def load_smrff(cls, pfile, pfptr=None, restrict=None):
'''
Given a parameter file, import the Morse 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)
(For programmer: The name of this parameter must be changed. It is hard to understand.)
**Returns**
Morse_objs: *list, Morse*, or *None*
Returns a list of Morse 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 pfptr is not None:
pfile = smrff_utils.parse_pfile(pfptr)
if MORSE_PFILE_ID not in pfile:
return []
pfile = pfile[pfile.index(MORSE_PFILE_ID):]
pfile = pfile[:pfile.index(END_ID)].split("\n")[1:-1]
pfile = [cls.parse_line(line) for line in pfile]
return [
cls(indices=indices, D0=D0, alpha=alpha, r0=r0, rc=rc, line=None)
for indices, D0, alpha, r0, rc in pfile
if check_restriction(indices, restrict)
]
def load_smrff(cls, pfile, pfptr=None, restrict=None):
'''
Given a parameter file, inport the LJ 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**
lj_objs: *list, 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 pfptr is not None:
pfile = smrff_utils.parse_pfile(pfptr)
if LJ_PFILE_ID not in pfile:
return []
pfile = pfile[pfile.index(LJ_PFILE_ID):]
pfile = pfile[:pfile.index(END_ID)].split("\n")[1:-1]
pfile = [cls.parse_line(line) for line in pfile]
return [
cls(index=index, sigma=sigma, epsilon=epsilon)
for index, sigma, epsilon in pfile
if check_restriction(index, restrict)
]
def load_smrff(cls,
parsed_file,
pfile_name=None,
restrict=None,
adjust_range=False):
'''
Given a parameter file, import the Morse 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 default bounds range to account for
read in values from a file being out of bounds.
**Returns**
Morse_objs: *list,* :class:`squid.forcefields.morse.Morse`, or *None*
Returns a list of Morse objects if possible, else None.
'''
import squid.forcefields.smrff as smrff_utils
# Ensure correct parsed_file format, and that we even need to parse it.
if pfile_name is not None:
parsed_file = smrff_utils.parse_pfile(pfile_name)
if MORSE_PFILE_ID not in parsed_file:
return []
parsed_file = parsed_file[parsed_file.index(MORSE_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(indices=indices,
D0=D0,
alpha=alpha,
r0=r0,
rc=rc,
line=None,
adjust_range=adjust_range)
for indices, D0, alpha, r0, rc in parsed_file
if check_restriction(indices, restrict)
]
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_smrff(cls, pfile, pfptr=None, restrict=None):
'''
Given a parameter file, inport the smooth 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**
smooth_objs: *list, smooth*, or *None*
Returns a list of smooth 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 pfptr is not None:
pfile = smrff_utils.parse_pfile(pfptr)
if SMOOTH_PFILE_ID not in pfile:
return []
pfile = pfile[pfile.index(SMOOTH_PFILE_ID):]
pfile = pfile[:pfile.index(END_ID)].split("\n")[1:-1]
pfile = [cls.parse_line(line) for line in pfile]
return [
cls(smooth_index,
atom_i,
atom_j,
r_in,
d_in,
gcut,
r_out=r_out,
d_out=d_out,
lr=lr,
c_r=c_r,
c_d=c_d,
c_lr=c_lr,
c_gcut=c_gcut,
c_s_index=c_s_index)
for smooth_index, atom_i, atom_j, r_in, d_in, r_out, d_out, c_r,
c_d, gcut, c_gcut, lr, c_lr, c_s_index in pfile
if check_restriction(atom_i, restrict)
and check_restriction(atom_j, restrict)
]
def load_smrff(cls, parsed_file, pfile_name=None, restrict=None):
'''
Given a parameter file, inport the smooth 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**
smooth_objs: *list,* :class:`squid.forcefields.sinSmooth.lr.SmoothSinInOut`, or *None*
Returns a list of smooth objects if possible, else None.
'''
import squid.forcefields.smrff as smrff_utils
# Ensure correct parsed_file format, and that we even need to parse it.
if pfile_name is not None:
parsed_file = smrff_utils.parse_pfile(pfile_name)
if SMOOTH_PFILE_ID not in parsed_file:
return []
parsed_file = parsed_file[parsed_file.index(SMOOTH_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
if is_numeric(line.split()[0]) and len(line.split()) == 9
]
return [
cls(smooth_index, atom_i, atom_j, r_in, d_in, gcut_in, r_out,
d_out, gcut_out) for smooth_index, atom_i, atom_j, r_in, d_in,
gcut_in, r_out, d_out, gcut_out in parsed_file
if check_restriction(atom_i, restrict)
and check_restriction(atom_j, 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_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)
]