def test():
testfile = "e_2_pdb.pdb"
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.pbc = [20.80, 20.80, 20.80, 90.0, 90.0, 90.0]
toReaxLammps(b)
def test():
testfile = "e_2_pdb.pdb"
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.pbc = [20.80, 20.80, 20.80, 90.0, 90.0, 90.0]
toReaxLammps(b)
def withPbc(testfile="supper.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
b.assignIdNumbers()
b.toFrac()
#b.translate(12.0, "z")
toXyz(b, "out.xyz")
toMusic(b, "out.music")
if len(b.pbc) == 0:
b.geotag = "BIOGRF 200"
else:
b.geotag = "XTLGRF 200"
toReaxLammps(b, "lammps.data")
toGeo(b, "sim.geo")
toMsd(b, "sim.msd")
toPoscar(b, )
toCfg(b, )
toJdft(b, )
toTowheecoords(b)
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
def monte_carlo():
""" a python shell for Monte Carlo reaxFF simulation'
"""
welcome()
mc = MC()
# read the pdb file
print("Reading input pdbfile")
pdbfile = "model.pdb"
a = Pdb(pdbfile)
sim = a.parser()
sim.assignEleTypes()
sim.assignAtomTypes()
# read the control file
read_control(mc)
# read index file
indexfile = "index.ndx"
grp = Group(indexfile)
# system init
log = open(mc.log, "w")
if mc.swap_flag == 1:
assign_swap_grps(mc, sim, grp)
print "Starting simulation:"
for i in range(mc.nsteps):
print("Running step %d" % i)
log.write("step %-6d" % i)
mc_moves(mc, sim, grp, log)
shutil.copy("out.data", "out.data.%06d" % i)
shutil.copy("dump.lmp", "dump.lmp.%06d" % i)
toReaxLammps(sim, "lammps.data.final")
log.close()
def monte_carlo():
""" a python shell for Monte Carlo reaxFF simulation'
"""
welcome()
mc = MC()
# read the pdb file
print("Reading input pdbfile")
pdbfile = "model.pdb"
a = Pdb(pdbfile)
sim = a.parser()
sim.assignEleTypes()
sim.assignAtomTypes()
# read the control file
read_control(mc)
# read index file
indexfile = "index.ndx"
grp = Group(indexfile)
# system init
log = open(mc.log, "w")
if mc.swap_flag == 1:
assign_swap_grps(mc, sim, grp)
print "Starting simulation:"
for i in range(mc.nsteps):
print("Running step %d"%i)
log.write("step %-6d"%i)
mc_moves(mc, sim, grp, log)
shutil.copy("out.data", "out.data.%06d"%i)
shutil.copy("dump.lmp", "dump.lmp.%06d"%i)
toReaxLammps(sim, "lammps.data.final")
log.close()
def read_pdb(pdbfile):
"""read pdb file
"""
a = Pdb(pdbfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
return b
def test():
testfile = "test.pdb"
a = Pdb(testfile)
b = a.parser()
atoms = b.atoms
print atoms[0].x
b.sortZ()
atoms = b.atoms
print atoms[0].x
def read_pdb(control):
print " Reading pdb file ..."
a = Pdb(control.pdbfile)
b = a.parser()
b.assignAtomTypes2()
print " cell parameters:"
print " a = %8.3f: "%b.pbc[0]
print " a = %8.3f: "%b.pbc[1]
print " a = %8.3f: "%b.pbc[2]
return b
def getBoxl(pdbfile, n, density):
density = density * 1000
a = Pdb(pdbfile)
b = a.parser()
b.getMass()
mass = b.mass
print "Molecule mass: ", mass
total = mass * n
vol = total * amc / density * 1e30 # here length is in A
print "Volume: ", vol
l = math.pow(vol, 1 / 3.0)
print "box a, b, c =", l
return l
def fortranOut(testfile="output.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
b.geotag = "XTLGRF 200"
toReaxLammps(b, "lammps.data")
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
toMsd(b, "sim.msd")
toGeo(b, "sim.geo")
def getBoxl(pdbfile, n, density):
density = density * 1000
a = Pdb(pdbfile)
b = a.parser()
b.getMass()
mass = b.mass
print "Molecule mass: ", mass
total = mass * n
vol = total*amc/density * 1e30 # here length is in A
print "Volume: ", vol
l = math.pow(vol, 1/3.0)
print "box a, b, c =", l
return l
def fortranOut(testfile = "output.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
b.geotag = "XTLGRF 200"
toReaxLammps(b, "lammps.data")
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
toMsd(b, "sim.msd")
toGeo(b, "sim.geo")
def main():
if len(sys.argv) < 4:
usage()
else:
pdbfile = sys.argv[1]
n = int(sys.argv[2])
density = float(sys.argv[3])
l = getBoxl(pdbfile, n, density)
writeInp(pdbfile, n, l)
os.system("packmol < inp")
if os.path.exists("sim.pdb"):
os.system("editconf -f sim.pdb -o sim.pdb -box %.4f" % (l / 10))
a = Pdb("sim.pdb")
b = a.parser()
b.assignAtomTypes()
toReaxLammps(b)
def main():
if len(sys.argv) < 4:
usage()
else:
pdbfile = sys.argv[1]
n = int(sys.argv[2])
density = float(sys.argv[3])
l = getBoxl(pdbfile, n, density)
writeInp(pdbfile, n, l)
os.system("packmol < inp")
if os.path.exists("sim.pdb"):
os.system("editconf -f sim.pdb -o sim.pdb -box %.4f"%(l/10))
a = Pdb("sim.pdb")
b = a.parser()
b.assignAtomTypes()
toReaxLammps(b)
def make_ndx(atp, lo, hi):
assert lo < hi
a = Pdb("model.pdb")
b = a.parser()
b.assignEleTypes()
b.assignAtomTypes()
n = 0
counter = 0
for i in b.atoms:
if i.element == atp:
z = i.x[2]
if z > lo and z <= hi:
print "%5d"%(n + 1),
if (counter + 1) % 15 == 0:
print ''
counter += 1
n+= 1
print ''
def make_ndx(atp, lo, hi):
assert lo < hi
a = Pdb("model.pdb")
b = a.parser()
b.assignEleTypes()
b.assignAtomTypes()
n = 0
counter = 0
for i in b.atoms:
if i.element == atp:
z = i.x[2]
if z > lo and z <= hi:
print "%5d" % (n + 1),
if (counter + 1) % 15 == 0:
print ''
counter += 1
n += 1
print ''
def withPbc(testfile="supper.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
#b.translate(12.0, "z")
toXyz(b, "out.xyz")
toMusic(b, "out.music")
if len(b.pbc) == 0:
b.geotag = "BIOGRF 200"
else:
b.geotag = "XTLGRF 200"
toReaxLammps(b, "lammps.data")
toGeo(b, "sim.geo")
toMsd(b, "sim.msd")
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
def sortXYZ(testfile="input.pdb", axis="z"):
a = Pdb(testfile)
b = a.parser()
atoms = b.atoms
b.sortXYZ(axis)
toPdb(b, "out_sorted.pdb")
1 3
improper
0
unit ntype
3 'H_' 0.4d0
vibration
1
2
improper
0
"""
if len(sys.argv) > 2:
nmol = int(sys.argv[2])
a = Pdb(sys.argv[1])
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
toTowheecoords(b)
rcut = 3.5
xx, xy, xz, yy, yz, zz = lattice2v(b.pbc)
la = [xx, 0.0, 0.0]
lb = [xy, yy, 0.0]
lc = [xz, yz, zz]
print la
print lb
print lc
o = open("towhee_input", "w")
o.write("inputformat\n")
def read_pdb():
a = Pdb("out_sorted.pdb")
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
return b
def sortXYZ(testfile="input.pdb", axis="z"):
a = Pdb(testfile)
b = a.parser()
atoms = b.atoms
b.sortXYZ(axis)
toPdb(b, "out_sorted.pdb")
def read_pdb():
a = Pdb("out_sorted.pdb")
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
return b
