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)
membrane.ymax - model.rod_length / 2, 0.0 + model.rod_length / 2,
run_args.Lz - model.rod_length / 2)
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))
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)
# 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',
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)