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 test_melt_using_groups(self):
""" 3d Lennard-Jones melt with two atom types """
L = PyLammps()
L.units('lj')
L.atom_style('atomic')
L.lattice('fcc', 0.8442) # NOTE: lattice command is different in LJ units
L.region('whole block', 0.0, 10.0, 0, 10, 0, 10)
L.create_box(2, 'whole')
L.region('upper block', 4.9, 10.1, 'EDGE EDGE EDGE EDGE')
L.region('lower block', 0.0, 4.9, 'EDGE EDGE EDGE EDGE')
# fill box with atoms according to lattice positions
L.create_atoms(1, 'region upper')
L.create_atoms(2, 'region lower')
L.mass(1, 1.0)
L.mass(2, 2.0)
L.group('gu', 'type', 1)
L.group('gl', 'type', 2)
L.velocity('gu', 'create 2.0 12345 mom no rot no')
L.velocity('gl', 'create 4.0 54321 mom no rot no')
L.timestep(0.002)
L.pair_style('lj/cut', 2.5)
L.pair_coeff('* *', 1.0, 1.0, 2.5)
L.fix('f1 all nve')
#L.dump('d1 all image 500 snap-03.*.jpg type type')
L.thermo(50)
L.run(500)
def test_melt(self):
""" 3d Lennard-Jones melt """
L = PyLammps()
L.units('lj')
L.atom_style('atomic')
L.lattice('fcc', 0.8442) # NOTE: lattice command is different in LJ units
# 0.8442 is density fraction
L.region('r1 block', 0, 10, 0, 10, 0, 10)
L.create_box(1, 'r1')
# fill box with atoms according to lattice positions
L.create_atoms(1, 'box')
L.mass(1, 1.0)
L.velocity('all create', 3.0, 87287, 'mom no')
L.timestep(0.002)
L.pair_style('lj/cut', 2.5)
L.pair_coeff(1, 1, 1.0, 1.0, 2.5)
L.fix('f1 all nve')
L.dump('d1 all image 500 snap-01.*.jpg type type')
L.thermo(50)
L.run(500)
self.assertTrue(os.path.exists('snap-01.0.jpg'))
self.assertTrue(os.path.exists('snap-01.500.jpg'))
os.remove('snap-01.0.jpg')
os.remove('snap-01.500.jpg')
def setUp(self):
"""create 3d rocksalt-like structure"""
L = PyLammps()
L.units('real') # kcal/mol, Angstrom, picoseconds
L.atom_style('charge') # atomic + charge
# lattice for Na+ ions and box
L.lattice('fcc', 6.0, 'origin', 0.0, 0.0, 0.0)
L.region('r1', 'block', -3, 3,-3, 3,-3, 3)
L.create_box(2, 'r1')
# fill box with Na+ ions according to lattice positions
L.create_atoms(1, 'box')
# new lattice for Cl- ions shifted by half box diagonal
L.lattice('fcc', 6.0, 'origin', 0.5, 0.5, 0.5)
L.create_atoms(2, 'box')
L.mass(1, 22.989770)
L.mass(2, 35.453)
L.set('type', 1, 'charge', 1.0)
L.set('type', 2, 'charge', -1.0)
L.group('na type', 1)
L.group('cl type', 2)
L.velocity('all create', 800.0, 12345, 'mom no rot no')
L.timestep(0.001)
self.L = L
def test_create_box(self):
L = PyLammps()
L.units('real')
L.lattice('fcc', 3.5)
L.region("a block", 0, 1, 0, 1, 0, 1)
L.create_box(1, 'a')
self.assertEqual(L.system.dimensions, 3)
self.assertEqual(L.system.orthogonal_box, [3.5, 3.5, 3.5])
self.assertEqual(L.system.boundaries, 'p,p p,p p,p')
self.assertEqual(L.system.xlo, 0.0)
self.assertEqual(L.system.ylo, 0.0)
self.assertEqual(L.system.zlo, 0.0)
self.assertEqual(L.system.xhi, 3.5)
self.assertEqual(L.system.yhi, 3.5)
self.assertEqual(L.system.zhi, 3.5)
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
#L.mass(1,196.96655) # molecular weight in g/mol Au
#L.mass(2,58.6934) # Ni
L.mass(3, 12.011) # C
L.create_atoms(1, "region",
"cluster") # fill cluster region with atoms of type 1
L.create_atoms(3, "random", nPartsub, 4723738,
"subst") # fill substrate region with atoms of type 3
L.group("substinteggr", "region", "substinteg")
class PythonPyLammps(unittest.TestCase):
def setUp(self):
machine = None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine = os.environ['LAMMPS_MACHINE_NAME']
self.pylmp = PyLammps(
name=machine,
cmdargs=['-nocite', '-log', 'none', '-echo', 'screen'])
self.pylmp.units("lj")
self.pylmp.atom_style("atomic")
self.pylmp.atom_modify("map array")
if 'LAMMPS_CMAKE_CACHE' in os.environ:
self.cmake_cache = {}
with open(os.environ['LAMMPS_CMAKE_CACHE'], 'r') as f:
for line in f:
line = line.strip()
if not line or line.startswith('#') or line.startswith(
'//'):
continue
parts = line.split('=')
key, value_type = parts[0].split(':')
if len(parts) > 1:
value = parts[1]
if value_type == "BOOL":
value = (value.upper() == "ON")
else:
value = None
self.cmake_cache[key] = value
def tearDown(self):
self.pylmp.close()
del self.pylmp
def test_version(self):
self.assertGreaterEqual(self.pylmp.version(), 20200824)
def test_create_atoms(self):
self.pylmp.region("box block", 0, 2, 0, 2, 0, 2)
self.pylmp.create_box(1, "box")
x = [1.0, 1.0, 1.0, 1.0, 1.0, 1.5]
types = [1, 1]
self.assertEqual(
self.pylmp.lmp.create_atoms(2, id=None, type=types, x=x), 2)
self.assertEqual(self.pylmp.system.natoms, 2)
self.assertEqual(len(self.pylmp.atoms), 2)
numpy.testing.assert_array_equal(self.pylmp.atoms[0].position,
tuple(x[0:3]))
numpy.testing.assert_array_equal(self.pylmp.atoms[1].position,
tuple(x[3:6]))
self.assertEqual(self.pylmp.last_run, None)
def test_write_script(self):
outfile = 'in.test_write_script'
self.pylmp.write_script(outfile)
self.assertTrue(os.path.exists(outfile))
os.remove(outfile)
def test_runs(self):
self.pylmp.lattice("fcc", 0.8442),
self.pylmp.region("box block", 0, 4, 0, 4, 0, 4)
self.pylmp.create_box(1, "box")
self.pylmp.create_atoms(1, "box")
self.pylmp.mass(1, 1.0)
self.pylmp.velocity("all create", 1.44, 87287, "loop geom")
self.pylmp.pair_style("lj/cut", 2.5)
self.pylmp.pair_coeff(1, 1, 1.0, 1.0, 2.5)
self.pylmp.neighbor(0.3, "bin")
self.pylmp.neigh_modify("delay 0 every 20 check no")
self.pylmp.fix("1 all nve")
self.pylmp.variable("fx atom fx")
self.pylmp.run(10)
self.assertEqual(len(self.pylmp.runs), 1)
self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
self.assertEqual(len(self.pylmp.last_run.thermo.Step), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.Press), 2)
def test_info_queries(self):
self.pylmp.lattice("fcc", 0.8442),
self.pylmp.region("box block", 0, 4, 0, 4, 0, 4)
self.pylmp.create_box(1, "box")
self.pylmp.variable("a equal 10.0")
self.pylmp.variable("b string value")
self.assertEqual(self.pylmp.variables['a'].value, 10.0)
self.assertEqual(self.pylmp.variables['b'].value, 'value')
self.assertEqual(len(self.pylmp.variables), 2)
self.assertEqual(self.pylmp.system.units, 'lj')
self.assertEqual(self.pylmp.system.atom_style, 'atomic')
self.assertEqual(self.pylmp.system.ntypes, 1)
self.assertEqual(self.pylmp.system.natoms, 0)
self.assertEqual(self.pylmp.communication.comm_style, 'brick')
self.assertEqual(self.pylmp.communication.comm_layout, 'uniform')
self.assertEqual(self.pylmp.communication.nprocs, 1)
self.assertEqual(len(self.pylmp.computes), 3)
self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp')
self.assertEqual(self.pylmp.computes[0]['style'], 'temp')
self.assertEqual(self.pylmp.computes[0]['group'], 'all')
self.assertEqual(self.pylmp.computes[1]['name'], 'thermo_press')
self.assertEqual(self.pylmp.computes[1]['style'], 'pressure')
self.assertEqual(self.pylmp.computes[1]['group'], 'all')
self.assertEqual(self.pylmp.computes[2]['name'], 'thermo_pe')
self.assertEqual(self.pylmp.computes[2]['style'], 'pe')
self.assertEqual(self.pylmp.computes[2]['group'], 'all')
self.assertEqual(len(self.pylmp.dumps), 0)
self.pylmp.fix('one', 'all', 'nve')
self.assertEqual(len(self.pylmp.fixes), 1)
self.assertEqual(self.pylmp.fixes[0]['name'], 'one')
self.assertEqual(self.pylmp.fixes[0]['style'], 'nve')
self.assertEqual(self.pylmp.fixes[0]['group'], 'all')
self.pylmp.group('none', 'empty')
self.assertEqual(len(self.pylmp.groups), 2)
#!/usr/bin/env python3
from lammps import PyLammps, lammps
import numpy as np
import sys
l = lammps()
lmp = PyLammps(ptr=l)
lmp.units("lj")
lmp.atom_style("atomic")
lmp.lattice("fcc", 0.8442)
lmp.region("box", "block", 0, 4, 0, 4, 0, 4)
lmp.create_box(1, "box")
lmp.create_atoms(1, "box")
lmp.mass(1, 1.0)
lmp.velocity("all", "create", 10, 87287)
lmp.pair_style("lj/cut", 2.5)
lmp.pair_coeff(1, 1, 1.0, 1.0, 2.5)
lmp.neighbor(0.3, "bin")
lmp.neigh_modify("delay", 0, "every", 20, "check no")
lmp.fix("1 all nve")
a = l.extract_fix("2",2,2)
print(a.contents)
#nlocal = l.extract_global("nlocal",0)
#print(nlocal)
#lmp.fix("2 all addforce 1.0 0.0 0.0")
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)
