO.write("POSCAR.CLUSTER%d"%len(atoms),array([v1,v2,v3])*val,[atom[:3] for atom in atoms],cs,"Cluster genearted by grabcluster.py")
print "POSCAR.CLUSTER%d written to."%len(atoms)
exit(0)
except ValueError:
if len(val)==0:
break
else:
if not(plotdisabled):
bthread=threading.Thread(target=plot3sphere,args=(md,ax,ay,az,afx,afy,afz,v1,v2,v3,rx,ry,rz,rr))
bthread.start()
bthread.join()
try:
val=raw_input("Good? (y/n):")
if val=="y" or val=="Y":
N=len(ax)
atoms=[[ax[i],ay[i],az[i],types[i]] for i in range(N) if sqrt((ax[i]-rx)**2+(ay[i]-ry)**2+(az[i]-rz)**2)<=rr]
atoms.sort(key=lambda x:x[3])
d1,d2,d3,types=zip(*atoms)
cs=[types.count(i) for i in range(N)]
#cut off types list after last non-zero number
last=0
for i,v in enumerate(cs):
if v>0:
last=i
cs=cs[:last+1]
print cs[:]
for atom in atoms:
print "% 5.5g % 5.5g % 5.5g" % (tuple(atom[:3]))
exit(0)
except ValueError:
pass
def outcar2poscar(outcar, outposcar, wantconfig):
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
outcar, wantconfig)
poscarIO.write(outposcar, basis, atoms, atypes, head)
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)
if configRequest > nSteps:
print "%d configurations available"%nSteps
exit(0)
if configRequest < 5:
print "Need more than 5 steps for backwards - finite difference method."
exit(0)
#Gather poscar information for last set of atoms
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcarFile,configRequest)
#Convert from fractional units to cartesian
def u2a(u):
a=list()
a.append(u[0]*basis[0][0]+u[0]*basis[1][0]+u[0]*basis[2][0])
a.append(u[0]*basis[0][1]+u[1]*basis[1][1]+u[1]*basis[2][1])
a.append(u[0]*basis[0][2]+u[2]*basis[1][2]+u[2]*basis[2][2])
return a
stepb0 = map(u2a,atoms)
stepb1 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-1)[2])
stepb2 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-2)[2])
stepb3 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-3)[2])
stepb4 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-4)[2])
velo5=list()
for b0,b1,b2,b3,b4 in zip(stepb0,stepb1,stepb2,stepb3,stepb4):
velo5.append( [(25*b0[i]-48*b1[i]+36*b2[i]-16*b3[i]+3*b4[i])/(12.0*timestep) for i in range(3)] )
poscarIO.write("VDATCAR",basis,atoms,atypes,head,velocities=velo5)