def load_smrff(cls,
parsed_file,
pfile_name=None,
restrict=None,
adjust_range=False):
'''
Given a parameter file, inport the coulomb parameters if possible.
**Parameters**
parsed_file: *str*
A parsed smrff parameter file input string (no comments or
trailing white spaces)
pfile_name: *str*
The name of a parameter file to be parsed. If specified,
then parsed_file is ignored (you may simply pass None as
parsed_file).
restrict: *list, str, optional*
A list of atom labels to include when loading. If not
specified, everything is loaded.
adjust_range: *bool, optional*
Whether to adjust the parameter bounds to account for read
in values, or not.
**Returns**
lj_objs: *list,* :class:`squid.forcefields.lj.LJ`, or *None*
Returns a list of LJ objects if possible, else None.
'''
import squid.forcefields.smrff as smrff_utils
# Ensure correct pfile format, and that we even need to parse it.
if pfile_name is not None:
parsed_file = smrff_utils.parse_pfile(pfile_name)
if LJ_PFILE_ID not in parsed_file:
return []
parsed_file = parsed_file[parsed_file.index(LJ_PFILE_ID):]
parsed_file = parsed_file[:parsed_file.index(END_ID)].split("\n")[1:-1]
parsed_file = [cls.parse_line(line) for line in parsed_file]
return [
cls(index=index,
sigma=sigma,
epsilon=epsilon,
adjust_range=adjust_range)
for index, sigma, epsilon in parsed_file
if check_restriction(index, restrict)
]
def load_opls(cls, dihedral_types, pfptr=None, restrict=None):
"""
Given a parameter file, inport the Dihedral parameters if possible.
**Parameters**
dihedral_types: *list,* :class:`structures.Struct`
Dihedral types from a parsed opls parameter file.
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
dihedral_objs: *list, Dihedral*, or *None*
Returns a list of Dihedral objects if possible, else None.
"""
import squid.forcefields.opls as opls_utils
if pfptr is not None:
_, _, _, dihedral_types = opls_utils.parse_pfile(pfptr)
return [
cls(indices=t.index2s, energies=t.e, equilibs=[])
for t in dihedral_types if check_restriction(t.index2s, restrict)
]
def load_smrff(cls, parsed_file, pfile_name=None, restrict=None):
'''
Given a parameter file, inport the coulomb parameters if possible.
**Parameters**
parsed_file: *str*
A parsed smrff parameter file input string (no comments or
trailing white spaces)
pfile_name: *str*
The name of a parameter file to be parsed. If specified,
then parsed_file is ignored (you may simply pass None as
parsed_file).
restrict: *list, str, optional*
A list of atom labels to include when loading. If not
specified, everything is loaded.
**Returns**
coul_objs: *list,* :class:`squid.forcefields.coulomb.Coul`, or *None*
Returns a list of Coul objects if possible, else None.
'''
import squid.forcefields.smrff as smrff_utils
# Ensure correct pfile format, and that we even need to parse it.
if pfile_name is not None:
parsed_file = smrff_utils.parse_pfile(pfile_name)
if COUL_PFILE_ID not in parsed_file:
return []
parsed_file = parsed_file[parsed_file.index(COUL_PFILE_ID):]
parsed_file = parsed_file[:parsed_file.index(END_ID)].split("\n")[1:-1]
parsed_file = [cls.parse_line(line) for line in parsed_file]
return [
cls(index=index, charge=charge, element=element, mass=mass)
for index, charge, element, mass in parsed_file
if check_restriction(index, restrict)
]
def load_opls(cls, atom_types, pfptr=None, restrict=None):
'''
Given a parameter file, inport the LJ parameters if possible.
**Parameters**
atom_types: *list,* :class:`structures.Struct`
Atom types from a parsed opls parameter file.
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
lj_objs: *list, LJ*, or *None*
Returns a list of LJ objects if possible, else None.
'''
# Ensure correct pfile format, and that we even need to parse it.
import squid.forcefields.opls as opls_utils
if pfptr is not None:
atom_types, _, _, _ = opls_utils.parse_pfile(pfptr)
return [
cls(index=t.index, sigma=t.vdw_r, epsilon=t.vdw_e)
for t in atom_types if check_restriction(t, restrict)
]
def dump_pair_coeffs(self, restricts, map_to_lmp_index=True):
'''
Get the smrff lammps input line for this smooth function. Specifically
the pair_coeff line.
**Parameters**
restricts: *list, str*
A list of the atom types and how they apply to LAMMPS. For
example, assume restricts = ["xA", "xB"], then atoms of
index xA will be 1 in LAMMPS dumps and atoms of xB will be
2 in LAMMPS dumps.
map_to_lmp_index: *bool, optional*
Whether to map the pair coeffs to the lmp indices or not.
**Returns**
pair_str: *str*
The pair coefficients in LAMMPS input script line format.
'''
self.validate()
# Handle restrict appropriately
if self.atom_i != "*" and not check_restriction(
self.atom_i, restricts):
return ""
if self.atom_j != "*" and not check_restriction(
self.atom_j, restricts):
return ""
if self.atom_i is None:
ai = "*"
else:
if map_to_lmp_index:
ai = restricts.index(self.atom_i) + 1
else:
ai = self.atom_i
if self.atom_j is None:
aj = "*"
else:
if map_to_lmp_index:
aj = restricts.index(self.atom_j) + 1
else:
aj = self.atom_j
if self.lr is None or 'inout' in self.lr:
style_name = 'sin_inout'
elif self.lr == 'l':
style_name = 'sin_l'
elif self.lr == 'r':
style_name = 'sin_r'
else:
raise Exception("Error - somehow style name is unknown")
dists = [self.r_in, self.d_in]
dists = ' '.join(["%.2f" % x for x in dists])
line = "pair_coeff %s %s %s %d %s"\
% (ai, aj, style_name, self.smooth_index, dists)
return line
def dump_pair_coeffs(self, restricts, skip_restricts=False):
'''
Get the smrff lammps input line for this smooth function. Specifically
the pair_coeff line.
'''
self.validate()
# Handle restrict appropriately
if self.atom_i is not "*" and not check_restriction(
self.atom_i, restricts):
return ""
if self.atom_j is not "*" and not check_restriction(
self.atom_j, restricts):
return ""
if self.atom_i is None:
ai = "*"
else:
if not skip_restricts:
ai = restricts.index(self.atom_i) + 1
else:
ai = self.atom_i
if self.atom_j is None:
aj = "*"
else:
if not skip_restricts:
aj = restricts.index(self.atom_j) + 1
else:
aj = self.atom_j
if self.lr is None or 'inout' in self.lr:
style_name = 'sin_inout'
elif self.lr == 'l':
style_name = 'sin_l'
elif self.lr == 'r':
style_name = 'sin_r'
else:
raise Exception("Error - somehow style name is unknown")
dists = [self.r_in, self.d_in]
if style_name == 'sin_inout':
dists += [self.r_out, self.d_out]
offset_couple = style_name == 'sin_inout'
dists = ' '.join(["%.2f" % x for x in dists])
line = "pair_coeff %s %s %s %d %s" % (ai, aj, style_name,
self.smooth_index, dists)
if self.coupled:
if self.c_lr is None or 'inout' in self.c_lr:
style_name = 'sin_inout'
elif self.c_lr == 'l':
style_name = 'sin_l'
elif self.c_lr == 'r':
style_name = 'sin_r'
else:
raise Exception("Error - somehow style name is unknown")
dists = [
self.r_in, self.d_in, self.r_out, self.d_out, self.c_r,
self.c_d
]
if offset_couple:
dists = dists[2:]
if None in dists:
dists = dists[:dists.index(None)]
dists = ' '.join(["%.2f" % x for x in dists])
line += "\n"
line += "pair_coeff %s %s %s %d %s" % (ai, aj, style_name,
self.c_s_index, dists)
return line
def load_smrff(cls, pfile, pfptr=None, restrict=None):
'''
Given a parameter file, inport the tersoff parameters if possible.
**Parameters**
pfile: *str*
A parsed smrff parameter file input string (no comments or
trailing white spaces)
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
tersoff_objs: *list, Tersoff*, or *None*
Returns a list of Tersoff objects if possible, else None.
'''
# Ensure correct pfile format, and that we even need to parse it.
if pfptr is not None:
pfile = smrff_utils.parse_pfile(pfptr)
if TERSOFF_PFILE_ID not in pfile:
return []
pfile = pfile[pfile.index(TERSOFF_PFILE_ID):]
pfile = pfile[:pfile.index(END_ID)].split("\n")[1:-1]
# Because Tersoff may be split into two lines, we need additional parsing
# Each line should have 17 things in it:
# 3 indices, 14 tersoff parameters
pfile = ' '.join(pfile).strip().split()
assert len(
pfile
) % 17 == 0, "Error - there appears to be an issue in how the Tersoff parameters are defined."
pfile = [
' '.join(pfile[i * 17:(i + 1) * 17])
for i in range(int(len(pfile) / 17))
]
pfile = [cls.parse_line(line) for line in pfile]
# indices, m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
return [
cls(indices=indices,
m=m,
gamma=gamma,
lambda3=lambda3,
c=c,
d=d,
costheta0=costheta0,
n=n,
beta=beta,
lambda2=lambda2,
B=B,
R=R,
D=D,
lambda1=lambda1,
A=A) for indices, m, gamma, lambda3, c, d, costheta0, n, beta,
lambda2, B, R, D, lambda1, A in pfile
if check_restriction(indices, restrict)
]