def poscar2dump(pcarFile, lmpFile, scale=None):
try:
poscar = open(pcarFile, "r").readlines()
lammps = open(lmpFile, "w")
except IOError:
print "Error: %s Unable to open POSCAR/Lammps file." % sys.argv[0].split("/")[-1]
usage()
exit(0)
if scale == None:
scale = 1.0
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
# Convert from POSCAR style basis vectors to LAMMPS style boundaries.
xhi, yhi, zhi, xy, xz, yz = basis2lohi(basis)
basis = matrix([[xhi, 0, 0], [xy, yhi, 0], [xz, yz, zhi]])
N = sum(atypes)
Ntypes = len(atypes)
types = [i for i in flatten([[i] * v for i, v in enumerate(atypes)])]
data = "#Generated by %s from %s\n\n" % (sys.argv[0].split("/")[-1], pcarFile)
data += "%d atoms\n" % N
data += "%d atom types\n\n" % Ntypes
data += "0.0000 %4f xlo xhi\n" % xhi
data += "0.0000 %4f ylo yhi\n" % yhi
data += "0.0000 %4f zlo zhi\n" % zhi
data += "% 4f % 4f % 4f xy xz yz\n\n" % (xy, xz, yz)
data += "Atoms\n\n"
for i, (t, atom) in enumerate(zip(types, atoms)):
x, y, z = atom # (atom*basis).tolist()[0]
data += "\t %d \t %d \t % 5f\t% 5f\t% 5f\n" % (i + 1, t + 1, x, y, z)
lammps.write(data)
lammps.close()
def poscar2dump(pcarFile, lmpFile, scale=None):
try:
poscar = open(pcarFile, "r").readlines()
lammps = open(lmpFile, "w")
except IOError:
print "Error: %s Unable to open POSCAR/Lammps file." % sys.argv[
0].split("/")[-1]
usage()
exit(0)
if scale == None:
scale = 1.0
[basis, atypes, atoms, head, poscar] = poscarIO.read(poscar)
#Convert from POSCAR style basis vectors to LAMMPS style boundaries.
xhi, yhi, zhi, xy, xz, yz = basis2lohi(basis)
basis = matrix([[xhi, 0, 0], [xy, yhi, 0], [xz, yz, zhi]])
N = sum(atypes)
Ntypes = len(atypes)
types = [i for i in flatten([[i] * v for i, v in enumerate(atypes)])]
data = "#Generated by %s from %s\n\n" % (sys.argv[0].split("/")[-1],
pcarFile)
data += "%d atoms\n" % N
data += "%d atom types\n\n" % Ntypes
data += "0.0000 %4f xlo xhi\n" % xhi
data += "0.0000 %4f ylo yhi\n" % yhi
data += "0.0000 %4f zlo zhi\n" % zhi
data += "% 4f % 4f % 4f xy xz yz\n\n" % (xy, xz, yz)
data += "Atoms\n\n"
for i, (t, atom) in enumerate(zip(types, atoms)):
x, y, z = atom #(atom*basis).tolist()[0]
data += "\t %d \t %d \t % 5f\t% 5f\t% 5f\n" % (i + 1, t + 1, x, y, z)
lammps.write(data)
lammps.close()
three = range(3)
while True:
mdcar.readline() #header
mdcar.readline() #volume ratio
v1 = map(float,mdcar.readline().split())
v2 = map(float,mdcar.readline().split())
v3 = map(float,mdcar.readline().split())
nAtom = int(mdcar.readline())
mdcar.readline() #direct
atoms = [map(float,mdcar.readline().split()) for i in range(nAtom)]
if len(atoms[nAtom-1])!=3:
break
types = [0 for i in range(nAtom)]
xhi,yhi,zhi,xy,xz,yz = lammpsIO.basis2lohi([v1,v2,v3])
bf=[xhi,yhi,zhi]
atoms = [map(lambda x: (a[x]+0.5)*bf[x],three) for a in atoms]
head= "ITEM: TIMESTEP\n%d\n"%count
head+="ITEM: NUMBER OF ATOMS\n%d\n"%nAtom
head+="ITEM: BOX BOUNDS\n"
head+=" 0.0000 % 6.6f\n"%(xhi)
head+=" 0.0000 % 6.6f\n"%(yhi)
head+=" 0.0000 % 6.6f\n"%(zhi)
head+="ITEM: ATOMS id type xs ys zs\n"
opdat.write(head)
atoms = zip(*atoms)
opdat.writelines([" ".join(map(str,line))+"\n" for line in zip(range(nAtom),types,atoms[0],atoms[1],atoms[2])])