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():
parser = argparse.ArgumentParser()
parser.add_argument("fname",
default="POSCAR",
nargs="?",
help="geo file name")
parser.add_argument("-n", type=int, help="number of fixed atoms")
parser.add_argument("-r",
action='store_true',
help="reverse the fixing order")
args = parser.parse_args()
if args.n:
n_fixed = int(args.n)
else:
n_fixed = int(input("number of fixed atoms: "))
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
shutil.copy(poscar_file, poscar_file + ".1")
coords = []
for i in range(len(b.atoms)):
coords.append([])
for i in range(len(b.atoms)):
coords[i].append(i)
for j in b.atoms[i].x:
coords[i].append(j)
coords.sort(key=lambda x: x[3])
if args.r:
coords.sort(key=lambda x: x[3], reverse=True)
for i in range(len(coords)):
if i < n_fixed:
coords[i].append("F")
else:
coords[i].append("T")
coords.sort(key=lambda x: x[0])
for i in range(len(b.atoms)):
b.atoms[i].xr = [0, 0, 0]
if coords[i][-1] == "F":
b.atoms[i].xr = [1, 1, 1]
toPoscar(b, "POSCAR_new")
def toPOSCAR(t0, conf, steps):
if not os.path.exists("poscars"):
os.mkdir("poscars")
os.chdir("poscars")
for i in range(len(conf)):
fname = "POSCAR_%06d"%steps[i]
t0.name = "step = %d"%steps[i]
for j in range(len(conf[i])):
tokens = conf[i][j].strip().split()
t0.atoms[j].xFrac[0] = float(tokens[0])
t0.atoms[j].xFrac[1] = float(tokens[1])
t0.atoms[j].xFrac[2] = float(tokens[2])
toPoscar(t0, fname)
os.chdir("..")
def toPOSCAR(t0, conf, steps):
if not os.path.exists("poscars"):
os.mkdir("poscars")
os.chdir("poscars")
for i in range(len(conf)):
fname = "POSCAR_%06d" % steps[i]
t0.name = "step = %d" % steps[i]
for j in range(len(conf[i])):
tokens = conf[i][j].strip().split()
t0.atoms[j].xFrac[0] = float(tokens[0])
t0.atoms[j].xFrac[1] = float(tokens[1])
t0.atoms[j].xFrac[2] = float(tokens[2])
toPoscar(t0, fname)
os.chdir("..")
def gen_input(scan, poscar):
n = len(scan.scan_points)
n_ref = scan.ref_atom - 1
for i in range(n):
folder = "s%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
z0 = poscar.atoms[n_ref].xFrac[2]
z1 = scan.scan_points[i]
dz = z1 - z0
# update the coords
poscar.atoms[n_ref].xFrac[2] += dz
for j in range(len(scan.grp_atoms)):
n_grp = scan.grp_atoms[j] - 1
poscar.atoms[n_grp].xFrac[2] += dz
# output the coords
toPoscar(poscar)
os.chdir("..")
def gen_input(scan, poscar):
n = len(scan.scan_points)
n_ref = scan.ref_atom - 1
for i in range(n):
folder = "s%02d" % i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
z0 = poscar.atoms[n_ref].xFrac[2]
z1 = scan.scan_points[i]
dz = z1 - z0
# update the coords
poscar.atoms[n_ref].xFrac[2] += dz
for j in range(len(scan.grp_atoms)):
n_grp = scan.grp_atoms[j] - 1
poscar.atoms[n_grp].xFrac[2] += dz
# output the coords
toPoscar(poscar)
os.chdir("..")
def gen_scan(s, args):
start = 0.7
end = 1.3
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
if os.path.exists('../pbs'):
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
def withPbc(testfile="supper.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
print b.atomtypes
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")
toPoscar(b,)
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
def gen_scan(s, args):
start = 0.8
end = 1.2
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
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,)
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, )
from mytype import System, Molecule, Atom
from poscar import Poscar
from output_conf import toPoscar
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()
toPoscar(b)
