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expand python module unit tests for extract_atom()

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Axel Kohlmeyer
2024-08-31 07:03:14 -04:00
parent 7d176cb66e
commit 2c05378815
1 changed files with 82 additions and 14 deletions
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96
unittest/python/python-numpy.py
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@ -160,31 +160,99 @@ class PythonNumpy(unittest.TestCase):
self.lmp.command("atom_style atomic") self.lmp.command("atom_style atomic")
self.lmp.command("atom_modify map array") self.lmp.command("atom_modify map array")
self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box") self.lmp.command("create_box 2 box")
x = [ x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5, 1.5, 1.0, 1.0 ]
1.0, 1.0, 1.0, types = [1, 2, 1]
1.0, 1.0, 1.5 ids = [1, 2, 3]
] self.assertEqual(self.lmp.create_atoms(3, id=ids, type=types, x=x), 3)
self.lmp.command("mass * 2.0")
self.lmp.command("pair_style zero 1.1")
self.lmp.command("pair_coeff * *")
self.lmp.command("fix props all property/atom i_one i2_two 2 d_three d2_four 2");
self.lmp.command("fix rmass all property/atom mol q rmass ghost yes");
self.lmp.command("fix 1 all nve")
self.lmp.command("run 0 post no")
ntypes = self.lmp.extract_setting("ntypes");
nlocal = self.lmp.extract_setting("nlocal");
nall = self.lmp.extract_setting("nall");
self.assertEqual(nlocal, 3)
self.assertEqual(ntypes, 2)
self.assertEqual(nall, 63)
types = [1, 1] self.lmp.command("set atom 1 charge -1");
self.lmp.command("set atom 2 charge 1");
self.lmp.command("set atom 3 charge 0");
self.lmp.command("set atom * mol 2");
self.lmp.command("set atom 2 mol 1");
self.lmp.command("set atom 1 i_one -3");
self.lmp.command("set atom 2 i_one 3");
self.lmp.command("set atom 2 d_three -1.3");
self.lmp.command("set atom 3 d_three 3.5");
self.lmp.command("set atom 1 i_two[1] -3");
self.lmp.command("set atom 2 i_two[2] 3");
self.lmp.command("set atom * d_four[1] -1.3");
self.lmp.command("set atom * d_four[2] 3.5");
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) mass = self.lmp.numpy.extract_atom("mass")
nlocal = self.lmp.extract_global("nlocal") self.assertEqual(len(mass), ntypes + 1)
self.assertEqual(nlocal, 2) self.assertTrue((mass == (0.0, 2.0, 2.0)).all())
rmass = self.lmp.numpy.extract_atom("rmass")
self.assertEqual(len(rmass), nall)
self.assertTrue((rmass[0:3] == (0.0, 0.0, 0.0)).all())
charge = self.lmp.numpy.extract_atom("q")
self.assertEqual(len(charge), nall)
self.assertTrue((charge[0:3] == (-1.0, 1.0, 0.0)).all())
molecule = self.lmp.numpy.extract_atom("molecule")
self.assertEqual(len(molecule), nall)
self.assertTrue((molecule[0:3] == (2, 1, 2)).all())
ident = self.lmp.numpy.extract_atom("id") ident = self.lmp.numpy.extract_atom("id")
self.assertEqual(len(ident), 2) self.assertEqual(len(ident), nall)
self.assertTrue((ident[0:3] == (1, 2, 3)).all())
ntypes = self.lmp.extract_global("ntypes") atype = self.lmp.numpy.extract_atom("type")
self.assertEqual(ntypes, 1) self.assertEqual(len(atype), nall)
self.assertTrue((atype[0:3] == (1, 2, 1)).all())
x = self.lmp.numpy.extract_atom("x") x = self.lmp.numpy.extract_atom("x")
v = self.lmp.numpy.extract_atom("v") v = self.lmp.numpy.extract_atom("v")
self.assertEqual(len(x), 2) self.assertEqual(len(x), nall)
self.assertEqual(len(x[0]), 3)
self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all())
self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
self.assertEqual(len(v), 2) self.assertTrue((x[2] == (1.5, 1.0, 1.0)).all())
self.assertEqual(len(v), nlocal)
self.assertEqual(len(v[0]), 3)
self.lmp.command("comm_modify vel yes");
self.lmp.command("run 0 post no")
v = self.lmp.numpy.extract_atom("v")
self.assertEqual(len(v), nall)
one = self.lmp.numpy.extract_atom("i_one")
two = self.lmp.numpy.extract_atom("i2_two")
three = self.lmp.numpy.extract_atom("d_three")
four = self.lmp.numpy.extract_atom("d2_four")
self.assertEqual(len(one), nlocal)
self.assertTrue((one == (-3, 3, 0)).all())
self.assertEqual(len(two), nlocal)
self.assertEqual(len(two[0]), 2)
self.assertTrue((two[0] == (-3, 0)).all())
self.assertTrue((two[1] == (0, 3)).all())
self.assertTrue((two[2] == (0, 0)).all())
self.assertEqual(len(three), nlocal)
self.assertTrue((three == (0.0, -1.3, 3.5)).all())
self.assertEqual(len(four), nlocal)
self.assertEqual(len(four[0]), 2)
self.assertTrue((four[0] == (-1.3, 3.5)).all())
self.assertTrue((four[1] == (-1.3, 3.5)).all())
self.assertTrue((four[2] == (-1.3, 3.5)).all())
@unittest.skipIf(not has_full,"Gather bonds test") @unittest.skipIf(not has_full,"Gather bonds test")
def testGatherBond_newton_on(self): def testGatherBond_newton_on(self):