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
#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")
L.group("clusterregiongr", "region", "cluster")
L.group("allintegrategr", "region", "allintegr")
L.set("region", "cluster", "type/fraction", 2, xNi, 1234)
L.group("clustergr", "type", 1, 2)
# mit Zhou-Potential:
L.pair_style("hybrid", "eam/alloy", "lj/cut", 10.0, "tersoff")
L.pair_coeff("* * eam/alloy NiAu_Zhou.eam.alloy Au Ni NULL")
L.pair_coeff(1, 3, "lj/cut", epsAuC, sigAuC, 10.0)
L.pair_coeff(2, 3, "lj/cut", epsNiC, sigNiC, 10.0)
L.pair_coeff("* *", "tersoff", "SiC.tersoff", "NULL NULL C")
# mit Ralf Meyers Potential:
# L.pair_style("hybrid","eam/fs","lj/cut",10.0,"tersoff")
# L.pair_coeff("* * eam/fs Ni_Au_SMATB.eam.fs Au Ni NULL")
# L.pair_coeff(1,3,"lj/cut",epsAuC,sigAuC,10.0)
# L.pair_coeff(2,3,"lj/cut",epsNiC,sigNiC,10.0)
# L.pair_coeff("* *","tersoff","SiC.tersoff","NULL NULL C")
