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)
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("thermofix2")
#initial equilibration procedure finished:
print("****************************************")
print("initial equilibration procedure finished, writing restart file")
print("****************************************")
L.write_restart("restart.equil")
L.write_restart("restartfromprevdispl.equil")
else:
L.read_restart("restart.equil")
L.velocity("all", "create", Temp, 12345, "dist", "gaussian", "mom", "yes",
"rot", "yes")
#L.fix("mainvartimestep","clustergr","dt/reset",10,"NULL","NULL",latticeconst/30,"emax",0.1,"units","box")
L.fix("mainvartimestep", "clustergr", "dt/reset", 1, "NULL", "NULL", 0.1,
"units", "box")
L.fix("linmomfix", "clustergr", "momentum", 1, "linear", 1, 1,
1) # remove linear momentum for better displacement detection
#L.fix("thermofix3","clustergr","langevin",Temp,Temp,0.05, 2614,"zero","yes")
#L.fix("thermofix3","clustergr","temp/csvr",Temp,Temp,0.1,12345)
nodispl = 0
nosputt = 0
displacement = False
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)
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("thermofix2")
#initial equilibration procedure finished:
print("****************************************")
print("initial equilibration procedure finished, writing restart file")
print("****************************************")
L.write_restart("restart.equil")
else:
L.read_restart("restart.equil")
L.velocity("all", "create", Temp, 12345, "dist", "gaussian", "mom", "yes",
"rot", "yes")
#L.fix("mainvartimestep","clustergr","dt/reset",10,"NULL","NULL",latticeconst/30,"emax",0.1,"units","box")
L.fix("mainvartimestep", "clustergr", "dt/reset", 1, "NULL", "NULL", 0.1,
"units", "box")
L.fix("linmomfix", "clustergr", "momentum", 1, "linear", 1, 1,
1) # remove linear momentum for better displacement detection
#L.fix("thermofix3","clustergr","langevin",Temp,Temp,0.05, 2614,"zero","yes")
#L.fix("thermofix3","clustergr","temp/csvr",Temp,Temp,0.1,12345)
nodispl = 0
nosputt = 0
displacement = False