def sep_xyz(n):
if not os.path.exists("conf"):
os.mkdir("conf")
shutil.copy("movie.xyz", "conf")
os.chdir("conf")
xyzBlock("movie.xyz", n+2, )
os.remove("movie.xyz")
os.chdir("..")
def sep_xyz(n):
if not os.path.exists("conf"):
os.mkdir("conf")
shutil.copy("movie.xyz", "conf")
os.chdir("conf")
xyzBlock(
"movie.xyz",
n + 2,
)
os.remove("movie.xyz")
os.chdir("..")
def replicate(xyz_info, args):
fname = args.f[0]
nlines = xyz_info.natoms + 2
nframe = xyzBlock(fname, nlines)
na, nb, nc = args.nbox
if nframe >= 0:
for i in range(nframe + 1):
if not xyz_info.restart:
a = Xyz("output%05d.xyz" % i)
b = a.parser()
b.pbc = xyz_info.pbc
b.step = i
toPdb(b, "output%05d.pdb" % i)
# replicate the box using external code (genconf in Gromacs)
subprocess.Popen([
"gmx", "genconf", "-f",
"output%05d.pdb" % i, "-o",
"s_%05d.pdb" % i, "-nbox",
"%d" % na,
"%d" % nb,
"%d" % nc
],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
subprocess.Popen(["cat s_*.pdb > movie_%d_%d_%d.pdb" % (na, nb, nc)],
shell=True)
# clear up
o = open("clear.sh", "w")
o.write("rm output*.xyz\n")
o.write("rm output*.pdb\n")
o.write("rm s_*.pdb\n")
o.close()
st = os.stat('clear.sh')
os.chmod('clear.sh', st.st_mode | stat.S_IEXEC)
def replicate(xyz_info, args):
fname = args.f[0]
nlines = xyz_info.natoms + 2
nframe = xyzBlock(fname, nlines)
na, nb, nc = args.nbox
if nframe >= 0:
for i in range(nframe+1):
if not xyz_info.restart:
a = Xyz("output%05d.xyz"%i)
b = a.parser()
b.pbc = xyz_info.pbc
b.step = i
toPdb(b, "output%05d.pdb"%i)
# replicate the box using external code (genconf in Gromacs)
subprocess.Popen(["genconf", "-f", "output%05d.pdb"%i,
"-o", "s_%05d.pdb"%i, "-nbox",
"%d"%na, "%d"%nb, "%d"%nc],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
subprocess.Popen(["cat s_*.pdb > movie_%d_%d_%d.pdb"%(na, nb, nc)],
shell=True)
# clear up
o = open("clear.sh", "w")
o.write("rm output*.xyz\n")
o.write("rm output*.pdb\n")
o.write("rm s_*.pdb\n")
o.close()
st = os.stat('clear.sh')
os.chmod('clear.sh', st.st_mode | stat.S_IEXEC)
def main():
print "Reading the xyz file ..."
shutil.copy("movie.xyz", "conf")
if not os.path.exists("conf"):
os.mkdir("conf")
os.chdir("conf")
n = 192
xyzBlock("movie.xyz", n, )
os.remove("movie.xyz")
os.chdir("..")
rlist = []
f = open("rxn.log", "r")
for i in f:
if i.strip().startswith("#"):
pass
else:
tokens = i.strip().split()
if len(tokens) > 1:
rxn = tokens[0]
rlist.append(rxn)
f.close()
for i in rlist:
find_rxn(i)
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
from mytype import System, Molecule, Atom
from xyz import Xyz
from output_conf import toDump
from block import xyzBlock
nframe = xyzBlock("movie.xyz", 194)
if nframe > 1:
for i in range(nframe):
a = Xyz("output%05d.xyz"%i)
b = a.parser()
b.pbc = [10.739, 11.747, 13.083, 90.00, 95.77, 90.00]
b.step = i
toDump(b, "output%05d.dump"%i)
o = open("total.dump", "w")
for i in range(nframe):
f = open("output%05d.dump"%i, "r")
for j in f:
o.write(j)
f.close()
o.close()
"""
testfile = "out.pdb"
a = Pdb(testfile)
b = a.parser()
toDump(b)
"""