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 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 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 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 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 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 get_energy(mc, sim, grp):
"""get reaxFF energy by calling LAMMPS externally
"""
ener = 0.0
toReaxLammps(sim)
f1, f2, f3 = popen2.popen3("%s %s -in lammps_input"%(mc.mpicode, mc.code))
for i in f1:
if i.strip().startswith("PotEng"):
tokens = i.strip().split()
n = tokens.index("PotEng")
ener = float(tokens[n + 2])
return ener
def get_energy(mc, sim, grp):
"""get reaxFF energy by calling LAMMPS externally
"""
ener = 0.0
toReaxLammps(sim)
f1, f2, f3 = popen2.popen3("%s %s -in lammps_input" %
(mc.mpicode, mc.code))
for i in f1:
if i.strip().startswith("PotEng"):
tokens = i.strip().split()
n = tokens.index("PotEng")
ener = float(tokens[n + 2])
return ener
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 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 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 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")
""" Replace the Ca in CaO crystal to creat a Ca-rich LDO (Ca:Al=7:1)
This is for LDH project
"""
from data import ReaxData
from output_conf import toReaxLammps
from tools import LdhProject
for i in range(100):
testfile = "a666.data"
a = ReaxData(testfile)
b = a.parser()
c = LdhProject(b)
c.re_al = 8
c.re1()
b.assignAtomTypes()
toReaxLammps(b, "case%02d.data" % i)
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 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 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, )