216 lines
7.0 KiB
Python
216 lines
7.0 KiB
Python
import sys,os,unittest
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from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL, \
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LMP_STYLE_ATOM, LMP_TYPE_VECTOR, LMP_TYPE_SCALAR, LMP_TYPE_ARRAY, \
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LMP_VAR_ATOM
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from ctypes import c_void_p
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try:
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import numpy
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NUMPY_INSTALLED = True
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except ImportError:
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NUMPY_INSTALLED = False
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@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
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class PythonNumpy(unittest.TestCase):
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def setUp(self):
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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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self.lmp = lammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo','screen'])
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def tearDown(self):
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del self.lmp
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def testLammpsPointer(self):
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self.assertEqual(type(self.lmp.lmp), c_void_p)
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def testExtractComputeGlobalScalar(self):
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# TODO
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pass
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def testExtractComputeGlobalVector(self):
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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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self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
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self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
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self.lmp.command("compute coordsum all reduce sum x y z")
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natoms = self.lmp.get_natoms()
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self.assertEqual(natoms,2)
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values = self.lmp.numpy.extract_compute("coordsum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
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self.assertEqual(len(values), 3)
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self.assertEqual(values[0], 2.0)
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self.assertEqual(values[1], 2.0)
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self.assertEqual(values[2], 2.5)
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def testExtractComputeGlobalArray(self):
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# TODO
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pass
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def testExtractComputePerAtomVector(self):
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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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self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
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self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
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self.lmp.command("compute ke all ke/atom")
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natoms = self.lmp.get_natoms()
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self.assertEqual(natoms,2)
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values = self.lmp.numpy.extract_compute("ke", LMP_STYLE_ATOM, LMP_TYPE_VECTOR)
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self.assertEqual(len(values), 2)
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self.assertEqual(values[0], 0.0)
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self.assertEqual(values[1], 0.0)
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def testExtractComputePerAtomArray(self):
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# TODO
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pass
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def testExtractComputeLocalScalar(self):
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# TODO
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pass
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def testExtractComputeLocalVector(self):
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# TODO
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pass
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def testExtractComputeLocalArray(self):
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# TODO
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pass
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def testExtractAtomDeprecated(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("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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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", LAMMPS_INT)
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self.assertEqual(nlocal, 2)
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ident = self.lmp.numpy.extract_atom_iarray("id", nlocal, dim=1)
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self.assertEqual(len(ident), 2)
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ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT)
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self.assertEqual(ntypes, 1)
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x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3)
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v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
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self.assertEqual(len(x), 2)
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self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all())
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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 testExtractAtom(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("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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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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ident = self.lmp.numpy.extract_atom("id")
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self.assertEqual(len(ident), 2)
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ntypes = self.lmp.extract_global("ntypes")
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self.assertEqual(ntypes, 1)
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x = self.lmp.numpy.extract_atom("x")
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v = self.lmp.numpy.extract_atom("v")
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self.assertEqual(len(x), 2)
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self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all())
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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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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.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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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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self.assertEqual(atom_i, 0)
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self.assertEqual(atom_j, 1)
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self.assertEqual(len(neighbors_i), 1)
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self.assertEqual(len(neighbors_j), 0)
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self.assertIn(1, neighbors_i)
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self.assertNotIn(0, neighbors_j)
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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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self.assertEqual(a, 100)
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self.lmp.command("variable a equal 3.14")
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a = self.lmp.numpy.extract_variable("a")
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self.assertEqual(a, 3.14)
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def test_extract_variable_atomstyle(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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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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self.lmp.command("variable a atom x*x+y*y+z*z")
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a = self.lmp.numpy.extract_variable("a", "all", LMP_VAR_ATOM)
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self.assertIs(type(a), numpy.ndarray)
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self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2])
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self.assertEqual(a[1], x[3]*x[3]+x[4]*x[4]+x[5]*x[5])
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if __name__ == "__main__":
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unittest.main()
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