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()
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():
"""
Test functionality of periodictable: 1) print atomic symbol and mass, 2) find an element with mass 12.0110
3) print it's properties, 4) find an element with symbol S and 5) print it's properties
"""
# Set periodic table element
pt = periodictable()
for el_symb in pt.elements:
print " symb %s mass %f " % (pt.elements[el_symb].symbol,
pt.elements[el_symb].mass)
find_mass = 12.0110
el = pt.getelementWithMass(find_mass)
print " Element with mass %f is %s " % (find_mass, el.symbol)
print " number ", el.number
print " mass", el.mass
print " cov_radii", el.cov_radii
print " vdw_radii", el.vdw_radii
atomic_symb = "S"
el = pt.getelementWithSymbol(atomic_symb)
print " Element with symbol %s is %s " % (atomic_symb, el.symbol)
print " number ", el.number
print " mass", el.mass
print " cov_radii", el.cov_radii
print " vdw_radii", el.vdw_radii
def find_composition(self):
"""
Find count of each element
"""
pt = periodictable()
self.composition = np.zeros(pt.maxgid)
for pid_i, ptclObj_i in self.ptclC:
atomic_number = ptclObj_i.tagsDict["number"]
self.composition[atomic_number] += 1
def find_composition(self):
"""
Find count of each element
"""
pt = periodictable()
self.composition = np.zeros(pt.maxgid)
for pid_i, ptclObj_i in self.ptclC:
atomic_number = ptclObj_i.tagsDict["number"]
self.composition[atomic_number] += 1
def guess_radii(self):
"""
Guess radii based on type
"""
from periodictable import periodictable
# Load periodic table
pt = periodictable()
for pid, ptclObj in self:
el = pt.getelementWithSymbol(ptclObj.tagsDict["symbol"])
ptclObj.radii = el.cov_radii
return
def guess_radii(self):
"""
Guess radii based on type
"""
from periodictable import periodictable
# Load periodic table
pt = periodictable()
for pid, ptclObj in self :
el = pt.getelementWithSymbol( ptclObj.tagsDict["symbol"] )
ptclObj.radii = el.cov_radii
return
def read_lmpdata( strucC , parmC , data_file):
"""
Read Lammps data file
Arguments:
strucC (StructureContainer)
parmC (ParameterContainer)
data_file (str) data file
ReturnS:
strucC (StructureContainer)
parmC (ParameterContainer)
"""
debug = 0
verbose = True
set_chain_numbers = True
if( not set_chain_numbers ):
print " Warning not reading in chain numbers!!! "
# Load periodic table
pt = periodictable()
F = open(data_file , 'r' )
lines = F.readlines()
F.close()
#
# Read in data header with number of parameters
#
for line in lines:
col = line.split()
if ( len(col) >=2 ):
# Read in number of each topolgical component
if( col[1] == "atoms" ):
n_atoms = int( col[0] )
elif( col[1] == "bonds" ):
n_bonds = int( col[0] )
elif( col[1] == "angles" ):
n_angles = int( col[0] )
elif( col[1] == "dihedrals" ):
n_dihedrals = int( col[0] )
elif( col[1] == "impropers" ):
n_impropers = int( col[0] )
if ( len(col) >= 3 ):
# Read in number of each parameter type
if( col[1] == "atom" and col[2] == "types" ):
n_atypes = int( col[0] )
elif( col[1] == "bond" and col[2] == "types" ):
n_btypes = int( col[0] )
elif( col[1] == "angle" and col[2] == "types" ):
n_angtypes = int( col[0] )
elif( col[1] == "dihedral" and col[2] == "types" ):
n_dtypes = int( col[0] )
elif( col[1] == "improper" and col[2] == "types" ):
n_imptypes = int( col[0] )
# Read in box size
if ( len(col) >= 4 ):
if( col[2] == "xlo" and col[3] == "xhi" ):
strucC.latvec[0][0] = float( col[1] ) - float( col[0] )
if( col[2] == "ylo" and col[3] == "yhi" ):
strucC.latvec[1][1] = float( col[1] ) - float( col[0] )
if( col[2] == "zlo" and col[3] == "zhi" ):
strucC.latvec[2][2] = float( col[1] ) - float( col[0] )
# Prind debug
if( verbose ):
print " atoms ",n_atoms
print " n_bonds ",n_bonds
print " n_angles ",n_angles
print " n_dihedrals ",n_dihedrals
print " n_impropers ",n_impropers
print ""
print "n_atom_types",n_atypes
print "n_bond_types",n_btypes
print "n_angle_types",n_angtypes
print "n_dihedral_types",n_dtypes
print "n_imp_dihedral_types",n_imptypes
# Check to see if a previous read has occured
pt_overwrite = False
if( len(strucC.ptclC) > 0 ):
pt_overwrite = True
# Check of conistent number of atoms
if( pt_overwrite ):
if( len(strucC.ptclC) != n_atoms):
print " %d atoms in passed structure "%(len(strucC.ptclC))
print " %d atoms in data file "%(n_atoms)
sys.exit(" Inconsistent number of atoms " )
else:
#
# Initialize particle container
#
for pid_i in range(n_atoms):
pt_i = Particle( )
strucC.ptclC.put(pt_i)
bonds_overwrite = False
if( len(strucC.bondC) > 0 ):
bonds_overwrite = True
if( len(strucC.bondC) != n_bonds):
print " %d bonds in passed structure "%(len(strucC.bondC))
print " %d bonds in data file "%(n_bonds)
sys.exit(" Inconsistent number of bonds " )
angles_overwrite = False
if( len(strucC.angleC) > 0 ):
angles_overwrite = True
if( len(strucC.angleC) != n_angles):
print " %d angles in passed structure "%(len(strucC.angleC))
print " %d angles in data file "%(n_angles)
sys.exit(" Inconsistent number of angles " )
dih_overwrite = False
if( len(strucC.dihC) > 0 ):
dih_overwrite = True
if( len(strucC.dihC) != n_dihedrals):
print " %d dihedrals in passed structure "%(len(strucC.dihC))
print " %d dihedrals in data file "%(n_dihedrals)
sys.exit(" Inconsistent number of dihedrals " )
imp_overwrite = False
if( len(strucC.impC) > 0 ):
imp_overwrite = True
if( len(strucC.impC) != n_impropers):
print " %d impropers in passed structure "%(len(strucC.impC))
print " %d impropers in data file "%(n_impropers)
sys.exit(" Inconsistent number of impropers " )
#
# Intialize
# - read in boolean to off
#
read_Masses = 0
read_Pair = 0
read_Bond_coeff = 0
read_Angle_coeff = 0
read_Dihedral_coeff = 0
read_Improper_coeff = 0
read_Atoms = 0
read_Bonds = 0
read_Angles = 0
read_Dihedrals = 0
read_Impropers = 0
# - lists as indecise can be out of order in data file
ATYPE_REF = n_atypes*[""]
ATYPE_MASS = np.zeros(n_atypes)
ATYPE_EP = np.zeros(n_atypes)
ATYPE_SIG = np.zeros(n_atypes)
BTYPE_REF = n_btypes*[2*[""]]
BONDTYPE_R0 = np.zeros(n_btypes)
BONDTYPE_K = np.zeros(n_btypes)
ANGTYPE_REF = n_angtypes*[3*[""]]
ANGLETYPE_R0 = np.zeros(n_angtypes)
ANGLETYPE_K = np.zeros(n_angtypes)
DTYPE_REF = n_dtypes*[4*[""]]
DIHTYPE_C = np.zeros((n_dtypes,4))
DIHTYPE_F = np.zeros(n_dtypes)
DIHTYPE_K = np.zeros(n_dtypes)
DIHTYPE_PN = np.zeros(n_dtypes)
DIHTYPE_PHASE = np.zeros(n_dtypes)
IMPTYPE_REF = n_imptypes*[4*[""]]
IMPTYPE_F = np.zeros(n_imptypes)
IMPTYPE_E0 = np.zeros(n_imptypes)
IMPTYPE_K = np.zeros(n_imptypes)
MOLNUMB = n_atoms*[0]
ATYPE_IND = n_atoms*[0]
CHARGES = np.zeros(n_atoms)
R = n_atoms*[np.zeros(3)]
ATYPE = n_atoms*[""]
BONDS = n_bonds*[[0,0]]
BTYPE_IND = n_bonds*[0]
ANGLES = n_angles*[[0,0,0]]
ANGTYPE_IND = n_angles*[0]
DIH = n_dihedrals*[[0,0,0,0]]
DTYPE_IND = n_dihedrals*[0]
#
# Check if values exist and need to be updated or don't and need to be created
#
ljtyp_update = False
ljtyp_cnt = 0
if( len(parmC.ljtypC) > 0 ):
print " LJ types will be updated "
ljtyp_update = True
btyp_update = False
btyp_cnt = 0
if( len(parmC.btypC) > 0 ):
print " Bond types will be updated "
btyp_update = True
atyp_update = False
atyp_cnt = 0
if( len(parmC.atypC) > 0 ):
print " Angle types will be updated "
atyp_update = True
dtyp_update = False
dtyp_cnt = 0
if( len(parmC.dtypC) > 0 ):
print " Dihedral types will be updated "
dtyp_update = True
imptyp_update = False
imptyp_cnt = 0
if( len(parmC.imptypC) > 0 ):
print " Improper dihedrals types will be updated "
imptyp_update = True
#
# Read in data parameters
#
for line in lines:
col = line.split()
if( read_Masses and len(col) >= 2 ):
cnt_Masses += 1
ind = int(col[0]) - 1
ATYPE_MASS[ind] = float(col[1])
if( len(col) >= 4 ):
ATYPE_REF[ind] = col[3]
ptype1 = col[3]
else:
ATYPE_REF[ind] = "??"
ptype1 = "??"
mass_i = float(col[1])
if( ljtyp_update ):
ljtyp_cnt = ind + 1
if( ljtyp_cnt > len(parmC.ljtypC) ):
print "Mass index %d larger then length of previously read ljtypC %d"%(ind,len(parmC.ljtypC))
ljtyp_i = parmC.ljtypC[ljtyp_cnt]
ljtyp_i.setmass(mass_i)
else:
ljtyp_i = ljtype(ptype1)
ljtyp_i.setmass(mass_i)
parmC.ljtypC.put(ljtyp_i)
# Turn of mass read
if(cnt_Masses == n_atypes ):
read_Masses = 0
if( read_Pair and len(col) >= 3 ):
cnt_Pair += 1
ind = int(col[0]) - 1
ATYPE_EP[ind] = float(col[1])
ATYPE_SIG[ind] = float(col[2])
epsilon = float(col[1])
sigma = float(col[2])
ljtyp_ind = int(col[0])
ljtyp_i = parmC.ljtypC[ljtyp_ind]
ljtyp_i.setparam(epsilon,sigma)
# Turn pair parameter read off
if(cnt_Pair >= n_atypes ):
read_Pair = 0
if( read_Bond_coeff and len(col) >= 3 ):
cnt_Bond_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
b_ind = int( col[0]) - 1
if( b_ind > n_btypes ):
error_line = " Error in data file index of bond parameter exceeds number of bond parameters specified with bond types "
sys.exit(error_line)
BTYPE_REF[b_ind][0] = "??"
BTYPE_REF[b_ind][1] = "??"
BONDTYPE_K[b_ind] = float(col[1])
BONDTYPE_R0[b_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
lmpindx = int( col[0])
kb = float(col[1])
r0 = float(col[2])
btype = "harmonic"
g_type = 1
if( btyp_update ):
btyp_cnt = b_ind + 1
btyp_i = parmC.btypC[btyp_cnt]
btyp_i.setharmonic(r0,kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
else:
btyp_i = bondtype(ptype1,ptype2,btype)
btyp_i.setharmonic(r0,kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
parmC.btypC.put(btyp_i)
if( cnt_Bond_coeff >= n_btypes ):
read_Bond_coeff = 0
if( read_Angle_coeff and len(col) >= 3 ):
cnt_Angle_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
a_ind = int( col[0]) - 1
if( a_ind > n_angtypes ):
print sys.exit(" Error in data file index of angle parameter exceeds number of angle parameters specified with angle types ")
ANGTYPE_REF[a_ind][0] = "??"
ANGTYPE_REF[a_ind][1] = "??"
ANGTYPE_REF[a_ind][2] = "??"
ANGLETYPE_K[a_ind] = float(col[1])
ANGLETYPE_R0[a_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
lmpindx = int( col[0])
theta0 = float( col[2] ) # degrees
kb = float( col[1] )
atype = "harmonic"
gfunc_type = 1
if( atyp_update ):
atyp_cnt = a_ind + 1
atyp_i = parmC.atypC[atyp_cnt]
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0,kb)
else:
atyp_i = angletype(ptype1,ptype2,ptype3,atype)
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0,kb)
parmC.atypC.put(atyp_i)
if( cnt_Angle_coeff >= n_angtypes ):
read_Angle_coeff = 0
if( read_Dihedral_coeff and len(col) >= 3 ):
cnt_Dihedral_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
d_ind = int( col[0]) - 1
if( debug): print " reading dih type ",d_ind," cnt ",cnt_Dihedral_coeff," of ",n_dtypes
if( d_ind > n_dtypes ):
error_line = " Error in data file index of dihedral parameter %d exceeds number of dihedral parameters %d "%(d_ind , n_dtypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
DTYPE_REF[d_ind][0] = "??"
DTYPE_REF[d_ind][1] = "??"
DTYPE_REF[d_ind][2] = "??"
DTYPE_REF[d_ind][3] = "??"
# Assume OPLS dihedral type
DIHTYPE_F[d_ind] = 3
DIHTYPE_C[d_ind][0] = float(col[1])
DIHTYPE_C[d_ind][1] = float(col[2])
DIHTYPE_C[d_ind][2] = float(col[3])
DIHTYPE_C[d_ind][3] = float(col[4])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
gfunc_type = 3
dtype = "opls"
lmpindx = int( col[0] )
k1 = float( col[1] )
k2 = float( col[2] )
k3 = float( col[3] )
k4 = float( col[4] )
if( dtyp_update ):
dtyp_cnt = d_ind + 1
dtyp_i = parmC.dtypC[dtyp_cnt]
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1,k2,k3,k4)
else:
dtyp_i = dihtype(ptype1,ptype2,ptype3,ptype4,dtype)
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1,k2,k3,k4)
parmC.dtypC.put(dtyp_i)
if( cnt_Dihedral_coeff >= n_dtypes ):
read_Dihedral_coeff = 0
if( read_Improper_coeff and len(col) >= 3 ):
cnt_Improper_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
imp_ind = int( col[0]) - 1
if( debug): print " reading imp dih type ",imp_ind," cnt ",cnt_Improper_coeff," of ",n_imptypes
if( imp_ind > n_imptypes ):
error_line = " Error in data file index of improper parameter %d exceeds number of improper parameters %d "%(imp_ind , n_imptypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
IMPTYPE_REF[imp_ind][0] = "??"
IMPTYPE_REF[imp_ind][1] = "??"
IMPTYPE_REF[imp_ind][2] = "??"
IMPTYPE_REF[imp_ind][3] = "??"
# Assume OPLS dihedral type
IMPTYPE_F[imp_ind] = 2
KE = float(col[1])
Eo = float(col[2])
IMPTYPE_E0[imp_ind] = Eo
IMPTYPE_K[imp_ind] = KE
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
g_indx = 2
dtype = "improper"
lmpindx = int( col[0] )
if( imptyp_update ):
imptyp_cnt = imp_ind + 1
imptyp_i = parmC.imptypC[imptyp_cnt]
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo,KE)
imptyp_i.set_lmpindx(lmpindx)
else:
imptyp_i = imptype(ptype1,ptype2,ptype3,ptype4,dtype)
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo,KE)
imptyp_i.set_lmpindx(lmpindx)
parmC.imptypC.put(imptyp_i)
if( cnt_Improper_coeff >= n_imptypes ):
read_Improper_coeff = 0
if( read_Atoms and len(col) >= 7 ):
cnt_Atoms += 1
ind = int( col[0]) - 1
if( ind > n_atoms ):
print sys.exit(" Error in data file index of atoms exceeds number of atoms specified with atoms ")
chain_i = int(col[1])
lmptype_i = int(col[2]) #- 1
indx = int(col[2]) - 1
q_i = float(col[3])
m_i = ATYPE_MASS[indx]
fftype_i = ATYPE_REF[indx]
el = pt.getelementWithMass(m_i)
if( el.symbol == "VS" ):
el.symbol = ATYPE_l[atom_indx].strip()
fftype_i = "VS"
m_i = 0.0
# HACK !!
if( ATYPE_MASS[indx] == 9.0 ):
el.symbol = "LP"
fftype_i = "LP"
m_i = 0.0
r_i = [ float(col[4]),float(col[5]),float(col[6])]
type_i = str(lmptype_i)
#tagsD = {"chain":chain_i,"symbol":el.symbol,"number":el.number,"mass":el.mass,"cov_radii":el.cov_radii,"vdw_radii":el.vdw_radii}
#if( pt_overwrite ):
pt_i = strucC.ptclC[ind+1]
pt_i.position = r_i
update_coord = True
if( not update_coord ):
pt_i.type = el.symbol
pt_i.charge = q_i
pt_i.mass = m_i
add_dict = pt_i.tagsDict
# Set properties read in data file
if( set_chain_numbers ): add_dict["chain"] = chain_i
add_dict["symbol"] = el.symbol
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = lmptype_i
add_dict["fftype"] = fftype_i
#
add_dict["ffmass"] = ATYPE_MASS[indx]
add_dict["residue"] = chain_i
add_dict["qgroup"] = chain_i
add_dict["resname"] = "MOLR"
add_dict["ring"] = 0
add_dict["label"] = add_dict["symbol"]
pt_i.setTagsDict(add_dict)
if( cnt_Atoms >= n_atoms ):
read_Atoms = 0
if(read_Bonds and len(col) >= 4 ):
cnt_Bonds += 1
ind = int( col[0]) - 1
if( ind > n_bonds ):
print sys.exit(" Error in data file index of bonds exceeds number of bonds specified with bonds ")
BTYPE_IND[ind] = int(col[1] ) - 1
BONDS[ind] = [int(col[2]) - 1 , int(col[3]) - 1 ]
i_o = int(col[2])
j_o = int(col[3])
if( bonds_overwrite ):
bondObj = strucC.bondC[cnt_Bonds]
bondObj.pgid1 = i_o
bondObj.pgid2 = j_o
bondObj.set_lmpindx(int(col[1] ))
else:
bondObj = Bond( i_o, j_o )
bondObj.set_lmpindx(int(col[1] ))
strucC.bondC.put(bondObj)
if( cnt_Bonds >= n_bonds ):
read_Bonds = 0
if(read_Angles and len(col) >= 5 ):
cnt_Angles += 1
ind = int( col[0]) - 1
ANGTYPE_IND[ind] = int(col[1] ) - 1
ANGLES[ind] = [int(col[2]) - 1, int(col[3]) - 1, int(col[4]) - 1 ]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
if( cnt_Angles >= n_angles ):
read_Angles = 0
if( angles_overwrite ):
angleObj = strucC.angleC[cnt_Angles]
angleObj.pgid1 = k_o
angleObj.pgid2 = i_o
angleObj.pgid3 = j_o
angleObj.set_lmpindx(int(col[1] ))
else:
angleObj = Angle( k_o,i_o, j_o )
angleObj.set_lmpindx(int(col[1] ))
strucC.angleC.put(angleObj)
if(read_Dihedrals and len(col) >= 6 ):
cnt_Dihedrals += 1
ind = int( col[0]) - 1
DTYPE_IND[ind] = int(col[1] ) - 1
DIH[ind] = [int(col[2]) - 1,int(col[3]) - 1, int(col[4]) - 1,int(col[5]) - 1]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if( dih_overwrite ):
dObj = strucC.dihC[cnt_Dihedrals]
dObj.pgid1 = k_o
dObj.pgid2 = i_o
dObj.pgid3 = j_o
dObj.pgid4 = l_o
dObj.set_lmpindx(int(col[1] ))
else:
dObj = Dihedral( k_o,i_o, j_o,l_o )
dObj.set_lmpindx(int(col[1] ))
strucC.dihC.put(dObj)
if( cnt_Dihedrals >= n_dihedrals ):
read_Dihedrals = 0
if(read_Impropers and len(col) >= 2 ):
cnt_Impropers += 1
ind = int( col[0]) - 1
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if( imp_overwrite ):
impObj = strucC.impC[cnt_Impropers]
impObj.pgid1 = k_o
impObj.pgid2 = i_o
impObj.pgid3 = j_o
impObj.pgid4 = l_o
impObj.set_lmpindx(int(col[1] ))
impObj.set_type("improper")
else:
impObj = Improper( k_o,i_o, j_o,l_o )
impObj.set_lmpindx(int(col[1] ))
impObj.set_type("improper")
strucC.impC.put(impObj)
if( cnt_Impropers >= n_impropers ):
read_Impropers = 0
if ( len(col) >= 1 ):
if( col[0] == "Masses" ):
read_Masses = 1
cnt_Masses = 0
if( col[0] == "Atoms" ):
read_Atoms = 1
cnt_Atoms = 0
if( col[0] == "Bonds" ):
read_Bonds = 1
cnt_Bonds = 0
if( col[0] == "Angles" ):
read_Angles = 1
cnt_Angles = 0
if( col[0] == "Dihedrals" ):
read_Dihedrals = 1
cnt_Dihedrals = 0
if( col[0] == "Impropers" ):
read_Impropers = 1
cnt_Impropers = 0
if ( len(col) >= 2 ):
if( col[0] == "Pair" and col[1] == "Coeffs" ):
read_Pair = 1
cnt_Pair = 0
if( col[0] == "Bond" and col[1] == "Coeffs" ):
read_Bond_coeff = 1
cnt_Bond_coeff = 0
if( col[0] == "Angle" and col[1] == "Coeffs" ):
read_Angle_coeff = 1
cnt_Angle_coeff = 0
if( col[0] == "Dihedral" and col[1] == "Coeffs" ):
read_Dihedral_coeff = 1
cnt_Dihedral_coeff = 0
if( col[0] == "Improper" and col[1] == "Coeffs" ):
read_Improper_coeff = 1
cnt_Improper_coeff = 0
# cnt_Bonds += 1
# ind = int( col[0]) - 1
# BTYPE_IND[ind] = int(col[1] ) - 1
# BONDS[ind][0] = int(col[2])
# if( cnt_Bonds >= n_atoms ):
# read_Bonds = 0
#
#
if( ljtyp_update ):
if( ljtyp_cnt != len(parmC.ljtypC) ):
print " Number of LJ types read in %d does not match previously read %d "%(ljtyp_cnt,len(parmC.ljtypC))
if( debug):
for ind in range(len(ATYPE_MASS)):
print ind+1,ATYPE_MASS[ind]
for ind in range(len(ATYPE_EP)):
print ind+1,ATYPE_EP[ind],ATYPE_SIG[ind]
for ind in range(n_btypes):
print ind+1,BONDTYPE_R0[ind],BONDTYPE_K[ind]
for ind in range(n_angtypes):
print ind+1,ANGLETYPE_R0[ind],ANGLETYPE_K[ind]
for ind in range(n_dtypes):
print ind+1,DIHTYPE_C[ind]
debug =0
if( debug):
for ind in range(len(BONDS)):
print ind+1,BONDS[ind]
if(debug):
sys.exit("debug 1 ")
#
#
return (strucC,parmC)
def read_lmpdata(strucC, parmC, data_file):
"""
Read Lammps data file
Arguments:
strucC (StructureContainer)
parmC (ParameterContainer)
data_file (str) data file
ReturnS:
strucC (StructureContainer)
parmC (ParameterContainer)
"""
debug = 0
verbose = True
set_chain_numbers = True
if (not set_chain_numbers):
print " Warning not reading in chain numbers!!! "
# Load periodic table
pt = periodictable()
F = open(data_file, 'r')
lines = F.readlines()
F.close()
#
# Read in data header with number of parameters
#
for line in lines:
col = line.split()
if (len(col) >= 2):
# Read in number of each topolgical component
if (col[1] == "atoms"):
n_atoms = int(col[0])
elif (col[1] == "bonds"):
n_bonds = int(col[0])
elif (col[1] == "angles"):
n_angles = int(col[0])
elif (col[1] == "dihedrals"):
n_dihedrals = int(col[0])
elif (col[1] == "impropers"):
n_impropers = int(col[0])
if (len(col) >= 3):
# Read in number of each parameter type
if (col[1] == "atom" and col[2] == "types"):
n_atypes = int(col[0])
elif (col[1] == "bond" and col[2] == "types"):
n_btypes = int(col[0])
elif (col[1] == "angle" and col[2] == "types"):
n_angtypes = int(col[0])
elif (col[1] == "dihedral" and col[2] == "types"):
n_dtypes = int(col[0])
elif (col[1] == "improper" and col[2] == "types"):
n_imptypes = int(col[0])
# Read in box size
if (len(col) >= 4):
if (col[2] == "xlo" and col[3] == "xhi"):
strucC.latvec[0][0] = float(col[1]) - float(col[0])
if (col[2] == "ylo" and col[3] == "yhi"):
strucC.latvec[1][1] = float(col[1]) - float(col[0])
if (col[2] == "zlo" and col[3] == "zhi"):
strucC.latvec[2][2] = float(col[1]) - float(col[0])
# Prind debug
if (verbose):
print " atoms ", n_atoms
print " n_bonds ", n_bonds
print " n_angles ", n_angles
print " n_dihedrals ", n_dihedrals
print " n_impropers ", n_impropers
print ""
print "n_atom_types", n_atypes
print "n_bond_types", n_btypes
print "n_angle_types", n_angtypes
print "n_dihedral_types", n_dtypes
print "n_imp_dihedral_types", n_imptypes
# Check to see if a previous read has occured
pt_overwrite = False
if (len(strucC.ptclC) > 0):
pt_overwrite = True
# Check of conistent number of atoms
if (pt_overwrite):
if (len(strucC.ptclC) != n_atoms):
print " %d atoms in passed structure " % (len(strucC.ptclC))
print " %d atoms in data file " % (n_atoms)
sys.exit(" Inconsistent number of atoms ")
else:
#
# Initialize particle container
#
for pid_i in range(n_atoms):
pt_i = Particle()
strucC.ptclC.put(pt_i)
bonds_overwrite = False
if (len(strucC.bondC) > 0):
bonds_overwrite = True
if (len(strucC.bondC) != n_bonds):
print " %d bonds in passed structure " % (len(strucC.bondC))
print " %d bonds in data file " % (n_bonds)
sys.exit(" Inconsistent number of bonds ")
angles_overwrite = False
if (len(strucC.angleC) > 0):
angles_overwrite = True
if (len(strucC.angleC) != n_angles):
print " %d angles in passed structure " % (len(strucC.angleC))
print " %d angles in data file " % (n_angles)
sys.exit(" Inconsistent number of angles ")
dih_overwrite = False
if (len(strucC.dihC) > 0):
dih_overwrite = True
if (len(strucC.dihC) != n_dihedrals):
print " %d dihedrals in passed structure " % (len(strucC.dihC))
print " %d dihedrals in data file " % (n_dihedrals)
sys.exit(" Inconsistent number of dihedrals ")
imp_overwrite = False
if (len(strucC.impC) > 0):
imp_overwrite = True
if (len(strucC.impC) != n_impropers):
print " %d impropers in passed structure " % (len(strucC.impC))
print " %d impropers in data file " % (n_impropers)
sys.exit(" Inconsistent number of impropers ")
#
# Intialize
# - read in boolean to off
#
read_Masses = 0
read_Pair = 0
read_Bond_coeff = 0
read_Angle_coeff = 0
read_Dihedral_coeff = 0
read_Improper_coeff = 0
read_Atoms = 0
read_Bonds = 0
read_Angles = 0
read_Dihedrals = 0
read_Impropers = 0
# - lists as indecise can be out of order in data file
ATYPE_REF = n_atypes * [""]
ATYPE_MASS = np.zeros(n_atypes)
ATYPE_EP = np.zeros(n_atypes)
ATYPE_SIG = np.zeros(n_atypes)
BTYPE_REF = n_btypes * [2 * [""]]
BONDTYPE_R0 = np.zeros(n_btypes)
BONDTYPE_K = np.zeros(n_btypes)
ANGTYPE_REF = n_angtypes * [3 * [""]]
ANGLETYPE_R0 = np.zeros(n_angtypes)
ANGLETYPE_K = np.zeros(n_angtypes)
DTYPE_REF = n_dtypes * [4 * [""]]
DIHTYPE_C = np.zeros((n_dtypes, 4))
DIHTYPE_F = np.zeros(n_dtypes)
DIHTYPE_K = np.zeros(n_dtypes)
DIHTYPE_PN = np.zeros(n_dtypes)
DIHTYPE_PHASE = np.zeros(n_dtypes)
IMPTYPE_REF = n_imptypes * [4 * [""]]
IMPTYPE_F = np.zeros(n_imptypes)
IMPTYPE_E0 = np.zeros(n_imptypes)
IMPTYPE_K = np.zeros(n_imptypes)
MOLNUMB = n_atoms * [0]
ATYPE_IND = n_atoms * [0]
CHARGES = np.zeros(n_atoms)
R = n_atoms * [np.zeros(3)]
ATYPE = n_atoms * [""]
BONDS = n_bonds * [[0, 0]]
BTYPE_IND = n_bonds * [0]
ANGLES = n_angles * [[0, 0, 0]]
ANGTYPE_IND = n_angles * [0]
DIH = n_dihedrals * [[0, 0, 0, 0]]
DTYPE_IND = n_dihedrals * [0]
#
# Check if values exist and need to be updated or don't and need to be created
#
ljtyp_update = False
ljtyp_cnt = 0
if (len(parmC.ljtypC) > 0):
print " LJ types will be updated "
ljtyp_update = True
btyp_update = False
btyp_cnt = 0
if (len(parmC.btypC) > 0):
print " Bond types will be updated "
btyp_update = True
atyp_update = False
atyp_cnt = 0
if (len(parmC.atypC) > 0):
print " Angle types will be updated "
atyp_update = True
dtyp_update = False
dtyp_cnt = 0
if (len(parmC.dtypC) > 0):
print " Dihedral types will be updated "
dtyp_update = True
imptyp_update = False
imptyp_cnt = 0
if (len(parmC.imptypC) > 0):
print " Improper dihedrals types will be updated "
imptyp_update = True
#
# Read in data parameters
#
for line in lines:
col = line.split()
if (read_Masses and len(col) >= 2):
cnt_Masses += 1
ind = int(col[0]) - 1
ATYPE_MASS[ind] = float(col[1])
if (len(col) >= 4):
ATYPE_REF[ind] = col[3]
ptype1 = col[3]
else:
ATYPE_REF[ind] = "??"
ptype1 = "??"
mass_i = float(col[1])
if (ljtyp_update):
ljtyp_cnt = ind + 1
if (ljtyp_cnt > len(parmC.ljtypC)):
print "Mass index %d larger then length of previously read ljtypC %d" % (
ind, len(parmC.ljtypC))
ljtyp_i = parmC.ljtypC[ljtyp_cnt]
ljtyp_i.setmass(mass_i)
else:
ljtyp_i = ljtype(ptype1)
ljtyp_i.setmass(mass_i)
parmC.ljtypC.put(ljtyp_i)
# Turn of mass read
if (cnt_Masses == n_atypes):
read_Masses = 0
if (read_Pair and len(col) >= 3):
cnt_Pair += 1
ind = int(col[0]) - 1
ATYPE_EP[ind] = float(col[1])
ATYPE_SIG[ind] = float(col[2])
epsilon = float(col[1])
sigma = float(col[2])
ljtyp_ind = int(col[0])
ljtyp_i = parmC.ljtypC[ljtyp_ind]
ljtyp_i.setparam(epsilon, sigma)
# Turn pair parameter read off
if (cnt_Pair >= n_atypes):
read_Pair = 0
if (read_Bond_coeff and len(col) >= 3):
cnt_Bond_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
b_ind = int(col[0]) - 1
if (b_ind > n_btypes):
error_line = " Error in data file index of bond parameter exceeds number of bond parameters specified with bond types "
sys.exit(error_line)
BTYPE_REF[b_ind][0] = "??"
BTYPE_REF[b_ind][1] = "??"
BONDTYPE_K[b_ind] = float(col[1])
BONDTYPE_R0[b_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
lmpindx = int(col[0])
kb = float(col[1])
r0 = float(col[2])
btype = "harmonic"
g_type = 1
if (btyp_update):
btyp_cnt = b_ind + 1
btyp_i = parmC.btypC[btyp_cnt]
btyp_i.setharmonic(r0, kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
else:
btyp_i = bondtype(ptype1, ptype2, btype)
btyp_i.setharmonic(r0, kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
parmC.btypC.put(btyp_i)
if (cnt_Bond_coeff >= n_btypes):
read_Bond_coeff = 0
if (read_Angle_coeff and len(col) >= 3):
cnt_Angle_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
a_ind = int(col[0]) - 1
if (a_ind > n_angtypes):
print sys.exit(
" Error in data file index of angle parameter exceeds number of angle parameters specified with angle types "
)
ANGTYPE_REF[a_ind][0] = "??"
ANGTYPE_REF[a_ind][1] = "??"
ANGTYPE_REF[a_ind][2] = "??"
ANGLETYPE_K[a_ind] = float(col[1])
ANGLETYPE_R0[a_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
lmpindx = int(col[0])
theta0 = float(col[2]) # degrees
kb = float(col[1])
atype = "harmonic"
gfunc_type = 1
if (atyp_update):
atyp_cnt = a_ind + 1
atyp_i = parmC.atypC[atyp_cnt]
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0, kb)
else:
atyp_i = angletype(ptype1, ptype2, ptype3, atype)
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0, kb)
parmC.atypC.put(atyp_i)
if (cnt_Angle_coeff >= n_angtypes):
read_Angle_coeff = 0
if (read_Dihedral_coeff and len(col) >= 3):
cnt_Dihedral_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
d_ind = int(col[0]) - 1
if (debug):
print " reading dih type ", d_ind, " cnt ", cnt_Dihedral_coeff, " of ", n_dtypes
if (d_ind > n_dtypes):
error_line = " Error in data file index of dihedral parameter %d exceeds number of dihedral parameters %d " % (
d_ind, n_dtypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
DTYPE_REF[d_ind][0] = "??"
DTYPE_REF[d_ind][1] = "??"
DTYPE_REF[d_ind][2] = "??"
DTYPE_REF[d_ind][3] = "??"
# Assume OPLS dihedral type
DIHTYPE_F[d_ind] = 3
DIHTYPE_C[d_ind][0] = float(col[1])
DIHTYPE_C[d_ind][1] = float(col[2])
DIHTYPE_C[d_ind][2] = float(col[3])
DIHTYPE_C[d_ind][3] = float(col[4])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
gfunc_type = 3
dtype = "opls"
lmpindx = int(col[0])
k1 = float(col[1])
k2 = float(col[2])
k3 = float(col[3])
k4 = float(col[4])
if (dtyp_update):
dtyp_cnt = d_ind + 1
dtyp_i = parmC.dtypC[dtyp_cnt]
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1, k2, k3, k4)
else:
dtyp_i = dihtype(ptype1, ptype2, ptype3, ptype4, dtype)
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1, k2, k3, k4)
parmC.dtypC.put(dtyp_i)
if (cnt_Dihedral_coeff >= n_dtypes):
read_Dihedral_coeff = 0
if (read_Improper_coeff and len(col) >= 3):
cnt_Improper_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
imp_ind = int(col[0]) - 1
if (debug):
print " reading imp dih type ", imp_ind, " cnt ", cnt_Improper_coeff, " of ", n_imptypes
if (imp_ind > n_imptypes):
error_line = " Error in data file index of improper parameter %d exceeds number of improper parameters %d " % (
imp_ind, n_imptypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
IMPTYPE_REF[imp_ind][0] = "??"
IMPTYPE_REF[imp_ind][1] = "??"
IMPTYPE_REF[imp_ind][2] = "??"
IMPTYPE_REF[imp_ind][3] = "??"
# Assume OPLS dihedral type
IMPTYPE_F[imp_ind] = 2
KE = float(col[1])
Eo = float(col[2])
IMPTYPE_E0[imp_ind] = Eo
IMPTYPE_K[imp_ind] = KE
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
g_indx = 2
dtype = "improper"
lmpindx = int(col[0])
if (imptyp_update):
imptyp_cnt = imp_ind + 1
imptyp_i = parmC.imptypC[imptyp_cnt]
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo, KE)
imptyp_i.set_lmpindx(lmpindx)
else:
imptyp_i = imptype(ptype1, ptype2, ptype3, ptype4, dtype)
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo, KE)
imptyp_i.set_lmpindx(lmpindx)
parmC.imptypC.put(imptyp_i)
if (cnt_Improper_coeff >= n_imptypes):
read_Improper_coeff = 0
if (read_Atoms and len(col) >= 7):
cnt_Atoms += 1
ind = int(col[0]) - 1
if (ind > n_atoms):
print sys.exit(
" Error in data file index of atoms exceeds number of atoms specified with atoms "
)
chain_i = int(col[1])
lmptype_i = int(col[2]) #- 1
indx = int(col[2]) - 1
q_i = float(col[3])
m_i = ATYPE_MASS[indx]
fftype_i = ATYPE_REF[indx]
el = pt.getelementWithMass(m_i)
if (el.symbol == "VS"):
el.symbol = ATYPE_l[atom_indx].strip()
fftype_i = "VS"
m_i = 0.0
# HACK !!
if (ATYPE_MASS[indx] == 9.0):
el.symbol = "LP"
fftype_i = "LP"
m_i = 0.0
r_i = [float(col[4]), float(col[5]), float(col[6])]
type_i = str(lmptype_i)
#tagsD = {"chain":chain_i,"symbol":el.symbol,"number":el.number,"mass":el.mass,"cov_radii":el.cov_radii,"vdw_radii":el.vdw_radii}
#if( pt_overwrite ):
pt_i = strucC.ptclC[ind + 1]
pt_i.position = r_i
pt_i.charge = q_i
pt_i.mass = m_i
add_dict = pt_i.tagsDict
# Set properties read in data file
if (set_chain_numbers): add_dict["chain"] = chain_i
add_dict["symbol"] = el.symbol
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = lmptype_i
add_dict["fftype"] = fftype_i
#
add_dict["ffmass"] = ATYPE_MASS[indx]
pt_i.setTagsDict(add_dict)
if (cnt_Atoms >= n_atoms):
read_Atoms = 0
if (read_Bonds and len(col) >= 4):
cnt_Bonds += 1
ind = int(col[0]) - 1
if (ind > n_bonds):
print sys.exit(
" Error in data file index of bonds exceeds number of bonds specified with bonds "
)
BTYPE_IND[ind] = int(col[1]) - 1
BONDS[ind] = [int(col[2]) - 1, int(col[3]) - 1]
i_o = int(col[2])
j_o = int(col[3])
if (bonds_overwrite):
bondObj = strucC.bondC[cnt_Bonds]
bondObj.pgid1 = i_o
bondObj.pgid2 = j_o
bondObj.set_lmpindx(int(col[1]))
else:
bondObj = Bond(i_o, j_o)
bondObj.set_lmpindx(int(col[1]))
strucC.bondC.put(bondObj)
if (cnt_Bonds >= n_bonds):
read_Bonds = 0
if (read_Angles and len(col) >= 5):
cnt_Angles += 1
ind = int(col[0]) - 1
ANGTYPE_IND[ind] = int(col[1]) - 1
ANGLES[ind] = [int(col[2]) - 1, int(col[3]) - 1, int(col[4]) - 1]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
if (cnt_Angles >= n_angles):
read_Angles = 0
if (angles_overwrite):
angleObj = strucC.angleC[cnt_Angles]
angleObj.pgid1 = k_o
angleObj.pgid2 = i_o
angleObj.pgid3 = j_o
angleObj.set_lmpindx(int(col[1]))
else:
angleObj = Angle(k_o, i_o, j_o)
angleObj.set_lmpindx(int(col[1]))
strucC.angleC.put(angleObj)
if (read_Dihedrals and len(col) >= 6):
cnt_Dihedrals += 1
ind = int(col[0]) - 1
DTYPE_IND[ind] = int(col[1]) - 1
DIH[ind] = [
int(col[2]) - 1,
int(col[3]) - 1,
int(col[4]) - 1,
int(col[5]) - 1
]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if (dih_overwrite):
dObj = strucC.dihC[cnt_Dihedrals]
dObj.pgid1 = k_o
dObj.pgid2 = i_o
dObj.pgid3 = j_o
dObj.pgid4 = l_o
dObj.set_lmpindx(int(col[1]))
else:
dObj = Dihedral(k_o, i_o, j_o, l_o)
dObj.set_lmpindx(int(col[1]))
strucC.dihC.put(dObj)
if (cnt_Dihedrals >= n_dihedrals):
read_Dihedrals = 0
if (read_Impropers and len(col) >= 2):
cnt_Impropers += 1
ind = int(col[0]) - 1
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if (imp_overwrite):
impObj = strucC.impC[cnt_Impropers]
impObj.pgid1 = k_o
impObj.pgid2 = i_o
impObj.pgid3 = j_o
impObj.pgid4 = l_o
impObj.set_lmpindx(int(col[1]))
impObj.set_type("improper")
else:
impObj = Improper(k_o, i_o, j_o, l_o)
impObj.set_lmpindx(int(col[1]))
impObj.set_type("improper")
strucC.impC.put(impObj)
if (cnt_Impropers >= n_impropers):
read_Impropers = 0
if (len(col) >= 1):
if (col[0] == "Masses"):
read_Masses = 1
cnt_Masses = 0
if (col[0] == "Atoms"):
read_Atoms = 1
cnt_Atoms = 0
if (col[0] == "Bonds"):
read_Bonds = 1
cnt_Bonds = 0
if (col[0] == "Angles"):
read_Angles = 1
cnt_Angles = 0
if (col[0] == "Dihedrals"):
read_Dihedrals = 1
cnt_Dihedrals = 0
if (col[0] == "Impropers"):
read_Impropers = 1
cnt_Impropers = 0
if (len(col) >= 2):
if (col[0] == "Pair" and col[1] == "Coeffs"):
read_Pair = 1
cnt_Pair = 0
if (col[0] == "Bond" and col[1] == "Coeffs"):
read_Bond_coeff = 1
cnt_Bond_coeff = 0
if (col[0] == "Angle" and col[1] == "Coeffs"):
read_Angle_coeff = 1
cnt_Angle_coeff = 0
if (col[0] == "Dihedral" and col[1] == "Coeffs"):
read_Dihedral_coeff = 1
cnt_Dihedral_coeff = 0
if (col[0] == "Improper" and col[1] == "Coeffs"):
read_Improper_coeff = 1
cnt_Improper_coeff = 0
# cnt_Bonds += 1
# ind = int( col[0]) - 1
# BTYPE_IND[ind] = int(col[1] ) - 1
# BONDS[ind][0] = int(col[2])
# if( cnt_Bonds >= n_atoms ):
# read_Bonds = 0
#
#
if (ljtyp_update):
if (ljtyp_cnt != len(parmC.ljtypC)):
print " Number of LJ types read in %d does not match previously read %d " % (
ljtyp_cnt, len(parmC.ljtypC))
if (debug):
for ind in range(len(ATYPE_MASS)):
print ind + 1, ATYPE_MASS[ind]
for ind in range(len(ATYPE_EP)):
print ind + 1, ATYPE_EP[ind], ATYPE_SIG[ind]
for ind in range(n_btypes):
print ind + 1, BONDTYPE_R0[ind], BONDTYPE_K[ind]
for ind in range(n_angtypes):
print ind + 1, ANGLETYPE_R0[ind], ANGLETYPE_K[ind]
for ind in range(n_dtypes):
print ind + 1, DIHTYPE_C[ind]
debug = 0
if (debug):
for ind in range(len(BONDS)):
print ind + 1, BONDS[ind]
if (debug):
sys.exit("debug 1 ")
#
#
return (strucC, parmC)
def read_cply(self,cply_file,debug = False):
"""
Read cply file
"""
# Load periodic table
pt = periodictable()
read_lattice = False
read_segment = False
with open(cply_file) as f:
for line in f:
col = line.split()
if( read_lattice ):
self.latvec[lv_cnt][0] = float( col[0] )
self.latvec[lv_cnt][1] = float( col[1] )
self.latvec[lv_cnt][2] = float( col[2] )
if( lv_cnt == 2 ):
read_lattice = False
lv_cnt += 1
elif( read_segment ):
if( debug ):
print " Readin degment line ",col
if( str(col[0]) == 'unit' ):
if( len(col) > 2 ):
error_line = "Each segment can only have 1 unit "
error_line += "\n {} in unit line will be ignored ".format(str(col[2::]))
print error_line
segment_i['unit'] = col[1]
if( str(col[0]) == 'func' ):
segment_i['func'] = col[1::]
if( str(col[0]) == 'end' ):
read_segment = False
elif( len(col) >= 4 and col[0] != "bond" and col[0] != "#" ):
pt_i = Particle()
pt_i.type = str(col[0])
pt_i.position = [ float(col[1]),float(col[2]),float(col[3]) ]
add_dict = pt_i.tagsDict
el = pt.getelementWithSymbol(str(col[0]))
add_dict["symbol"] = str(col[0])
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cplytag"] = ""
add_dict["linkid"] = ""
add_dict["link"] = ""
pt_i.mass = el.mass
add_dict["chain"] = 1
add_dict["ring"] = 0
add_dict["residue"] = 1
add_dict["resname"] = "RES"
add_dict["qgroup"] = 1
add_dict["fftype"] = "??"
add_dict["label"] = el.symbol
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = -1
if (len(col) >= 14 ):
add_dict["label"] = str(col[4])
add_dict["fftype"] = str(col[5])
add_dict["mass"] = float(col[6])
pt_i.mass = float(col[6])
pt_i.charge = float(col[7])
add_dict["qgroup"] = int(col[8])
add_dict["ring"] = int(col[9])
add_dict["residue"] = int(col[10])
add_dict["resname"] = str(col[11])
add_dict["chain"] = int(col[12])
add_dict["cplytag"] = str(col[13])
elif (len(col) == 13 ):
add_dict["label"] = str(col[4])
add_dict["fftype"] = str(col[5])
add_dict["mass"] = float(col[6])
pt_i.mass = float(col[6])
pt_i.charge = float(col[7])
add_dict["qgroup"] = int(col[8])
add_dict["ring"] = int(col[9])
add_dict["residue"] = int(col[10])
add_dict["resname"] = str(col[11])
add_dict["chain"] = int(col[12])
elif (len(col) == 8 ):
add_dict["residue"] = int(col[5])
add_dict["resname"] = str(col[6])
add_dict["cplytag"] = str(col[7])
elif (len(col) == 7 ):
pt_i.charge = float(col[4])
add_dict["residue"] = int(col[5])
add_dict["resname"] = str(col[6])
elif (len(col) == 5 ):
add_dict["cplytag"] = str(col[4])
pt_i.setTagsDict(add_dict)
self.ptclC.put(pt_i)
# # # print "debug pt_i ",len(col),pt_i
elif(len(col) >= 3 ):
if( col[0] == "bond"):
b_i = int(col[1])
b_j = int(col[2])
bnd = Bond(b_i,b_j)
#print "process_line bond line ",col
self.bondC.put(bnd)
# Key word search
if( len(col) > 0 ):
if( str(col[0]) == 'lattice' ):
read_lattice = True
lv_cnt = 0
if( str(col[0]) == 'segment' ):
read_segment = True
segment_i = {} #segment(str(col[1]))
# segment_i = segment()
segment_i['tag'] = str(col[1])
segment_i['segment'] = {}
self.segments.append(segment_i)
if( debug ):
print segments
sys.exit("debug in read_cply is 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_cply(options.in_cply)
search_i = dict()
search_i = create_search(search_i,options.symbol,options.label,options.fftype,options.residue,options.resname,options.chain,options.ring)
if( len(search_i) > 0 ):
if( options.verbose ):
log_line = "\n Searching group i {} {} ".format(search_i,len(search_i))
#log_out.write(log_line)
if( options.verbose ): print log_line
list_i = bb_o.ptclC.getParticlesWithTags(search_i)
bb_i = bb_o.getSubStructure(list_i, particlesOnly=False )
else:
bb_i = bb_o
if( len(bb_i.bondC) == 0 or options.rebond ):
bb_i.bondC.clear()
bb_i.ptclC.guess_radii()
bb_i.build_bonded_nblist(max_nn=12.0,radii_buffer=1.25)
bb_i.nblist_bonds()
else:
bb_i.bondC_nblist()
if( options.setqgroup ): bb_i.set_chargegroups()
bb_i.find_max_qgroup_id()
if( options.setresidues ): bb_i.set_residues()
if( options.setlabel ): bb_i.set_label()
if( options.setmass ): bb_i.set_mass()
if( options.setrings ): bb_i.find_rings()
if( options.setfftype ):
bb_i.oplsaa_atomtypes()
bb_i.atomtypes()
set_biaryl = False
if(set_biaryl):
bb_i.biaryl_types()
bb_i.interring_types()
bb_i.write_qgroup()
# Set connecting termcap particles to lay along the x axis and the second connecter term to be at origin
bb_i.align_termcaps()
print bb_i
comment = "Read in from {} to output {} ".format(options.in_cply,options.out_id)
append = False
bb_i.ptclC.write_xmol("{}.xyz".format(options.out_id),comment,append)
bb_i.write_cply("{}.cply".format(options.out_id),write_ff=True,write_bonds=True)
del bb_i
def read_cply(self, cply_file, debug=False):
"""
Read cply file
"""
# Load periodic table
pt = periodictable()
read_lattice = False
read_segment = False
with open(cply_file) as f:
for line in f:
col = line.split()
if (read_lattice):
self.latvec[lv_cnt][0] = float(col[0])
self.latvec[lv_cnt][1] = float(col[1])
self.latvec[lv_cnt][2] = float(col[2])
if (lv_cnt == 2):
read_lattice = False
lv_cnt += 1
elif (read_segment):
if (debug):
print " Readin degment line ", col
if (str(col[0]) == 'unit'):
if (len(col) > 2):
error_line = "Each segment can only have 1 unit "
error_line += "\n {} in unit line will be ignored ".format(
str(col[2::]))
print error_line
segment_i['unit'] = col[1]
if (str(col[0]) == 'func'):
segment_i['func'] = col[1::]
if (str(col[0]) == 'end'):
read_segment = False
elif (len(col) >= 4 and col[0] != "bond" and col[0] != "#"):
pt_i = Particle()
pt_i.type = str(col[0])
pt_i.position = [
float(col[1]),
float(col[2]),
float(col[3])
]
add_dict = pt_i.tagsDict
el = pt.getelementWithSymbol(str(col[0]))
add_dict["symbol"] = str(col[0])
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cplytag"] = ""
add_dict["linkid"] = ""
add_dict["link"] = ""
pt_i.mass = el.mass
add_dict["chain"] = 1
add_dict["ring"] = 0
add_dict["residue"] = 1
add_dict["resname"] = "RES"
add_dict["qgroup"] = 1
add_dict["fftype"] = "??"
add_dict["label"] = el.symbol
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = -1
if (len(col) >= 14):
add_dict["label"] = str(col[4])
add_dict["fftype"] = str(col[5])
add_dict["mass"] = float(col[6])
pt_i.mass = float(col[6])
pt_i.charge = float(col[7])
add_dict["qgroup"] = int(col[8])
add_dict["ring"] = int(col[9])
add_dict["residue"] = int(col[10])
add_dict["resname"] = str(col[11])
add_dict["chain"] = int(col[12])
add_dict["cplytag"] = str(col[13])
elif (len(col) == 13):
add_dict["label"] = str(col[4])
add_dict["fftype"] = str(col[5])
add_dict["mass"] = float(col[6])
pt_i.mass = float(col[6])
pt_i.charge = float(col[7])
add_dict["qgroup"] = int(col[8])
add_dict["ring"] = int(col[9])
add_dict["residue"] = int(col[10])
add_dict["resname"] = str(col[11])
add_dict["chain"] = int(col[12])
elif (len(col) == 8):
add_dict["residue"] = int(col[5])
add_dict["resname"] = str(col[6])
add_dict["cplytag"] = str(col[7])
elif (len(col) == 7):
pt_i.charge = float(col[4])
add_dict["residue"] = int(col[5])
add_dict["resname"] = str(col[6])
elif (len(col) == 5):
add_dict["cplytag"] = str(col[4])
pt_i.setTagsDict(add_dict)
self.ptclC.put(pt_i)
# # # print "debug pt_i ",len(col),pt_i
elif (len(col) >= 3):
if (col[0] == "bond"):
b_i = int(col[1])
b_j = int(col[2])
bnd = Bond(b_i, b_j)
#print "process_line bond line ",col
self.bondC.put(bnd)
# Key word search
if (len(col) > 0):
if (str(col[0]) == 'lattice'):
read_lattice = True
lv_cnt = 0
if (str(col[0]) == 'segment'):
read_segment = True
segment_i = {} #segment(str(col[1]))
# segment_i = segment()
segment_i['tag'] = str(col[1])
segment_i['segment'] = {}
self.segments.append(segment_i)
if (debug):
print segments
sys.exit("debug in read_cply is True ")
