def test_change_potential(self):
L = PyLammps()
L.file(IncludeTests.ATOMS_SETUP_FILE)
# set non-bonded potential
L.pair_style('lj/cut', 5.0)
L.pair_coeff(1, 1, 1.0, 1.0)
# set different non-bonded potential
L.velocity('all create', 1.0, 54321, 'mom no rot no')
# import time integration setting from include file
L.file(IncludeTests.VERLET_CONFIG_FILE)
L.minimize(1.0e-10, 1.0e-10, 100, 1000)
L.reset_timestep(0) # set timestep counter to zero
L.thermo(10) # thermo output every 10 steps
L.run(100, 'post no')
# continue run with different potential
L.pair_style('morse', 5.0)
L.pair_coeff(1, 1, 1.0, 5.0, 1.12)
L.run(100)
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 test_read_restart(self):
L = self.L
pe = L.eval("pe")
L.write_restart('/tmp/test_read_restart.restart')
del L
L2 = PyLammps()
L2.read_restart('/tmp/test_read_restart.restart')
L2.run(0)
os.remove('/tmp/test_read_restart.restart')
self.assertEqual(L2.system.natoms, 2)
self.assertEqual(L2.atoms[0].position, (-1.0, 0.0, 0.0))
self.assertEqual(L2.atoms[1].position, (1.0, 0.0, 0.0))
self.assertEqual(L2.eval("pe"), pe)
def test_morse_potential(self):
L = PyLammps()
L.file(IncludeTests.ATOMS_SETUP_FILE)
# set different non-bonded potential
L.pair_style('morse', 5.0)
L.pair_coeff(1, 1, 1.0, 5.0, 1.12)
L.velocity('all create', 1.0, 54321, 'mom no rot no')
# import time integration setting from include file
L.file(IncludeTests.VERLET_CONFIG_FILE)
L.thermo(10) # thermo output every 10 steps
L.run(100)
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 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
def test_run_post_no_pre_no(self):
L = PyLammps()
L.file(IncludeTests.ATOMS_SETUP_FILE)
# set non-bonded potential
L.pair_style('lj/cut', 5.0)
L.pair_coeff(1, 1, 1.0, 1.0)
# set different non-bonded potential
L.velocity('all create', 1.0, 54321, 'mom no rot no')
# import time integration setting from include file
L.file(IncludeTests.VERLET_CONFIG_FILE)
L.minimize(1.0e-10, 1.0e-10, 100, 1000)
L.reset_timestep(0) # set timestep counter to zero
L.thermo(10) # thermo output every 10 steps
L.run(100, 'post no') # don't print post run information
L.run(100, 'pre no') # don't to pre-run preparation (not needed, if no change)
L.thermo(1000)
L.thermo_modify("lost", "ignore", "flush", "yes")
L.echo("none")
L.velocity("all", "create", Temp, 12345, "dist", "gaussian", "mom", "yes",
"rot", "yes")
#L.fix("thermofix","all","temp/csvr",Temp,Temp,0.1,12345) # does not perform time integration !
L.fix("thermofix1", "allintegrategr", "langevin", 1, 1, 0.1, 699483,
"zero", "yes")
#L.fix("nveintegration","allintegrategr","nve/limit",0.05) # performs time integration with modified velocities in micro-canonical ensemble
L.fix("nveintegration", "allintegrategr", "nve")
# initial equilibration:
starttime = time.time()
L.run(20000)
print("dt at start: {} fs".format(L.eval("dt") * 1000))
print("T at start: {} K".format(L.eval("temp")))
print("elapsed time: {} s".format(time.time() - starttime))
L.unfix("nveintegration") # remove time integration fix
L.unfix("thermofix1")
L.velocity("all", "create", Temp, 12345, "dist", "gaussian", "mom", "yes",
"rot", "yes")
L.fix("thermofix", "clustergr", "langevin", Temp, Temp, 0.1, 12345, "zero",
"yes") # does not perform time integration !
L.fix("nveintegration", "clustergr", "nve") # move only cluster atoms
L.timestep(0.002)
starttime = time.time()
L.run(50000)
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)
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")
#f = l.extract_atom("f",3)
#a = np.ctypeslib.as_array(f.contents,shape=(natoms, 3))
#print(a)
lmp.dump("id all atom 50 dumpT10.0.lammpstrj")
lmp.thermo(50)
lmp.run(10000)
-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)
# THERMALIZE INITIAL CONFIGURATION
simulation.deactivate_state(0, vx_eps=5.0)
py_lmp.run(1000)
simulation.activate_state(0)
py_lmp.reset_timestep(0)
# GROUPS & COMPUTES
if hasattr(run_args, 'label_micelles'):
micelle_group = 'sol_tips'
sol_tip_bead_type = model.state_structures[0][0][-1]
py_lmp.variable(micelle_group, 'atom',
'"type == {:d}"'.format(sol_tip_bead_type))
py_lmp.group(micelle_group, 'dynamic', simulation.rods_group, 'var',
micelle_group, 'every', out_freq)
micelle_compute = "micelle_ID"
if hasattr(run_args, 'micelle_cutoff'):
micelle_cutoff = run_args.micelle_cutoff
else:
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)
concentration = run_args.conc / model.rod_length**3
simulation.set_state_concentration(
0, concentration, 10, 10, opt=['region', 'gcmc_init', 'tfac_insert', 1.65])
# TEST DUMP...
# py_lmp.thermo_style('custom', 'step atoms', 'pe temp')
# py_lmp.variable('thermo_var', 'equal', '"stagger({:d}, 1)"'.format(out_freq))
# py_lmp.thermo('v_thermo_var')
# py_lmp.dump('test_dump', 'all', 'custom', out_freq, dump_path+'_init',
# 'id x y z type mol c_'+cluster_compute)
# py_lmp.dump_modify('test_dump', 'sort id')
# GENERATING INITIAL CONFIGURATION
py_lmp.neigh_modify('every', 1, 'delay', 1)
py_lmp.timestep(run_args.dt)
py_lmp.run(1000)
simulation.unset_state_concentration(0)
py_lmp.unfix(zwalls_fix)
py_lmp.reset_timestep(0)
# ===== MEMBRANE ========================================================================
# create membrane (box update, create membrane & groups, ...)
membrane.create_membrane(py_lmp, seed, append=True)
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))
# GROUPS & COMPUTES
adsorbed_group = 'mem_and_tips'
concentration = run_args.conc / run_args.cell_size**3
mc_exchange_tries = int(0.01 * mc_tries + 1)
simulation.set_state_concentration(0,
concentration,
run_args.mc_every,
mc_exchange_tries,
opt=["overlap_cutoff", overlap])
# OUTPUT
dump_elems = "id x y z type mol"
py_lmp.dump("dump_cmd", "all", "custom", out_freq, '"' + dump_path + '"',
dump_elems)
py_lmp.dump_modify("dump_cmd", "sort id")
py_lmp.thermo_style(
"custom",
"step atoms",
"pe temp",
" ".join([
"v_{}".format(group_var) for group_var in simulation.state_group_vars
]),
"f_{}[2]".format(simulation.state_trans_fix), # state change successes
"f_{}[1]".format(simulation.state_trans_fix)) # state change attempts
py_lmp.thermo(out_freq)
# RUN
py_lmp.neigh_modify("every 1 delay 1")
py_lmp.timestep(run_args.dt)
py_lmp.run(args.simlen)
MPI.Finalize()
