def gen_msd(log, dr):
a0 = Dump("t0.lammpstrj")
b0 = a0.parser()
a1 = Dump("t1.lammpstrj")
b1 = a1.parser()
n0 = len(b0.atoms)
n1 = len(b1.atoms)
log.write
log.write("t0 has %d atoms\n"%n0)
log.write("t1 has %d atoms\n"%n1)
if n0 != n1:
sys.stderr.write("Atom numbers are different!")
sys.stderr.flush()
sys.exit()
else:
natom = n0
neb_atoms = []
o = open("detail.dat", "w")
for i in range(natom):
r2 = 0
for j in range(3):
d = (b0.atoms[i].x[j] - b1.atoms[i].x[j])
r2 += d * d
if r2 > dr*dr:
neb_atoms.append(b1.atoms[i])
o.write("%d\t%.4f\t%.4f\t%.4f\t%.4f\n"
%(i+1, math.sqrt(r2), b1.atoms[i].x[0],
b1.atoms[i].x[1], b1.atoms[i].x[2]))
o.close()
o = open("final.coords", "w")
o.write("%d\n"%len(neb_atoms))
for i in neb_atoms:
o.write("%d\t%.4f\t%.4f\t%.4f\n"
%(i.an, i.x[0], i.x[1], i.x[2]))
o.close()
def gen_msd(log, dr):
a0 = Dump("t0.lammpstrj")
b0 = a0.parser()
a1 = Dump("t1.lammpstrj")
b1 = a1.parser()
n0 = len(b0.atoms)
n1 = len(b1.atoms)
log.write
log.write("t0 has %d atoms\n" % n0)
log.write("t1 has %d atoms\n" % n1)
if n0 != n1:
sys.stderr.write("Atom numbers are different!")
sys.stderr.flush()
sys.exit()
else:
natom = n0
neb_atoms = []
o = open("detail.dat", "w")
for i in range(natom):
r2 = 0
for j in range(3):
d = (b0.atoms[i].x[j] - b1.atoms[i].x[j])
r2 += d * d
if r2 > dr * dr:
neb_atoms.append(b1.atoms[i])
o.write("%d\t%.4f\t%.4f\t%.4f\t%.4f\n" %
(i + 1, math.sqrt(r2), b1.atoms[i].x[0], b1.atoms[i].x[1],
b1.atoms[i].x[2]))
o.close()
o = open("final.coords", "w")
o.write("%d\n" % len(neb_atoms))
for i in neb_atoms:
o.write("%d\t%.4f\t%.4f\t%.4f\n" % (i.an, i.x[0], i.x[1], i.x[2]))
o.close()
from block import dumpBlock
from dump import Dump
from output_conf import toXyz, toPdb
lmpfile = "dump.lammpstrj"
sepfile = "dump.sep"
dt = 1
# parse the dump file with multi configurations into seperated dump files
nframe = dumpBlock(lmpfile, sepfile, dt)
nframe += 1
for i in range(0, nframe, dt):
#for i in range(10):
a = Dump("%s%05d.dump"%(sepfile,i))
b = a.parser()
#toXyz(b, "xyz%05d.xyz"%i)
#b.sortXYZ("z")
toPdb(b, "pdb%05d.pdb"%i)
from block import dumpBlock
from dump import Dump
from output_conf import toXyz, toPdb, toPoscar, toReaxLammps
lmpfile = "dump.lammpstrj"
sepfile = "dump.sep"
dt = 1
# parse the dump file with multi configurations into seperated dump files
nframe = dumpBlock(lmpfile, sepfile, dt)
nframe += 1
for i in range(0, nframe, dt):
#for i in range(10):
a = Dump("%s%05d.dump" % (sepfile, i))
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
b.toFrac()
toXyz(b, "xyz%05d.xyz" % i)
#b.sortXYZ("z")
toPdb(b, "pdb%05d.pdb" % i)
toReaxLammps(b, "lammps.data")
toPoscar(b, )
