def data(i):
lmp1 = lammps()
polymer = PyLammps(ptr=lmp1)
x = 60
y = 30
z = 30
t = 1
polymer.units("lj")
polymer.dimension(3)
polymer.atom_style("bond")
polymer.bond_style("harmonic")
polymer.pair_style("lj/cut", 3)
polymer.read_data("data.polymer")
polymer.region("void cylinder x", 15, 15, 2, 29, 31)
polymer.pair_coeff(1, 2, 2.5, 3)
polymer.pair_coeff(1, 3, 2.5, 1.12)
polymer.pair_coeff(2, 3, 2.5, 1.12)
polymer.velocity("all create", t, 97287)
polymer.group("polymer type", 1, 2)
polymer.group("first type", 1)
polymer.region("box block", 0, x, 0, y, 0, z)
polymer.region("spherein sphere", 29, 15, 15, 2)
polymer.region("boxin block", 27, 29, 13, 17, 13, 17)
polymer.region("hemiin intersect", 2, "boxin spherein")
x0 = polymer.atoms[0].position[0]
y0 = polymer.atoms[0].position[1]
z0 = polymer.atoms[0].position[2]
r = lambda x0, y0, z0: np.sqrt((x0 - 29)**2 + (y0 - 15)**2 + (z0 - 15)**2)
fx = lambda x0, y0, z0: 5 * (x0 - 29) / r(x0, y0, z0)
fy = lambda x0, y0, z0: 5 * (y0 - 15) / r(x0, y0, z0)
fz = lambda x0, y0, z0: 5 * (z0 - 15) / r(x0, y0, z0)
polymer.fix(1, "polymer nve")
polymer.fix(2, "polymer langevin", t, t, 1.5,
np.random.randint(2, high=200000))
polymer.fix(3, "polymer spring tether", 10, i, "NULL NULL", 0)
polymer.timestep(0.01)
polymer.compute("com polymer com")
polymer.variable("ftotal equal fcm(polymer,x)")
polymer.variable("c equal c_com[1]")
polymer.thermo_style("custom v_ftotal v_c")
polymer.thermo(1)
polymer.run(500000)
l = polymer.runs[0][0][1][20000:] + [i]
u = [np.mean(polymer.runs[0][0][0][20000:]), i]
np.savetxt("trial%dmean.txt" % i, u)
np.savetxt("trial%dall.txt" % i, l)
return u
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)
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
