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_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 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.compute("P", "all", "pe/atom")
L.compute(
"coordno", "all", "coord/atom", "cutoff", NNthresh
) # calculate coordination no between all atoms of type 1 or 2 (exclude substrate atoms (type 3)
#L.dump("d1","all","xyz",1000,"output.xyz")
#L.dump("d1","all","custom",1000,"output.out", "id", "type","x","y","z","vx","vy","vz","c_K","c_P","c_coordno")
#L.dump("d1","xtc","atom",100,"T" + str(Temp) + "_Fulltrajectories.xtc",100) # last value gives precision, a value of 100 means that coordinates are stored to 1/100 nanometer accuracy
#L.dump_modify("d1","element","Au","Ni","C")
#L.dump_modify("d1","pbc","yes") # remap atoms via periodic boundary conditions
#L.dump("trajectory","all","atom",100, "T" + str(Temp) + "_Fulltrajectories.lammpstrj")
# Set thermo output to log file
L.thermo_style("custom", "step", "atoms", "temp", "etotal", "pe", "ke",
"dt")
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)
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)
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:
SS_tip_int_key = model.eps[(sol_tip_bead_type, sol_tip_bead_type)][1]
SS_tip_int_range = model.int_types[SS_tip_int_key][1]
micelle_cutoff = 2 * model.rod_radius + SS_tip_int_range
py_lmp.compute(micelle_compute, micelle_group, 'aggregate/atom',
micelle_cutoff)
# OUTPUT
dump_elems = "id x y z type mol"
try:
dump_elems += " c_" + micelle_compute
except:
pass
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")
py_lmp.thermo(out_freq)
# RUN ...
py_lmp.run(args.simlen)
MPI.Finalize()
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)
