def main():
"""
Read in data file and replicate it
"""
#
# Read options
#
options, args = get_options()
#
# Initialize mpi
#
p = mpiBase.getMPIObject()
pt = periodictable()
#
# Read in cply file into a structure container object
#
bb_o = Buildingblock()
bb_o.read_xmol(options.in_xyz)
if( options.setlabel ): bb_o.set_label()
if( options.setmass ): bb_o.set_mass()
print bb_o
comment = "Read in from {} to output {} ".format(options.in_xyz,options.out_id)
append = False
bb_o.ptclC.write_xmol("{}.xyz".format(options.out_id),comment,append)
bb_o.write_cply("{}.cply".format(options.out_id),write_ff=True,write_bonds=True)
del bb_o
def main():
"""
Read in gaussian fchk file and create an xyz file
"""
#
# Read options
#
options, args = get_options()
#
# Initialize blank system
#
bb_o = Buildingblock()
bb_o.read_cply(options.in_cply)
param_o = ParameterContainer()
bb_o,param_o = read_lmpdata( bb_o , param_o , options.in_data)
print bb_o
print param_o
if( options.mol_pbcs ):
bb_o.bondC_nblist()
molpbcs(bb_o,bb_o.bonded_nblist, bb_o.bonded_nbindx,debug=False)
comment = " From data file {} ".format( options.in_data)
append = False
out_xyz = "{}.xyz".format(options.out_id)
bb_o.ptclC.write_xmol("{}".format(out_xyz),comment,append)
if( options.verbose ): print " Writing cply file {}.cply".format(options.out_id)
bb_o.write_cply("{}.cply".format(options.out_id),write_ff=True,write_bonds=True)
def main():
"""
Read in gaussian fchk file and create an xyz file
"""
#
# Read options
#
options, args = get_options()
#
# Initialize blank system
#
bb_o = Buildingblock()
bb_o.read_cply(options.in_cply)
param_o = ParameterContainer()
bb_o, param_o = read_lmpdata(bb_o, param_o, options.in_data)
print bb_o
print param_o
if (options.mol_pbcs):
bb_o.bondC_nblist()
molpbcs(bb_o, bb_o.bonded_nblist, bb_o.bonded_nbindx, debug=False)
comment = " From data file {} ".format(options.in_data)
append = False
out_xyz = "{}.xyz".format(options.out_id)
bb_o.ptclC.write_xmol("{}".format(out_xyz), comment, append)
if (options.verbose):
print " Writing cply file {}.cply".format(options.out_id)
bb_o.write_cply("{}.cply".format(options.out_id),
write_ff=True,
write_bonds=True)
def main():
"""
Read in data file and replicate it
"""
#
# Read options
#
options, args = get_options()
#
# Initialize mpi
#
p = mpiBase.getMPIObject()
pt = periodictable()
#
# Read in cply file into a structure container object
#
bb_o = Buildingblock()
bb_o.read_xmol(options.in_xyz)
if (options.setlabel): bb_o.set_label()
if (options.setmass): bb_o.set_mass()
print bb_o
comment = "Read in from {} to output {} ".format(options.in_xyz,
options.out_id)
append = False
bb_o.ptclC.write_xmol("{}.xyz".format(options.out_id), comment, append)
bb_o.write_cply("{}.cply".format(options.out_id),
write_ff=True,
write_bonds=True)
del bb_o
def main():
"""
Read in data file and replicate it
"""
#
# Read options
#
options, args = get_options()
#
# Initialize mpi
#
p = mpiBase.getMPIObject()
#
# Read in fchk file into a simulation object
#
sim_o = SimulationGaussian(options.out_id)
sim_o.readfchk(options.in_fchk)
print sim_o
write_xyz = True
if (write_xyz):
comment = " adf"
append = False
sim_o.write_xmol("{}.xyz".format(options.out_id), comment, append)
struc_o = sim_o.getstrucC()
param_o = sim_o.getparamC()
# initialize_fftags(struc_o)
struc_o.build_bonded_nblist(max_nn=12.0, radii_buffer=1.25)
struc_o.nblist_bonds()
struc_o.nblist_angles()
limdih = False
limitdih_n = 0
struc_o.nblist_dih(limdih, limitdih_n)
#
# Use oplsaa types as fftype guess
# These should be checked and edited in the cply file
#
ring_nblist, ring_nbindex = find_rings(struc_o, struc_o.bonded_nblist,
struc_o.bonded_nbindx)
oplsaa_atomtypes(struc_o, struc_o.bonded_nblist, struc_o.bonded_nbindx)
set_chargegroups(struc_o, ring_nblist, ring_nbindex, struc_o.bonded_nblist,
struc_o.bonded_nbindx)
print " Charge groups set "
bb_o = Buildingblock()
print " bb_o created "
bb_o.setStructureContainer(struc_o)
print " bb_o strucC set to struc_o "
bb_o.set_cply_tags()
# struc_o.zero_unitq()
print " cply tags set "
bb_o.write_cply("{}.cply".format(options.out_id),
write_ff=True,
write_bonds=True)
del sim_o
def main():
"""
Read in data file and replicate it
"""
#
# Read options
#
options, args = get_options()
#
# Initialize mpi
#
p = mpiBase.getMPIObject()
#
# Read in fchk file into a simulation object
#
sim_o = SimulationGaussian(options.out_id)
sim_o.readfchk(options.in_fchk)
print sim_o
write_xyz = True
if( write_xyz ):
comment = " adf"
append = False
sim_o.write_xmol("{}.xyz".format(options.out_id),comment,append)
struc_o = sim_o.getstrucC()
param_o = sim_o.getparamC()
# initialize_fftags(struc_o)
struc_o.build_bonded_nblist(max_nn=12.0,radii_buffer=1.25)
struc_o.nblist_bonds()
struc_o.nblist_angles()
limdih = False
limitdih_n = 0
struc_o.nblist_dih(limdih,limitdih_n)
#
# Use oplsaa types as fftype guess
# These should be checked and edited in the cply file
#
ring_nblist, ring_nbindex = find_rings(struc_o,struc_o.bonded_nblist, struc_o.bonded_nbindx)
oplsaa_atomtypes(struc_o,struc_o.bonded_nblist, struc_o.bonded_nbindx)
set_chargegroups(struc_o , ring_nblist, ring_nbindex,struc_o.bonded_nblist, struc_o.bonded_nbindx)
print " Charge groups set "
bb_o = Buildingblock()
print " bb_o created "
bb_o.setStructureContainer(struc_o)
print " bb_o strucC set to struc_o "
bb_o.set_cply_tags()
# struc_o.zero_unitq()
print " cply tags set "
bb_o.write_cply("{}.cply".format(options.out_id),write_ff=True,write_bonds=True)
del sim_o
