forked from lijiext/lammps
numpy version of neighbor list tests
This commit is contained in:
Axel Kohlmeyer
parent
85a5698c1b
commit
d3b2ccf9dd
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@ -4,6 +4,17 @@ from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL, \
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LMP_VAR_ATOM
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from ctypes import c_void_p
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has_manybody=False
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try:
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machine=None
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if 'LAMMPS_MACHINE_NAME' in os.environ:
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machine=os.environ['LAMMPS_MACHINE_NAME']
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lmp=lammps(name=machine)
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has_manybody = lmp.has_style("pair","sw")
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lmp.close()
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except:
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pass
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try:
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import numpy
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NUMPY_INSTALLED = True
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@ -137,36 +148,34 @@ class PythonNumpy(unittest.TestCase):
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self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
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self.assertEqual(len(v), 2)
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def testNeighborList(self):
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self.lmp.command("units lj")
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self.lmp.command("atom_style atomic")
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self.lmp.command("atom_modify map array")
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self.lmp.command("boundary f f f")
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self.lmp.command("region box block 0 2 0 2 0 2")
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self.lmp.command("create_box 1 box")
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x = [
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1.0, 1.0, 1.0,
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1.0, 1.0, 1.5
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]
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def testNeighborListSimple(self):
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self.lmp.commands_string("""
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units lj
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atom_style atomic
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atom_modify map array
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boundary f f f
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region box block 0 2 0 2 0 2
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create_box 1 box""")
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x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ]
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types = [1, 1]
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self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
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nlocal = self.lmp.extract_global("nlocal")
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self.assertEqual(nlocal, 2)
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self.lmp.command("mass 1 1.0")
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self.lmp.command("velocity all create 3.0 87287")
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self.lmp.command("pair_style lj/cut 2.5")
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self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5")
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self.lmp.command("neighbor 0.1 bin")
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self.lmp.command("neigh_modify every 20 delay 0 check no")
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self.lmp.commands_string("""
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mass 1 1.0
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velocity all create 3.0 87287
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.1 bin
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neigh_modify every 20 delay 0 check no
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run 0 post no""")
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self.lmp.command("run 0")
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self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0)
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nlist = self.lmp.numpy.get_neighlist(0)
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idx = self.lmp.find_pair_neighlist("lj/cut")
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self.assertNotEqual(idx, -1)
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nlist = self.lmp.numpy.get_neighlist(idx)
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self.assertEqual(len(nlist), 2)
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atom_i, neighbors_i = nlist[0]
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atom_j, neighbors_j = nlist[1]
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@ -180,6 +189,190 @@ class PythonNumpy(unittest.TestCase):
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self.assertIn(1, neighbors_i)
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self.assertNotIn(0, neighbors_j)
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def testNeighborListHalf(self):
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self.lmp.commands_string("""
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boundary f f f
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units real
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region box block -5 5 -5 5 -5 5
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create_box 1 box
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mass 1 1.0
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pair_style lj/cut 4.0
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pair_coeff 1 1 0.2 2.0
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""")
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x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
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0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
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0.0, 0.0, 1.0 ]
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tags = [1, 2, 3, 4, 5, 6, 7]
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types = [1, 1, 1, 1, 1, 1, 1]
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self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
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nlocal = self.lmp.extract_global("nlocal")
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self.assertEqual(nlocal, 7)
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self.lmp.command("run 0 post no")
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self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),0)
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nlist = self.lmp.numpy.get_neighlist(0)
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self.assertEqual(nlist.size, 7)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(idx,i)
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self.assertEqual(neighs.size,nlocal-1-i)
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# look up neighbor list by atom index
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neighs = nlist.find(2)
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self.assertEqual(neighs.size,4)
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self.assertIsNotNone(neighs,None)
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# this one will fail
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neighs = nlist.find(10)
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self.assertIsNone(neighs,None)
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@unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential")
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def testNeighborListFull(self):
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self.lmp.commands_string("""
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boundary f f f
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units metal
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region box block -5 5 -5 5 -5 5
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create_box 1 box
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mass 1 1.0
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pair_style sw
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pair_coeff * * Si.sw Si
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""")
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x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
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0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
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0.0, 0.0, 1.0 ]
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tags = [1, 2, 3, 4, 5, 6, 7]
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types = [1, 1, 1, 1, 1, 1, 1]
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self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
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nlocal = self.lmp.extract_global("nlocal")
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self.assertEqual(nlocal, 7)
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self.lmp.command("run 0 post no")
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self.assertEqual(self.lmp.find_pair_neighlist("sw"),0)
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nlist = self.lmp.numpy.get_neighlist(0)
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self.assertEqual(nlist.size, 7)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(idx,i)
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self.assertEqual(neighs.size,nlocal-1)
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@unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential")
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def testNeighborListHybrid(self):
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self.lmp.commands_string("""
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boundary f f f
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units metal
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region box block -5 5 -5 5 -5 5
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create_box 2 box
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mass * 1.0
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pair_style hybrid/overlay morse 4.0 lj/cut 4.0 lj/cut 4.0 sw
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pair_coeff * * sw Si.sw Si NULL
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pair_coeff 1 2 morse 0.2 2.0 2.0
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pair_coeff 2 2 lj/cut 1 0.1 2.0
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pair_coeff * * lj/cut 2 0.01 2.0
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""")
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x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
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0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
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0.0, 0.0, 1.0 ]
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tags = [1, 2, 3, 4, 5, 6, 7]
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types = [1, 1, 1, 1, 2, 2, 2]
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self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
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nlocal = self.lmp.extract_global("nlocal")
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self.assertEqual(nlocal, 7)
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self.lmp.command("run 0 post no")
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# valid and invalid lookups
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self.assertNotEqual(self.lmp.find_pair_neighlist("sw"),-1)
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self.assertNotEqual(self.lmp.find_pair_neighlist("morse"),-1)
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self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=1),-1)
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self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=2),-1)
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self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
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self.assertEqual(self.lmp.find_pair_neighlist("hybrid/overlay"),-1)
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self.assertNotEqual(self.lmp.numpy.get_neighlist(4).size,0)
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self.assertEqual(self.lmp.numpy.get_neighlist(5).size,-1)
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# full neighbor list for 4 type 1 atoms
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# all have 3 type 1 atom neighbors
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nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("sw"))
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self.assertEqual(nlist.size, 4)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(idx,i)
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self.assertEqual(neighs.size,3)
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# half neighbor list for all pairs between type 1 and type 2
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# 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors
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nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("morse"))
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self.assertEqual(nlist.size, 7)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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if (i < 4): self.assertEqual(neighs.size,3)
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else: self.assertEqual(neighs.size,0)
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# half neighbor list between type 2 atoms only
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# 3 pairs with 2, 1, 0 neighbors
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nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1))
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self.assertEqual(nlist.size, 3)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(neighs.size,2-i)
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# half neighbor list between all pairs. same as simple lj/cut case
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nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2))
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self.assertEqual(nlist.size, 7)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(neighs.size,nlocal-1-i)
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def testNeighborListCompute(self):
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self.lmp.commands_string("""
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boundary f f f
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units real
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region box block -5 5 -5 5 -5 5
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create_box 1 box
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mass 1 1.0
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pair_style lj/cut 4.0
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pair_coeff 1 1 0.2 2.0
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compute dist all pair/local dist
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fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector
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thermo_style custom f_dist[*]
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""")
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x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
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0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
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0.0, 0.0, 1.0 ]
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tags = [1, 2, 3, 4, 5, 6, 7]
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types = [1, 1, 1, 1, 1, 1, 1]
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self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
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nlocal = self.lmp.extract_global("nlocal")
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self.assertEqual(nlocal, 7)
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self.lmp.command("run 0 post no")
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# check compute data from histogram summary
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nhisto = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=0)
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nskip = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=1)
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minval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=2)
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maxval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=3)
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# 21 pair distances counted, none skipped, smallest 1.0, largest 2.1
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self.assertEqual(nhisto,21)
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self.assertEqual(nskip,0)
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self.assertEqual(minval,1.0)
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self.assertEqual(maxval,2.1)
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self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
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self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
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# the compute has a half neighbor list
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nlist = self.lmp.numpy.get_neighlist(self.lmp.find_compute_neighlist("dist"))
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self.assertEqual(nlist.size, 7)
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for i in range(0,nlist.size):
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idx, neighs = nlist.get(i)
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self.assertEqual(idx,i)
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self.assertEqual(neighs.size,nlocal-1-i)
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def test_extract_variable_equalstyle(self):
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self.lmp.command("variable a equal 100")
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a = self.lmp.numpy.extract_variable("a")
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