def test_default_settings(self):
L = PyLammps()
# verify default settings
self.assertEqual(L.system.natoms, 0)
self.assertEqual(L.system.ntypes, 0)
self.assertEqual(L.system.style, 'none')
self.assertEqual(L.system.units, 'lj')
self.assertEqual(L.system.kspace_style, 'none')
self.assertEqual(L.system.atom_style, 'atomic')
self.assertEqual(L.system.atom_map, 'none')
# now explicitly set them and check if nothing changed
L.units('lj')
L.boundary("p p p")
L.lattice("none 1.0")
L.atom_style("atomic")
self.assertEqual(L.system.natoms, 0)
self.assertEqual(L.system.ntypes, 0)
self.assertEqual(L.system.style, 'none')
self.assertEqual(L.system.units, 'lj')
self.assertEqual(L.system.kspace_style, 'none')
self.assertEqual(L.system.atom_style, 'atomic')
self.assertEqual(L.system.atom_map, 'none')
def test_real_units(self):
L = PyLammps()
L.units('real') # angstrom, kcal/mol, femtoseconds
L.atom_style('atomic')
L.boundary('p p p')
L.lattice('none', 1.0)
# create simulation cell
L.region('r1 block', -15.0, 15.0, -15.0, 15.0, -15.0, 15.0)
L.create_box(1, 'r1')
# argon
L.mass(1, 39.948002)
L.pair_style('lj/cut', 8.5)
L.pair_coeff(1, 1, 0.2379, 3.405)
L.timestep(10.0)
L.create_atoms(1, 'single', -1.0, 0.0, 0.0)
L.create_atoms(1, 'single', 1.0, 0.0, 0.0)
L.velocity('all create', 250.0, 54321, 'mom no rot no')
L.minimize(1.0e-10, 1.0e-10, 100, 1000)
L.reset_timestep(0)
L.thermo(100)
L.fix('f1 all nve')
L.run(1000)
def setUp(self):
L = PyLammps()
L.units('lj')
L.atom_style('atomic')
L.boundary('p p p')
L.atom_modify("map array")
L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0)
L.create_box(1, 'r1')
L.mass(1, 1.0)
L.create_atoms(1, 'single', -1.0, 0.0, 0.0)
L.create_atoms(1, 'single', 1.0, 0.0, 0.0)
L.pair_style('lj/cut', 5.0)
L.pair_coeff(1, 1, 1.0, 1.0)
L.run(0)
self.L = L
# generate cumulative distribution function considering given angular ranges
# set theta range:
thetamin = 2 * math.asin(math.sqrt(Etmin / Etmax2)) * 180 / math.pi
thetamax = 180
X2 = scatterangle2[scatterangle2 >= thetamin]
X2 = X2[X2 <= thetamax]
indmin = np.where(scatterangle2 == min(X2))
indmin = np.asarray(indmin).item()
indmax = np.where(scatterangle2 == max(X2))
indmax = np.asarray(indmax).item()
cdf2 = np.cumsum(scattercross2[indmin:indmax])
if continueprevsim == False:
L.boundary("p", "p", "f") # "f" non-periodic and fixed
L.region("cluster", "block", (Lsub - dCluster) / 2,
Lsub - (Lsub - dCluster) / 2, (Lsub - dCluster) / 2,
Lsub - (Lsub - dCluster) / 2, dsub, dsub + dCluster)
L.region("subst", "block", 0, Lsub, 0, Lsub, 2, dsub)
L.region("substinteg", "block", 0, Lsub, 0, Lsub, dsub - 4, dsub)
L.region("simregion", "block", 0, Lsub, 0, Lsub, 0, dCluster * 3)
L.region("allintegr", "union", 2, "substinteg", "cluster")
L.lattice("fcc", latticeconst)
L.create_box(
3, "simregion"
) # create box containing 3 elements over full simulation region
else:
py_lmp = PyLammps(cmdargs=['-echo', 'both'], comm=mpi_comm)
py_lmp.log('"' + log_path + '"')
rod_params = rods.Rod_params()
if mpi_rank == 0:
rod_params.from_file(args.cfg_file)
rod_params = mpi_comm.bcast(rod_params, root=0)
# CREATE BASE OBJECTS
model = rods.Rod_model(rod_params)
simulation = rods.Simulation(py_lmp, model, run_args.temp, seed, output_folder)
py_lmp.units("lj")
py_lmp.dimension(3)
py_lmp.boundary("p p p")
py_lmp.lattice("sc", 1 / (run_args.cell_size**3))
py_lmp.region("box", "block", -run_args.num_cells / 2, run_args.num_cells / 2,
-run_args.num_cells / 2, run_args.num_cells / 2,
-run_args.num_cells / 2, run_args.num_cells / 2)
simulation.setup("box")
simulation.create_rods(box=None)
# ROD DYNAMICS
py_lmp.fix("thermostat", "all", "langevin", run_args.temp, run_args.temp,
run_args.damp, seed) #, "zero yes")
simulation.set_rod_dynamics("nve", opt=["mol", model.rod_states[0]])
py_lmp.neigh_modify("every 1 delay 1")
py_lmp.timestep(run_args.dt)
class RealUnitsLatticeBoxTests(unittest.TestCase):
def setUp(self):
self.L = PyLammps()
self.L.units('real') # default, use reduced units
self.L.atom_style('atomic') # default, point particles with mass and type
self.L.boundary('p p p') # default, periodic boundaries in 3-d
self.L.processors('* * *') # default, automatic domain decomposition
self.L.newton('on') # default, use newton's 3rd law for ghost particles
def assertAlmostEqualList(self, a_list, b_list):
for a, b in zip(a_list, b_list):
self.assertAlmostEqual(a, b, places=3)
def test_real_none_box(self):
self.L.lattice('none', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units box')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertEqual(self.L.system.xlo, -5.0)
self.assertEqual(self.L.system.ylo, -5.0)
self.assertEqual(self.L.system.zlo, -5.0)
self.assertEqual(self.L.system.xhi, 5.0)
self.assertEqual(self.L.system.yhi, 5.0)
self.assertEqual(self.L.system.zhi, 5.0)
def test_real_sc_box(self):
self.L.lattice('sc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units box')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertEqual(self.L.system.xlo, -5.0)
self.assertEqual(self.L.system.ylo, -5.0)
self.assertEqual(self.L.system.zlo, -5.0)
self.assertEqual(self.L.system.xhi, 5.0)
self.assertEqual(self.L.system.yhi, 5.0)
self.assertEqual(self.L.system.zhi, 5.0)
def test_real_fcc_box(self):
self.L.lattice('fcc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units box')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertEqual(self.L.system.xlo, -5.0)
self.assertEqual(self.L.system.ylo, -5.0)
self.assertEqual(self.L.system.zlo, -5.0)
self.assertEqual(self.L.system.xhi, 5.0)
self.assertEqual(self.L.system.yhi, 5.0)
self.assertEqual(self.L.system.zhi, 5.0)
def test_real_bcc_box(self):
self.L.lattice('bcc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units box')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertEqual(self.L.system.xlo, -5.0)
self.assertEqual(self.L.system.ylo, -5.0)
self.assertEqual(self.L.system.zlo, -5.0)
self.assertEqual(self.L.system.xhi, 5.0)
self.assertEqual(self.L.system.yhi, 5.0)
self.assertEqual(self.L.system.zhi, 5.0)
def test_real_none_lattice(self):
self.L.lattice('none', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units lattice')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertEqual(self.L.system.xlo, -5.0)
self.assertEqual(self.L.system.ylo, -5.0)
self.assertEqual(self.L.system.zlo, -5.0)
self.assertEqual(self.L.system.xhi, 5.0)
self.assertEqual(self.L.system.yhi, 5.0)
self.assertEqual(self.L.system.zhi, 5.0)
def test_real_sc_lattice(self):
self.L.lattice('sc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units lattice')
self.L.create_box(1, 'r1')
self.assertEqual(self.L.system.orthogonal_box, [10, 10, 10])
self.assertAlmostEqual(self.L.system.xlo, -5.0)
self.assertAlmostEqual(self.L.system.ylo, -5.0)
self.assertAlmostEqual(self.L.system.zlo, -5.0)
self.assertAlmostEqual(self.L.system.xhi, 5.0)
self.assertAlmostEqual(self.L.system.yhi, 5.0)
self.assertAlmostEqual(self.L.system.zhi, 5.0)
def test_real_fcc_lattice(self):
self.L.lattice('fcc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units lattice')
self.L.create_box(1, 'r1')
lattice_spacing = 1.0
self.assertAlmostEqualList(self.L.system.orthogonal_box, [10*lattice_spacing, 10*lattice_spacing, 10*lattice_spacing])
self.assertAlmostEqual(self.L.system.xlo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.ylo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.zlo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.xhi, 5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.yhi, 5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.zhi, 5.0 * lattice_spacing, places=3)
def test_real_bcc_lattice(self):
self.L.lattice('bcc', 1.0)
self.L.region('r1 block', -5.0, 5.0, -5.0, 5.0, -5.0, 5.0, 'units lattice')
self.L.create_box(1, 'r1')
lattice_spacing = 1.0
self.assertAlmostEqualList(self.L.system.orthogonal_box, [10*lattice_spacing, 10*lattice_spacing, 10*lattice_spacing])
self.assertAlmostEqual(self.L.system.xlo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.ylo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.zlo, -5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.xhi, 5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.yhi, 5.0 * lattice_spacing, places=3)
self.assertAlmostEqual(self.L.system.zhi, 5.0 * lattice_spacing, places=3)
def test_use_data_file(self):
L = PyLammps()
L.units('real') # angstrom, kcal/mol, femtoseconds
L.atom_style('atomic')
L.boundary('p p p')
L.lattice('none', 1.0)
# create simulation cell
L.region('r1 block', -15.0, 15.0, -15.0, 15.0, -15.0, 15.0)
L.create_box(1, 'r1')
# argon
L.mass(1, 39.948002)
L.pair_style('lj/cut', 8.5)
L.pair_coeff(1, 1, 0.2379, 3.405)
L.timestep(10.0)
L.create_atoms(1, 'single', -1.0, 0.0, 0.0)
L.create_atoms(1, 'single', 1.0, 0.0, 0.0)
L.velocity('all create', 250.0, 54321, 'mom no rot no')
L.minimize(1.0e-10, 1.0e-10, 100, 1000)
L.reset_timestep(0)
L.thermo(100)
L.fix('f1 all nve')
L.run(1000)
L.write_restart('run.restart')
L.write_data('run.data')
L2 = PyLammps()
L2.units('real') # angstrom, kcal/mol, femtoseconds
L2.atom_style('atomic')
L2.boundary('p p p')
L2.pair_style('lj/cut', 8.5)
L2.read_data('run.data')
L2.timestep(10.0)
L2.thermo(100)
L2.fix('f1 all nve')
L2.run(1000)
# reset status. forget all settings. delete system
L2.clear()
L2.read_restart('run.restart')
L2.thermo(100)
L2.fix('f1 all nve')
L2.run(1000)
os.remove('run.restart')
os.remove('run.data')
self.assertEqual(L.system, L2.system)
model.rod_length / 2, 5.0)
# ===== LAMMPS setup ====================================================================
if mpi_rank == 0:
py_lmp = PyLammps(cmdargs=['-echo', 'both'],
comm=mpi_comm,
verbose=args.verbose)
else:
py_lmp = PyLammps(cmdargs=['-echo', 'both'], comm=mpi_comm)
py_lmp.log('"' + log_path + '"')
simulation = rods.Simulation(py_lmp, model, run_args.temp, seed, output_folder)
py_lmp.units('lj')
py_lmp.dimension(3)
py_lmp.boundary('p p f')
py_lmp.region('box', 'block', membrane.xmin, membrane.xmax, membrane.ymin,
membrane.ymax, 0.0, run_args.Lz)
simulation.setup('box',
type_offset=max(membrane.bead_types),
extra_pair_styles=[('cosine/squared', model.global_cutoff)],
bond_offset=membrane.bond_type,
extra_bond_styles=['fene'],
opt=['angle/types', 1, 'extra/angle/per/atom', 1])
py_lmp.angle_style('harmonic')
zwalls_fix = 'zwalls'
py_lmp.fix(zwalls_fix, 'all', 'wall/lj126', 'zlo EDGE', 1.0, model.rod_radius,
model.rod_radius * pow(2, 1. / 6), 'zhi EDGE', 1.0,
model.rod_radius, model.rod_radius * pow(2, 1. / 6))
def elastic():
""" Compute elastic constant tensor for a crystal
In order to calculate the elastic constants correctly, care must be taken to specify
the correct units (units). It is also important to verify that the minimization of energy
w.r.t atom positions in the deformed cell is fully converged.
One indication of this is that the elastic constants are insensitive
to the choice of the variable ${up}. Another is to check
the final max and two-norm forces reported in the log file. If you know
that minimization is not required, you can set maxiter = 0.0 """
parser = ArgumentParser(
description=
'A python script to compute elastic properties of bulk materials')
parser.add_argument("input_data_file",
help="The full path & name of the lammps data file.")
parser.add_argument(
"kim_model",
help="the KIM ID of the interatomic model archived in OpenKIM")
parser.add_argument(
"elements",
nargs='+',
default=['Au'],
help=
"a list of N chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM model"
)
parser.add_argument(
"--min_style",
default="cg",
help="which algorithm will be used for minimization from lammps")
parser.add_argument("--minimize",
type=float,
nargs=4,
default=[1.0e-4, 1.0e-6, 100, 1000],
help="minimization parameters")
parser.add_argument("--up",
type=float,
default=1.0e-6,
help="the deformation magnitude (in strain units)")
args = parser.parse_args()
L = PyLammps()
L.units("metal")
# Define the finite deformation size.
#Try several values to verify that results do not depend on it.
L.variable("up equal {}".format(args.up))
# Define the amount of random jiggle for atoms. It prevents atoms from staying on saddle points
atomjiggle = 1.0e-5
# metal units, elastic constants in GPa
cfac = 1.0e-4
# Define minimization parameters
L.variable("dmax equal 1.0e-2")
L.boundary("p", "p",
"p") # periodic boundary conditions in all three directions
L.box(
"tilt large"
) # to avoid termination if the final simulation box has a high tilt factor
# use the OpenKIM model to set the energy interactions
L.kim("init", args.kim_model, "metal", "unit_conversion_mode")
L.read_data(args.input_data_file)
potential(L, args)
# Need to set mass to something, just to satisfy LAMMPS
mass_dictionary = {
'H': 1.00797,
'He': 4.00260,
'Li': 6.941,
'Be': 9.01218,
'B': 10.81,
'C': 12.011,
'N': 14.0067,
'O': 15.9994,
'F': 18.998403,
'Ne': 20.179,
'Na': 22.98977,
'Mg': 24.305,
'Al': 26.98154,
'Si': 28.0855,
'P': 30.97376,
'S': 32.06,
'Cl': 35.453,
'K': 39.0983,
'Ar': 39.948,
'Ca': 40.08,
'Sc': 44.9559,
'Ti': 47.90,
'V': 50.9415,
'Cr': 51.996,
'Mn': 54.9380,
'Fe': 55.847,
'Ni': 58.70,
'Co': 58.9332,
'Cu': 63.546,
'Zn': 65.38,
'Ga': 69.72,
'Ge': 72.59,
'As': 74.9216,
'Se': 78.96,
'Br': 79.904,
'Kr': 83.80,
'Rb': 85.4678,
'Sr': 87.62,
'Y': 88.9059,
'Zr': 91.22,
'Nb': 92.9064,
'Mo': 95.94,
'Tc': 98,
'Ru': 101.07,
'Rh': 102.9055,
'Pd': 106.4,
'Ag': 107.868,
'Cd': 112.41,
'In': 114.82,
'Sn': 118.69,
'Sb': 121.75,
'I': 126.9045,
'Te': 127.60,
'Xe': 131.30,
'Cs': 132.9054,
'Ba': 137.33,
'La': 138.9055,
'Ce': 140.12,
'Pr': 140.9077,
'Nd': 144.24,
'Pm': 145,
'Sm': 150.4,
'Eu': 151.96,
'Gd': 157.25,
'Tb': 158.9254,
'Dy': 162.50,
'Ho': 164.9304,
'Er': 167.26,
'Tm': 168.9342,
'Yb': 173.04,
'Lu': 174.967,
'Hf': 178.49,
'Ta': 180.9479,
'W': 183.85,
'Re': 186.207,
'Os': 190.2,
'Ir': 192.22,
'Pt': 195.09,
'Au': 196.9665,
'Hg': 200.59,
'Tl': 204.37,
'Pb': 207.2,
'Bi': 208.9804,
'Po': 209,
'At': 210,
'Rn': 222,
'Fr': 223,
'Ra': 226.0254,
'Ac': 227.0278,
'Pa': 231.0359,
'Th': 232.0381,
'Np': 237.0482,
'U': 238.029
}
for itype in range(1, len(args.elements) + 1):
L.mass(itype, mass_dictionary.get(args.elements[itype - 1], 1.0e-20))
# Compute initial state at zero pressure
L.fix(3, "all", "box/relax", "aniso", 0.0)
L.min_style(args.min_style)
L.minimize(args.minimize[0], args.minimize[1], int(args.minimize[2]),
int(args.minimize[3]))
L.variable("lx0 equal {}".format(L.eval("lx")))
L.variable("ly0 equal {}".format(L.eval("ly")))
L.variable("lz0 equal {}".format(L.eval("lz")))
# These formulas define the derivatives w.r.t. strain components
L.variable("d1 equal -(v_pxx1-{})/(v_delta/v_len0)*{}".format(
L.eval("pxx"), cfac))
L.variable("d2 equal -(v_pyy1-{})/(v_delta/v_len0)*{}".format(
L.eval("pyy"), cfac))
L.variable("d3 equal -(v_pzz1-{})/(v_delta/v_len0)*{}".format(
L.eval("pzz"), cfac))
L.variable("d4 equal -(v_pyz1-{})/(v_delta/v_len0)*{}".format(
L.eval("pyz"), cfac))
L.variable("d5 equal -(v_pxz1-{})/(v_delta/v_len0)*{}".format(
L.eval("pxz"), cfac))
L.variable("d6 equal -(v_pxy1-{})/(v_delta/v_len0)*{}".format(
L.eval("pxy"), cfac))
L.displace_atoms("all", "random", atomjiggle, atomjiggle, atomjiggle,
87287, "units box")
# Write restart
L.unfix(3)
L.write_restart("restart.equil")
for idir in range(1, 7):
displace(L, args, idir)
postprocess_and_output(L)
return
class LammpsKernel(IGMKernel):
def __init__(self, model, cfg, runid):
self.cfg = cfg
self.model = model
self.runid = runid
self.tmp_dir = self.cfg.tmpdir('optimization')
self.randseed = int(self.cfg["optimization/kernel_opts/lammps/seed"])
self.initLammps()
self.setupSimulationBox()
self.setupParticles()
self.setCoordinates()
self.setRadii()
self.setupNeighbor()
def initLammps(self):
"""
setup lammps python interface, log file
"""
if self.cfg["optimization/kernel_opts/lammps/keep_logs"]:
self.Lmp = PyLammps(cmdargs=["-log",os.path.join(self.tmp_dir, self.runid+".log")])
else:
self.Lmp = PyLammps(cmdargs=["-log","none"])
self.Lmp.atom_style("bond")
self.Lmp.boundary('s','s','s')
def setupSimulationBox(self):
"""
setup lammps simulation box
"""
atom_types = 1
bond_types = 0
bond_per_atom = 0
for Res in self.model.restraints:
atom_types += Res.extra_atom_types
bond_types += Res.extra_bond_types
bond_per_atom += Res.extra_bond_per_atom
if res.type == "Envelope":
xx , yy, zz = Res.a*1.2, Res.b*1.2, Res.c*1.2
self.Lmp.region("IGMBOX", "block", -xx, xx, -yy, yy, -zz, zz)
self.Lmp.create_box(1, "IGMBOX", "bond/types", bond_types, "extra/bond/per/atom", bond_per_atom)
def setupParticles(self):
"""
initialize particles with random position
"""
#add user define per-atom property: radius(double)
self.Lmp.fix("UserProperty","all","property/atom","d_radius")
#number of particles
self.nbead = len(self.model.particles)
self.atom_style_index = 1
self.Lmp.create_atoms(1, "random", self.nbead, self.randseed, "IGMBOX")
#set particle mass 1.0
self.Lmp.mass('*', 1.0)
#group particle NORMAL
self.lmp_group_NORMAL = "NORMAL"
self.Lmp.group(self.lmp_group_NORMAL, "type", 1)
#get numpy view of per atom array
self.particle_id = self.Lmp.lmp.numpy.extract_atom_iarray('id', n, 1)
self._coordinates = self.Lmp.lmp.numpy.extract_atom_darray('x', n, 3)
self._radii = self.lmp.lmp.numpy.extract_atom_darray('d_radius', n, 1)
def indexMapping(self):
"""
particle mapping from lammps index to original index
"""
return np.argsort( self.particle_id[:, 0] )
def setCoordinates(self, crd = None):
"""
assign xyz values to lammps
"""
if crd:
self.coordinates[self.indexMapping(), :] = crd[:]
else:
self.coordinates[self.indexMapping(), :] = self.model.particles.coordinates[:]
def setRadii(self, radii = None):
"""
assign radius values to lammps
"""
if radii:
self.radii[self.indexMapping(), :] = radii[:]
else:
self.radii[self.indexMapping(), :] = self.model.particles.radii[:]
self.maxrad = max(self.radii)
def setupNeighbor(self):
"""
setup neighbor list rules
"""
if hasattr(self, "maxrad"):
self.Lmp.neighbor(self.maxrad, 'bin')
else:
raise RuntimeError("Radii not set before setupNeighbor()")
max_neighbor = int(self.cfg["optimization/kernel_opts/lammps/max_neigh"])
self.Lmp.neigh_modify('every',1,'check','yes')
self.Lmp.neigh_modify("one", max_neighbor, 'page', 20*max_neighbor)
def addRestraints(self):
"""
add restraints to lammps one by one
"""
#lammps bond style definition
bond_styles = set()
n = 1
for Res in self.model.restraints:
if hasattr(Res, "bond_style"):
bond_styles.add(Res.bond_style)
#give_bond_id
Res.setBondId(n)
n += 1
if len(bond_styles) == 1:
self.Lmp.bond_style(bond_styles.pop())
elif len(bond_styles) > 1:
cmd = ["bond_style", "hybrid"]
while bond_styles:
cmd.append(bond_styles.pop())
self.Lmp.command(" ".join(cmd))
#define variable for fast communication/avoid input string parsing
self.Lmp.variable("batoms","string","EMPTY")
bond_variable = "batoms"
#loop all restraints and apply lammps code
for Res in self.model.restraints:
Res.Lammps(self.Lmp, runid = self.runid,
tmp_dir = self.tmp_dir,
randseed = self.randseed,
normal_group = self.lmp_group_NORMAL,
bond_variable = bond_variable)
