def compute(self, gpos=None, vtens=None):
'''
Consider a rotation of the entire system such that the ``a`` vector
is aligned with the X-axis, the ``b`` vector is in the XY-plane, and
the ``c`` vector chosen such that a right-handed basis is formed.
The rotated cell is lower-diagonal in the Yaff notation.
In this rotated system, it is fairly simple to compute the required
projections and derivatives, because the projections are simply the
Cartesian components. Values obtained in the rotated system are then
transformed back to the original system.
'''
# Compute rotation that makes cell lower diagonal
_, R = cell_lower(self.system.cell.rvecs)
# The projected vector of centers of mass difference (aka the
# collective variable) in the rotated system
cv_orig = np.sum(self.weights.reshape((-1, 1)) * self.system.pos,
axis=0)
# Transform back to the original system
cv = np.dot(R, cv_orig)
self.value = cv[self.index]
if gpos is not None:
gpos[:] = 0.0
gpos[:, self.index] = self.weights
# Forces (vector) need to be rotated back to original system
gpos[:] = np.einsum('ij,kj', gpos, R.T)
if vtens is not None:
vtens[:] = 0.0
vtens[self.index, self.index:] = cv[self.index:]
vtens[self.index:, self.index] = cv[self.index:]
# Virial (tensor) needs to be rotated back to original system
vtens[:] = np.dot(R.T, np.dot(vtens[:], R))
return self.value
def update_rvecs(self, rvecs):
# Find cell vectors in LAMMPS format
self.rvecs[:], self.rot[:] = cell_lower(rvecs)
self.cell.update_rvecs(self.rvecs)
if self.triclinic:
self.lammps.command("change_box all x final %f %30.20f y final %f %30.20f z final %f %30.20f xy final %30.20f xz final %30.20f yz final %30.20f\n" %
(0.0,self.rvecs[0,0],0.0,self.rvecs[1,1], 0.0, self.rvecs[2,2], self.rvecs[1,0],self.rvecs[2,0],self.rvecs[2,1]))
else:
self.lammps.command("change_box all x final %f %30.20f y final %f %30.20f z final %f %30.20f\n" %
(0.0,self.rvecs[0,0],0.0,self.rvecs[1,1], 0.0, self.rvecs[2,2]))
def write_lammps_system_data(system,
ff=None,
fn='lammps.data',
triclinic=True):
'''
Write information about a Yaff system to a LAMMPS data file
Following information is written: cell vectors, atom type ids
and topology (as defined by the bonds)
**Arguments**
system
Yaff system
fn
Filename to write the LAMMPS data to
triclinic
Boolean, specify whether a triclinic cell will be used during
the simulation. If the cell is orthogonal, set it to False
as LAMMPS should run slightly faster.
Default: True
'''
if system.cell.nvec != 3:
raise ValueError(
'The system must be 3D periodic for Lammps calculations.')
if system.ffatypes is None:
raise ValueError('Atom types need to be defined.')
if system.bonds is None:
raise ValueError('Bonds need to be defined')
if system.charges is None:
if log.do_warning:
log.warn(
"System has no charges, writing zero charges to LAMMPS file")
charges = np.zeros((system.natom, ))
else:
charges = system.charges
if ff is None:
ffatypes, ffatype_ids = system.ffatypes, system.ffatype_ids
else:
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
fdat = open(fn, 'w')
fdat.write(
"Generated by Yaff\n\n%20d atoms\n%20d bonds\n%20d angles \n%20d dihedrals\n%20d impropers\n\n"
% (system.natom, system.nbond, 0, 0, 0))
fdat.write(
"%20d atom types\n%20d bond types\n%20d angle types\n%20d dihedral types\n%20d improper types\n\n"
% (np.amax(ffatype_ids) + 1, 1, 0, 0, 0))
rvecs, R = cell_lower(system.cell.rvecs)
pos = np.einsum('ij,kj', system.pos, R)
fdat.write(
"%30.24f %30.24f xlo xhi\n%30.24f %30.24f ylo yhi\n%30.24f %30.24f zlo zhi\n"
% (0.0, rvecs[0, 0], 0.0, rvecs[1, 1], 0.0, rvecs[2, 2]))
if triclinic:
fdat.write("%30.24f %30.24f %30.24f xy xz yz\n" %
(rvecs[1, 0], rvecs[2, 0], rvecs[2, 1]))
fdat.write("Atoms\n\n")
for i in range(system.natom):
fdat.write("%5d %3d %3d %30.24f %30.24f %30.24f %30.24f\n" %
(i + 1, 1, ffatype_ids[i] + 1, charges[i], pos[i, 0],
pos[i, 1], pos[i, 2]))
fdat.write("\nBonds\n\n")
for i in range(system.nbond):
fdat.write("%5d %3d %5d %5d\n" %
(i + 1, 1, system.bonds[i, 0] + 1, system.bonds[i, 1] + 1))
fdat.close()
def ff2lammps(system,
parameter_fns,
dn,
triclinic=True,
rcut=12.0 * angstrom,
switch=4.0 * angstrom,
smooth_ei=False,
tailcorrections=True,
mode='md',
unit_style='electron',
tabulated=False):
'''
Convert a Yaff ForceField parameter file and accompanying System instance
to LAMMPS input files. Not all potentials available in Yaff are
transferable to LAMMPS.
**Arguments:**
system
Yaff system instance
parameter_fns
A single filename or a list of filenames
dn
Directory where files will be saved. Existing files will be
overwritten without warning.
**Optional arguments:**
triclinic
Boolean, specify whether a triclinic cell will be used during
the simulation. If the cell is orthogonal, set it to False
as LAMMPS should run slightly faster.
Default: True
rcut
The real space cutoff used by all pair potentials.
switch
The width of the Switch3 truncation. Set to 0 to turn off truncation.
smooth_ei
Flag for smooth truncations for the electrostatic interactions.
Currently not available in LAMMPS, so has to be False
tailcorrections
Boolean: if true, apply a correction for the truncation of the
pair potentials assuming the system is homogeneous in the
region where the truncation modifies the pair potential
mode
One of ``md``, ``library``, or ``test``, indicating the input
directives for LAMMPS
``md``: generic input file for MD simulations
``library``: generic input file for using LAMMPS as a library
``test``: provide excessive output in order to debug things
unit_style
One of ``real`` or ``electron``, see
https://lammps.sandia.gov/doc/units.html for details
tabulated
Boolean; if True, the van der Waals interactions will be read from
a lammps.table file, which can be generated with the
``write_lammps_table`` function.
'''
# Check some properties of the supplied system
if system.cell.nvec != 3:
raise ValueError(
'The system must be 3d periodic for Lammps calculations.')
if system.ffatypes is None:
raise ValueError('Atom types need to be defined.')
if system.bonds is None:
raise ValueError('Bonds need to be defined')
if system.masses is None:
if log.do_high:
log("Setting standard masses")
system.set_standard_masses()
if not unit_style in lammps_units.keys():
raise ValueError('Invalid unit style selected')
if smooth_ei:
raise ValueError(
'smooth_ei should be set to False. '
'Note that using smooth_ei=True in YAFF introduces an artificial '
'effect, that however should be very small when using proper settings.'
)
# Select the LAMMPS units
units = lammps_units[unit_style]
# Apply the parameters of the force field to the system
parameters = apply_lammps_generators(system,
Parameters.from_file(parameter_fns))
if system.charges is None: charges = np.zeros((system.natom, ))
else: charges = system.charges
if system.radii is None: radii = np.zeros((system.natom, ))
else: radii = system.radii
# Use atom types compatible with tables
if tabulated:
ff = ForceField.generate(system, parameter_fns)
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
else:
ffatypes, ffatype_ids = system.ffatypes, system.ffatype_ids
# The following dictionary maps prefixes appearing in the Yaff ForceField
# file to corresponding LAMMPS potentials, including the type of potential
# and the dimensions of the paramters.
all_prefixes = {
'MM3QUART':
('Bond', 'mm3',
[units['energy'] / units['distance']**2 / 0.5, units['distance']]),
'BONDTABLE': ('Bond', 'table', []),
'BONDHARM':
('Bond', 'harmonic',
[units['energy'] / units['distance']**2 / 0.5, units['distance']]),
'BONDMORSE':
('Bond', 'morse',
[units['energy'], 1.0 / units['distance'], units['distance']]),
'MM3BENDA': ('Angle', 'mm3', [units['energy'] / rad**2 / 0.5, deg]),
'BENDAHARM':
('Angle', 'harmonic', [units['energy'] / rad**2 / 0.5, deg]),
'BENDCOS': ('Angle', 'cosine/periodic',
[1, units['energy'] * 4.0, deg]),
'BENDCHARM': ('Angle', 'cosine/squared', [units['energy'] / 0.5, deg]),
'CROSS': ('Angle', 'cross', [
units['energy'] / units['distance']**2,
units['energy'] / units['distance'] / rad,
units['energy'] / units['distance'] / rad, units['distance'],
units['distance'], deg
]),
'TORSION': ('Dihedral', 'fourier', [1, units['energy'], deg]),
'OOPDIST':
('Improper', 'distharm',
[units['energy'] / units['distance']**2 / 0.5, units['distance']]),
'SQOOPDIST':
('Improper', 'sqdistharm',
[units['energy'] / units['distance']**4 / 0.5, units['distance']**2]),
'MM3': ('Pair', 'mm3'),
'LJ': ('Pair', 'lj'),
'FIXQ': ('Charge', 'coul')
}
# Find out which prefixes need to be treated and how
present_prefixes = {
'Bond': [],
'Angle': [],
'Dihedral': [],
'Improper': [],
'Pair': [],
'Charge': []
}
for prefix in parameters.keys():
present_prefixes[all_prefixes[prefix][0]].append(prefix)
assert len(
present_prefixes['Pair']
) <= 1, "There should be at most one van der Waals contribution!"
assert len(present_prefixes['Charge']
) == 1, "There should be one electrostatic contribution!"
# Count how many different coefficients and terms are present for each
# type of internal coordinate
counters = {}
for term in ['Bond', 'Angle', 'Dihedral', 'Improper']:
ncoeffs, nterms = 0, 0
for prefix in present_prefixes[term]:
ncoeffs += len(parameters[prefix][1])
nterms += len(parameters[prefix][0])
counters[term] = (ncoeffs, nterms)
if tabulated and not np.all(system.radii == 0.0):
# Potential messy situation: if a table is used to specify vdW
# interactions and Gaussian electrostatics is used, the correction
# due to Gaussian electrostatics is included in the vdW table. This
# poses a problem when different scaling rules for vdW and EI are used.
# If this is the case, we correct for this by including the scaled
# electrostatics as bonded terms. Note that this possibly messes up the
# topology LAMMPS uses, as for instance 1-3 neighbors will become
# pseudo-bonded.
scales_lj = parameters[present_prefixes['Pair'][0]][1]
scales_ei = parameters[present_prefixes['Charge'][0]][1]
# Get unique combinations of charges and radii
ei_terms, ei_data = [], []
parameters['BONDTABLE'] = [[], []]
dists = []
npoints_table, rmin, rmax = 1000, 0.5 * angstrom, 5.5 * angstrom
# Add 1-2 electrostatics to the bond terms
if scales_ei[1] != scales_lj[1]:
rescale = scales_ei[1] - scales_lj[1]
for i, j in system.bonds:
gamma = np.sqrt(system.radii[i]**2 + system.radii[j]**2)
comb = (rescale * system.charges[i] * system.charges[j], gamma)
if not comb in ei_data:
parameters['BONDTABLE'][1].append(
("btab%03d" % len(ei_data)))
ei_data.append(comb)
ei_terms.append([i, j, ei_data.index(comb)])
parameters['BONDTABLE'][0].append((ei_data.index(comb), [i,
j]))
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
dists.append(np.linalg.norm(delta))
# Add 1-3 electrostatic interactions as bond terms
if scales_ei[2] != scales_lj[2]:
rescale = scales_ei[2] - scales_lj[2]
realangles = []
for i, _, k in system.iter_angles():
if [i, k] in realangles: continue
realangles.append([i, k])
for i, k in realangles:
gamma = np.sqrt(system.radii[i]**2 + system.radii[k]**2)
comb = (rescale * system.charges[i] * system.charges[k], gamma)
if not comb in ei_data:
parameters['BONDTABLE'][1].append(
("btab%03d" % len(ei_data)))
ei_data.append(comb)
ei_terms.append([i, k, ei_data.index(comb)])
parameters['BONDTABLE'][0].append((ei_data.index(comb), [i,
k]))
delta = system.pos[i] - system.pos[k]
system.cell.mic(delta)
dists.append(np.linalg.norm(delta))
dists = np.asarray(dists)
if np.amin(dists) < rmin: raise ValueError
if np.amax(dists) > rmax: raise ValueError
# Update general bond information
ncoeffs, nterms = counters["Bond"]
ncoeffs += len(ei_data)
nterms += len(ei_terms)
counters["Bond"] = (ncoeffs, nterms)
present_prefixes['Bond'].append('BONDTABLE')
# Write the tables
fn_table = os.path.join(dn, 'eibonded.table')
with open(fn_table, 'w') as f:
f.write("#Table containing 1-3 electrostatic interactions\n")
rval = np.linspace(rmin, rmax, npoints_table)
for icomb, pars in enumerate(ei_data):
qprod, gamma = pars
f.write("btab%03d\nN %d\n\n" % (icomb, npoints_table))
for ir, r in enumerate(rval):
y = r / gamma
e = qprod * erf(y) / r
g = -qprod * (2.0 / np.sqrt(np.pi) * np.exp(-y**2) / r /
gamma - erf(y) / r**2)
f.write("%5d %12.4f %20.12f %20.12f\n" %
(ir + 1, r / lammps_units[unit_style]['distance'],
e / lammps_units[unit_style]['energy'],
g / lammps_units[unit_style]['energy'] *
lammps_units[unit_style]['distance']))
# Check that there is a bond term for every bond
if not counters['Bond'][1] >= system.nbond:
raise ValueError(
"Please ensure that there is a bond term "
"(possibly with force constant 0) for each bond in the system")
# Write the headers to file
with open(os.path.join(dn, 'lammps.data'), 'w') as fdat:
fdat.write("Generated by Yaff\n\n%20d atoms\n%20d bonds\n%20d "
"angles \n%20d dihedrals\n%20d impropers\n\n" %
(system.natom, counters['Bond'][1], counters['Angle'][1],
counters['Dihedral'][1], counters['Improper'][1]))
fdat.write("%20d atom types\n%20d bond types\n%20d angle types\n "
"%20d dihedral types\n%20d improper types\n\n" %
(np.amax(ffatype_ids) + 1, counters['Bond'][0],
counters['Angle'][0], counters['Dihedral'][0],
counters['Improper'][0]))
# Write cell vectors (in LAMMPS format) to file
rvecs, _ = cell_lower(system.cell.rvecs)
fdat.write("%40.34f %40.34f xlo xhi\n%40.34f %40.34f ylo yhi\n"
"%40.34f %40.34f zlo zhi\n" %
(0.0, rvecs[0, 0] / units['distance'], 0.0, rvecs[1, 1] /
units['distance'], 0.0, rvecs[2, 2] / units['distance']))
if triclinic:
fdat.write("%40.34f %40.34f %40.34f xy xz yz\n" %
(rvecs[1, 0] / units['distance'], rvecs[2, 0] /
units['distance'], rvecs[2, 1] / units['distance']))
else:
# Make sure that cell is not triclinic
if not np.all(
np.abs(rvecs.ravel()[[3, 6, 7]]) < 1e-10 *
units['distance']):
raise ValueError(
"Cell is triclinic, but triclinic was set to False!")
# Write atomic masses, add the atom type as comment (not read by LAMMPS)
fdat.write("\nMasses\n\n")
for iffa, ffa in enumerate(ffatypes):
mask = ffatype_ids == iffa
mass = system.masses[mask][0]
assert np.all(mass == system.masses[mask])
fdat.write("%5d %15.8f # %15s\n" %
(iffa + 1, mass / units['mass'], ffa))
# Write coefficients of the covalent terms
for term in ['Bond', 'Angle', 'Dihedral', 'Improper']:
counter = 1
if len(present_prefixes[term]) == 0: continue
fdat.write("\n%s Coeffs\n\n" % term)
for prefix in present_prefixes[term]:
par_units = all_prefixes[prefix][2]
for pars in parameters[prefix][1]:
fdat.write("%8d" % counter)
if len(present_prefixes[term]) > 1:
fdat.write("%20s" % (all_prefixes[prefix][1]))
if prefix == 'TORSION':
fdat.write(
"%5d %15.8f %5d %15.8f" %
(1, 0.5 * pars[1] / par_units[1], pars[0],
(pars[0] * pars[2] - np.pi) / par_units[2]))
elif prefix == 'BENDCHARM':
fdat.write(
"%15.8f %15.8f" %
(pars[0] / par_units[0], np.arccos(pars[1]) / deg))
elif prefix == 'BENDCOS':
if pars[2] == 0.0:
fdat.write("%15.8f %5d %5d" %
(pars[1] / par_units[1] * pars[0]**2,
(-1.0)**(pars[0]), pars[0]))
elif pars[2] == np.pi:
fdat.write("%15.8f %5d %5d" %
(pars[1] / par_units[1] * pars[0]**2,
(-1.0)**(pars[0] + 1), pars[0]))
else:
raise NotImplementedError
elif prefix == 'BONDTABLE':
fdat.write("%20s %15s" % ("eibonded.table", pars))
else:
for ipar, par in enumerate(pars):
fdat.write(" %15.8f" % (par / par_units[ipar]))
counter += 1
fdat.write("\n")
# Write coefficients of the non-covalent terms
if len(present_prefixes['Pair']) > 0 and (not tabulated):
paircoeff_prefix = present_prefixes['Pair'][0]
mapping = parameters[paircoeff_prefix][0][0]
fdat.write("\nPair Coeffs\n\n")
for iffa, ffa in enumerate(ffatypes):
mask = ffatype_ids == iffa
radius = radii[mask][0]
if not np.all(radius == system.radii[mask]):
raise ValueError("All atoms with the same ffatype should "
"have the same radius")
index = mapping[(ffa, )][0]
tpars = parameters[paircoeff_prefix][0][1][index]
# Check that onlypauli is turned off, not yet present in LAMMPS
if paircoeff_prefix == 'MM3': assert tpars[2] == 0
fdat.write(
"%5d %20.12f %20.12f %20.12f # %15s\n" %
(iffa + 1, tpars[1] / units['energy'], tpars[0] /
units['distance'], radius / units['distance'], ffa))
else:
if not tabulated:
if not np.all(radii == 0.0):
raise ValueError(
"When no vdW contribution is provided, "
" Gaussian charge distributions are not supported")
# Write atom types, atomic charges and positions
fdat.write("\nAtoms\n\n")
for i in range(system.natom):
# Coordinates need to be rotated, because LAMMPS uses a different cell
pos = np.dot(rvecs.T, np.dot(system.cell.gvecs, system.pos[i]))
fdat.write("%5d %3d %3d %40.34f %40.34f %40.34f %40.34f\n" %
(i + 1, 1, ffatype_ids[i] + 1, charges[i],
pos[0] / units['distance'], pos[1] / units['distance'],
pos[2] / units['distance']))
# Write covalent terms
for term in ['Bond', 'Angle', 'Dihedral', 'Improper']:
counter = 1
type_counter = 1
if len(present_prefixes[term]) == 0: continue
fdat.write("\n%ss\n\n" % term)
for prefix in present_prefixes[term]:
for coeff_type, indexes in parameters[prefix][0]:
fdat.write("%5d %5d" %
(counter, coeff_type + type_counter))
for index in indexes:
fdat.write(" %5d" % (index + 1))
counter += 1
fdat.write("\n")
type_counter += len(parameters[prefix][1])
# Write a partial LAMMPS input file
with open(os.path.join(dn, 'lammps.in'), 'w') as fin:
fin.write("#" * 30)
fin.write("General settings")
fin.write("#" * 30 + "\n")
fin.write("units %s\n" % (unit_style))
fin.write("atom_style full\n")
fin.write("boundary p p p\n")
fin.write("dielectric 1\n\n")
if len(present_prefixes['Pair']) > 0:
lj = present_prefixes['Pair'][0]
scales_lj = parameters[lj][1]
if tabulated:
scales_lj[1] = scales_lj[2]
scales_lj[2] = 1.0
else:
scales_lj = {1: 0, 2: 0, 3: 0}
ei = present_prefixes['Charge'][0]
scales_ei = parameters[ei][1]
if tabulated: scales_ei[1] = 0.0
if 4 in scales_lj.keys(): assert scales_lj[4] == 1.0
if 4 in scales_ei.keys(): assert scales_ei[4] == 1.0
fin.write("#" * 30)
fin.write("Force field and system specification")
fin.write("#" * 30 + "\n")
fin.write("special_bonds lj %f %f %f coul %f %f %f\n" % \
(scales_lj[1],scales_lj[2],scales_lj[3],scales_ei[1],scales_ei[2],scales_ei[3]) )
fin.write(
"#Note that when a table is used, it is possible that the\n"
"#topology might have been adapted to correctly include\n"
"#Gaussian electrostatics in LAMMPS. The scaling rules might\n"
"#need to be different from what is specified in the Yaff parameter file\n"
)
if tabulated:
fin.write(
"pair_style hybrid/overlay coul/long %13.8f table spline 5000\n"
% (rcut / units['distance']))
pass
else:
if len(present_prefixes['Pair']) > 0:
fin.write("%-15s %s/%s/%s/%s %13.8f" %
("pair_style", all_prefixes[lj][1], "switch3",
"coulgauss", "long", rcut / units['distance']))
fin.write("%8.4f" % (switch / units['distance']))
fin.write("\n")
else:
fin.write("pair_style coul/long %13.8f\n" %
(rcut / units['distance']))
fin.write(
"pair_modify table 16 # Accuracy of the table used for real space electrostatics\n"
)
fin.write("pair_modify mix arithmetic\n")
fin.write("pair_modify tail %s\n" %
("yes" if tailcorrections else "no"))
for term in ['Bond', 'Angle', 'Dihedral', 'Improper']:
if len(present_prefixes[term]) == 0: continue
fin.write("%-15s" % ("%s_style" % (term.lower())))
if len(present_prefixes[term]) > 1: fin.write(" hybrid")
for prefix in present_prefixes[term]:
fin.write(" %s" % (all_prefixes[prefix][1]))
if all_prefixes[prefix][1] == 'table':
fin.write(" spline %d" % npoints_table)
fin.write("\n")
fin.write("box tilt large\n")
fin.write("\n%-15s %s # Data file location\n" %
("read_data", "lammps.data"))
if len(present_prefixes['Pair']) == 0:
fin.write("pair_coeff * *\n")
if tabulated:
fin.write("pair_coeff * * coul/long\n")
for iffa, ffai in enumerate(ffatypes):
for jffa, ffaj in enumerate(ffatypes):
if jffa < iffa: continue
if ffai > ffaj:
name = '%s---%s' % (str(ffai), str(ffaj))
else:
name = '%s---%s' % (str(ffaj), str(ffai))
fin.write("pair_coeff %d %d table %s %s\n" %
(iffa + 1, jffa + 1, 'lammps.table', name))
if system.natom > 2000: kspace = 'pppm'
else: kspace = 'ewald'
if mode == 'library':
fin.write("kspace_style %s 1e-7 # Ewald accuracy\n" %
kspace)
fin.write(
'\nthermo_style custom pe ebond eangle edihed eimp evdwl ecoul elong etail pxx pyy pzz pxy pxz pyz\n'
)
fin.write('neigh_modify delay 0 every 1 check no\n')
fin.write('variable eng equal pe\n')
fin.write('compute virial all pressure NULL virial\n')
fin.write('fix 1 all nve\n')
fin.write('run 0\n')
elif mode == 'test':
fin.write("kspace_style %s 1e-7 # Ewald accuracy\n" %
kspace)
fin.write(
'\ncompute Pmol all pressure NULL bond angle dihedral improper\n'
)
fin.write('compute Ppair all pressure NULL pair kspace\n')
fin.write(
'thermo_style custom step emol evdwl ecoul elong etail c_Pmol[1] c_Pmol[2] c_Pmol[3] c_Pmol[4] c_Pmol[5] c_Pmol[6] c_Ppair[1] c_Ppair[2] c_Ppair[3] c_Ppair[4] c_Ppair[5] c_Ppair[6]\n'
)
fin.write('neigh_modify delay 0 every 1 check no\n')
fin.write('variable eng equal pe\n')
fin.write('compute virial all pressure NULL virial\n')
fin.write('fix 1 all nve\n')
fin.write('run 0\n')
elif mode == 'md':
fin.write("kspace_style %s 1e-7 # Ewald accuracy\n" %
kspace)
fin.write("neighbor 2.0 multi\n")
fin.write("neigh_modify every 2 delay 4 check yes\n\n")
fin.write("#" * 30)
fin.write("Output settings")
fin.write("#" * 30 + "\n")
fin.write("thermo 10 # Provide output every n steps\n")
fin.write(
"thermo_style custom step time etotal ke temp pe emol evdwl ecoul elong etail pxx pyy pzz pxy pxz pyz vol press\n"
)
fin.write("#dump 1 all custom 10 positions.dat id type x y z\n")
fin.write(
"#dump 2 all custom 10 velocities.dat id type vx vy vz\n\n")
fin.write("#" * 30)
fin.write("Sampling options")
fin.write("#" * 30 + "\n")
fin.write("timestep 0.5 # in time units\n")
fin.write(
"velocity all create 0.0 5 # initial temperature in Kelvin and random seed\n"
)
fin.write(
"#fix 1 all npt temp 300.0 300.0 100.0 tri 1.0 1.0 1000.0 tchain 3 mtk yes nreset 1000 volconstraint no\n"
)
fin.write(
"#fix_modify 1 energy yes # Add thermo/barostat contributions to energy\n"
)
fin.write("run 0\n")
else:
raise NotImplementedError