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 main(args):
xyz_info = XyzInfo()
if args.f:
fname = args.f[0]
else:
fname = "movie.xyz"
sys.stderr.write("Using default xyz file: movie.xyz\n")
if args.c:
a = Xyz(fname)
b = a.parser()
if args.pbc:
b.pbc = args.pbc
else:
b.pbc = [20, 20, 23, 90, 90, 90]
toPdb(b)
if args.s:
config = ConfigParser.ConfigParser()
config.read(args.s[0])
read_info(xyz_info, config)
if args.nbox:
if not args.s:
sys.stderr.write("No configure file found!\n")
sys.stderr.write("Prepare a sample configure file (test.ini)\n")
write_config()
sys.exit()
else:
replicate(xyz_info, args)
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(args):
xyz_info = XyzInfo()
if args.f:
fname = args.f[0]
else:
fname = "movie.xyz"
sys.stderr.write("Using default xyz file: movie.xyz\n")
if args.c:
a = Xyz(fname)
b = a.parser()
b.pbc = [100, 100, 100, 90, 90, 90]
toPdb(b)
if args.s:
config = ConfigParser.ConfigParser()
config.read(args.s[0])
read_info(xyz_info, config)
if args.nbox:
if not args.s:
sys.stderr.write("No configure file found!\n")
sys.stderr.write("Prepare a sample configure file (test.ini)\n")
write_config()
sys.exit()
else:
replicate(xyz_info, args)
""" 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)
"""