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 sort_with_connect(fname):
"""Sort the atoms: gather the same atoms, and atoms in same
molecules according to connectivity (.mdf). This is very good
for generating gromacs input files, and organize the atoms into
a well defined order.
"""
mdffile = "%s.mdf" % fname
carfile = "%s.car" % fname
mdf = Mdf(mdffile)
car = Car(carfile)
a = car.parser()
Li = []
Ge = []
P = []
atom_names = mdf.atom_names
for i in range(len(mdf.atoms)):
if mdf.atoms[i].element == "Li":
Li.append(i)
elif mdf.atoms[i].element == "Ge":
Ge.append(i)
for j in mdf.atoms[i].connect:
Ge.append(atom_names.index(j))
elif mdf.atoms[i].element == "P":
P.append(i)
for j in mdf.atoms[i].connect:
P.append(__get_index(atom_names, j))
seq_new = Li + Ge + P
a.sortNdx(seq_new)
toPdb(a)
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 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)
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 add_h(b, centers, cn):
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
n_cut = 10
for i in range(len(cn)):
n = int(cn[i])
print "processing %d"%(n*1.0/8183*100)
if n < n_cut:
a = Atom()
a.name = "H"
a.element = "H"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + 1.5
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a.x[0] = x
a.x[1] = y
a.x[2] = z
b1.atoms.append(a)
toPdb(b1, "add_h.pdb")
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 convertors(b):
#toGeo(b, b.name+'.geo')
toGeo(b, 'geo')
toXyz(b, b.name+'.xyz')
toGjf(b, b.name+'.gjf')
toPdb(b, b.name+'.pdb')
toReaxLammps(b)
def sort_with_connect(fname):
"""Sort the atoms: gather the same atoms, and atoms in same
molecules according to connectivity (.mdf). This is very good
for generating gromacs input files, and organize the atoms into
a well defined order.
"""
mdffile = "%s.mdf" % fname
carfile = "%s.car" % fname
mdf = Mdf(mdffile)
car = Car(carfile)
a = car.parser()
Li = []
Ge = []
P = []
atom_names = mdf.atom_names
for i in range(len(mdf.atoms)):
if mdf.atoms[i].element == "Li":
Li.append(i)
elif mdf.atoms[i].element == "Ge":
Ge.append(i)
for j in mdf.atoms[i].connect:
Ge.append(atom_names.index(j))
elif mdf.atoms[i].element == "P":
P.append(i)
for j in mdf.atoms[i].connect:
P.append(__get_index(atom_names, j))
seq_new = Li + Ge + P
a.sortNdx(seq_new)
toPdb(a)
def convert(fname):
a = Jaguar(fname)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
toXyz(b, "out.xyz")
toPdb(b, "output.pdb", 1)
toReaxLammps(b, "lammps.data")
def convert(fname):
a = Jaguar(fname)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
toXyz(b, "out.xyz")
toPdb(b, "output.pdb", 1)
toReaxLammps(b, "lammps.data")
def surface_atoms_read(b):
sur = np.loadtxt("sur_sas.dat")
b1 = copy.deepcopy(b)
atoms = []
for i in range(len(sur)):
if int(sur[i]) == 1:
atoms.append(b.atoms[i])
b1.atoms = atoms
toPdb(b1, "surface_atoms.pdb")
toXyz(b1, "surface_atoms.xyz")
def main(log):
d1_file = "lammps.data.3"
d2_file = "./slice_03/conf2/lammps.data"
d1 = read_data(d1_file)
d2 = read_data(d2_file)
logfile = "./slice_03/conf2/build.log"
z0, ndx = read_build_log(logfile)
toPdb(d1, "t0.pdb")
update_coords(d1, d2, z0, ndx)
toPdb(d1, "t1.pdb")
toReaxLammps(d1, "lammps.data.4")
def main(log):
d1_file = "lammps.data.3"
d2_file = "./slice_03/conf2/lammps.data"
d1 = read_data(d1_file)
d2 = read_data(d2_file)
logfile = "./slice_03/conf2/build.log"
z0, ndx = read_build_log(logfile)
toPdb(d1, "t0.pdb")
update_coords(d1, d2, z0, ndx)
toPdb(d1, "t1.pdb")
toReaxLammps(d1, "lammps.data.4")
def filter_center(center, dx, nl, b):
o = open("ndx_original.dat", "w")
atoms = []
for i in range(len(b.atoms)):
x = b.atoms[i].x[0]
z = b.atoms[i].x[2]
an = b.atoms[i].an
zn = int(z/dx)
if x >= center[zn][0]:
atoms.append(b.atoms[i])
o.write("%d\n"%an)
o.close()
b.atoms = atoms
toPdb(b)
def filter_center(center, dx, nl, b):
o = open("ndx_original.dat", "w")
atoms = []
for i in range(len(b.atoms)):
x = b.atoms[i].x[0]
z = b.atoms[i].x[2]
an = b.atoms[i].an
zn = int(z / dx)
if x >= center[zn][0]:
atoms.append(b.atoms[i])
o.write("%d\n" % an)
o.close()
b.atoms = atoms
toPdb(b)
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 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 surface_atoms_read(b):
sur = np.loadtxt("sur_sas.dat")
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
atoms_sur = []
atoms_bulk = []
for i in range(len(sur)):
if int(sur[i]) == 1:
atoms_sur.append(b.atoms[i])
else:
atoms_bulk.append(b.atoms[i])
b1.atoms = atoms_sur
b2.atoms = atoms_bulk
toPdb(b1, "surface_atoms.pdb")
toXyz(b1, "surface_atoms.xyz")
toPdb(b2, "bulk_atoms.pdb")
toXyz(b2, "bulk_atoms.xyz")
def surface_atoms_read(b):
sur = np.loadtxt("sur_sas.dat")
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
atoms_sur = []
atoms_bulk = []
for i in range(len(sur)):
if int(sur[i]) == 1:
atoms_sur.append(b.atoms[i])
else:
atoms_bulk.append(b.atoms[i])
b1.atoms = atoms_sur
b2.atoms = atoms_bulk
toPdb(b1, "surface_atoms.pdb")
toXyz(b1, "surface_atoms.xyz")
toPdb(b2, "bulk_atoms.pdb")
toXyz(b2, "bulk_atoms.xyz")
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
args = parser.parse_args()
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
print b.getVol()
#print b.pbc
toXyz(b)
toGeo(b, "geo")
toPdb(b, "sim.pdb")
toReaxLammps(b, "lammps.data")
toJdft(b, "coords")
def output_pdb(control, b, ndx):
"""Output the atoms in ndx to pdb file
"""
c = copy.deepcopy(b)
c.atoms = []
sphere = []
void = []
for i in range(len(ndx)):
for j in range(len(ndx[i])):
sphere.append((ndx[i][j]))
for i in range(len(b.atoms)):
if i not in sphere:
void.append(i)
if control.void == "yes":
for i in void:
c.atoms.append(b.atoms[i])
else:
for i in sphere:
c.atoms.append(b.atoms[i])
toPdb(c, control.output)
def surface_atoms_cut_off(b):
"""
"""
cn = np.loadtxt("cn.dat")
o = open("sur.dat", "w")
n_cut = 10
sur = np.where(cn <= 10, 1, 0)
b1 = copy.deepcopy(b)
atoms = []
for i in range(len(sur)):
if sur[i] == 1:
atoms.append(b.atoms[i])
o.write("1\n")
else:
o.write("0\n")
o.close()
b1.atoms = atoms
toPdb(b1, "surface_atoms.pdb")
toXyz(b1, "surface_atoms.xyz")
def surface_atoms_cut_off(b):
"""
"""
cn = np.loadtxt("cn.dat")
o = open("sur.dat", "w")
n_cut = 10
sur = np.where(cn <= 10, 1, 0)
b1 = copy.deepcopy(b)
atoms = []
for i in range(len(sur)):
if sur[i] == 1:
atoms.append(b.atoms[i])
o.write("1\n")
else:
o.write("0\n")
o.close()
b1.atoms = atoms
toPdb(b1, "surface_atoms.pdb")
toXyz(b1, "surface_atoms.xyz")
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 main():
parser = argparse.ArgumentParser()
parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
args = parser.parse_args()
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
vol = b.getVol()
mass = b.getMass()
density = mass/vol*ATOMIC_MASS_CONSTANT*1e27
print density
#print b.pbc
toXyz(b, "contcar.xyz")
toGeo(b, "geo")
toPdb(b, "sim.pdb")
toReaxLammps(b, "lammps.data")
toJdft(b, "coords")
def main(counter):
# Set up
x = np.linspace(1,32,32)
delta = 6.0
miu = 17.0
# get the distribution
al_natoms, o_natoms = gaussian(x, delta, miu)
# read pdb
a = read_pdb()
# build the atoms list
ca_list, o_list = build_list(a)
# replace
al_list, ignore_list = replace(ca_list, o_list, al_natoms, o_natoms)
# do the replace
process(a, al_list, ignore_list)
# output the data
toPdb(a, "case%02d.pdb"%counter)
def main(counter):
# Set up
x = np.linspace(1, 32, 32)
delta = 6.0
miu = 17.0
# get the distribution
al_natoms, o_natoms = gaussian(x, delta, miu)
# read pdb
a = read_pdb()
# build the atoms list
ca_list, o_list = build_list(a)
# replace
al_list, ignore_list = replace(ca_list, o_list, al_natoms, o_natoms)
# do the replace
process(a, al_list, ignore_list)
# output the data
toPdb(a, "case%02d.pdb" % counter)
def add_o(b, centers, cn):
"""add o
"""
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
n_cut = 10
for i in range(len(cn)):
print "processing %d"%(i*1.0/8183*100)
n = int(cn[i])
token = random.random()
if n < n_cut and token > 0.9:
a = Atom()
a.name = "O"
a.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + 2.0
s = r/r1
x = s*(x0-x1) + x1 + 1.0
y = s*(y0-y1) + y1 + 1.0
z = s*(z0-z1) + z1
a.x[0] = x
a.x[1] = y
a.x[2] = z
b1.atoms.append(a)
toPdb(b1, "add_o.pdb")
def fconv(fname):
a = FullData(fname)
b = a.parser()
b.assignAtomTypes()
toPdb(b)
def fconv(fname):
a = FullData(fname)
b = a.parser()
b.assignAtomTypes()
toPdb(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")
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03LogConf
from output_conf import toXyz, toGeo, toPdb
usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
print usage
else:
for i in sys.argv[1:]:
outfile = i.split(".")[0]
if os.path.exists(i):
a = G03LogConf(i)
b = a.parser()
b.assignEleTypes()
b.geotag = "BIOGRF 200"
toXyz(b, outfile + ".xyz")
toGeo(b, outfile + ".geo")
b.pbc = [50, 50, 50, 90.0, 90.0, 90.0]
toPdb(b, outfile + ".pdb")
else:
print "missing file %s" % i
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03LogConf
from output_conf import toXyz, toGeo, toPdb
usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
print usage
else:
for i in sys.argv[1:]:
outfile = i.split(".")[0]
if os.path.exists(i):
a = G03LogConf(i)
b = a.parser()
b.assignEleTypes()
b.geotag = "BIOGRF 200"
toXyz(b, outfile+".xyz")
toGeo(b, outfile+".geo")
b.pbc = [50, 50, 50, 90.0, 90.0, 90.0]
toPdb(b, outfile+".pdb")
else:
print "missing file %s"%i
def add_oh(b, centers, cn, n_ignore, ndx):
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
a = Atom()
a.name = "O"
a.element = "O"
b2.atoms.append(a)
a = Atom()
a.name = "H"
a.element = "H"
b2.atoms.append(a)
n_cut = 10
r_pt_oh = 2.0
r_oh = 1.0
for i in range(len(cn)):
#print "processing %d"%(i*1.0/len(cn)*100)
token = random.random()
n = int(cn[i])
if n < n_cut and token >= 0.0:
a1 = Atom()
a1.name = "O"
a1.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + r_pt_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a1.x[0] = x
a1.x[1] = y
a1.x[2] = z
b1.atoms.append(a1)
b2.atoms[-2].x[0] = x
b2.atoms[-2].x[1] = y
b2.atoms[-2].x[2] = z
a2 = Atom()
a2.name = "H"
a2.element = "H"
r = r1 + r_pt_oh + r_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a2.x[0] = x
a2.x[1] = y
a2.x[2] = z
b1.atoms.append(a2)
b2.atoms[-1].x[0] = x
b2.atoms[-1].x[1] = y
b2.atoms[-1].x[2] = z
if i >= n_ignore - 1:
toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))
toPdb(b1, "add_oh.pdb")
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)
def sortXYZ(testfile="input.pdb", axis="z"):
a = Pdb(testfile)
b = a.parser()
atoms = b.atoms
b.sortXYZ(axis)
toPdb(b, "out_sorted.pdb")
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, )
""" read the geo file and output to data (LAMMPS), geo and xyz file. """ from mytype import System, Molecule, Atom from data import ReaxData from output_conf import toPdb testfile = "e_2_data.data" a = ReaxData(testfile) b = a.parser() b.assignAtomTypes() toPdb(b)
def get_slice(b, id0):
logfile = "build.log"
o = open(logfile, "w")
a0 = b.atoms[id0-1]
id0 = a0.an
x0, y0, z0 = a0.x
o.write("Reference atoms is %d.\n"%id0)
o.write("The coordination of reference atom is %.4f %.4f %.4f.\n"%
(x0, y0, z0))
o.write("Cut from z direction.\n")
zl = b.pbc[2]
z0 = z0 - int(z0/zl)*zl
dz1 = DELTA_Z1
dz2 = DELTA_Z2
z1 = z0 - dz1
z2 = z0 + dz1
z1 = z1 - math.floor(z1/zl)*zl
z2 = z2 - math.floor(z2/zl)*zl
b1 = copy.deepcopy(b)
o.write("Starting from %.4f to %.4f.\n"%(z1, z2))
o.write("Cut radius is %.4f.\n"%dz1)
#o.write("Buffer distance is %.4f.\n"%dz2)
#o.write("Fixed L1 from %.4f to %.4f\n"%(z1, z2))
#o.write("Fixed L2 from %.4f to %.4f\n"%(z3, z4))
ca = []
a_ref = []
for i in range(len(b.atoms)):
id = b.atoms[i].an
z = b.atoms[i].x[2]
z = z - math.floor(z/zl)*zl #pbc
b1.atoms[i].x[2] = z
if id == id0:
a_ref.append(b1.atoms[i])
else:
if z1 < z2:
if z >= z1 and z < z2:
ca.append(b1.atoms[i])
else:
if z >= 0 and z < z2:
ca.append(b1.atoms[i])
elif z >= z1 and z < zl:
ca.append(b1.atoms[i])
# Shift the atoms according to reference atom
for i in range(len(ca)):
z = ca[i].x[2]
z = z - z1
z = z - math.floor(z/zl)*zl
ca[i].x[2] = z
z = a_ref[0].x[2]
z = z - z1
z = z - math.floor(z/zl)*zl
a_ref[0].x[2] = z
o.write("Sort the atom index according to z.\n")
ca.sort(key=lambda x: x.x[2])
c1 = []
c2 = []
for i in ca:
z = i.x[2]
if z <= dz2:
c1.append(i)
elif z > 2*dz1 - dz2:
c1.append(i)
else:
c2.append(i)
o.write("Fixed atoms is %d.\n"%(len(c1)))
ca = ca + a_ref
o.write("Total number of atoms is %d.\n"%len(ca))
o.write("Index is as following:\n")
counter = 0
for i in ca:
if counter % 10 == 0:
o.write("\n")
o.write("%8d"%i.an)
counter += 1
o.write("\n")
b1.atoms = c1 + c2 + a_ref
b1.pbc[2] = 2*dz1
o.write("Output to pdb.\n")
toPdb(b1, "input.pdb")
toReaxLammps(b1)
o.close()
return ca, c1, c2, a_ref
from mytype import System, Molecule, Atom
from poscar import Poscar
from output_conf import toXyz, toGeo, toPdb, toReaxLammps
import sys
if len(sys.argv) > 1:
fname = sys.argv[1]
else:
fname = "CONTCAR"
a = Poscar(fname)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
print b.getVol()
toXyz(b)
toGeo(b, "geo")
toPdb(b, "sim.pdb")
toReaxLammps(b, "lammps.data")
def add_oh(b, centers, cn, n_ignore, ndx):
"""add oh
"""
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
a = Atom()
a.name = "O"
a.element = "O"
b2.atoms.append(a)
a = Atom()
a.name = "H"
a.element = "H"
b2.atoms.append(a)
n_cut = 10
r_pt_oh = 2.0
r_oh = 1.0
for i in range(len(cn)):
#print "processing %d"%(i*1.0/len(cn)*100)
token = random.random()
n = int(cn[i])
if n < n_cut and token >= 0.0:
a1 = Atom()
a1.name = "O"
a1.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + r_pt_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a1.x[0] = x
a1.x[1] = y
a1.x[2] = z
b1.atoms.append(a1)
b2.atoms[-2].x[0] = x
b2.atoms[-2].x[1] = y
b2.atoms[-2].x[2] = z
a2 = Atom()
a2.name = "H"
a2.element = "H"
r = r1 + r_pt_oh + r_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a2.x[0] = x
a2.x[1] = y
a2.x[2] = z
b1.atoms.append(a2)
b2.atoms[-1].x[0] = x
b2.atoms[-1].x[1] = y
b2.atoms[-1].x[2] = z
if i >= n_ignore - 1:
toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))
toPdb(b1, "add_oh.pdb")