import sys,os,unittest from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL, \ LMP_STYLE_ATOM, LMP_TYPE_VECTOR, LMP_TYPE_SCALAR, LMP_TYPE_ARRAY, \ LMP_VAR_ATOM from ctypes import c_void_p try: import numpy NUMPY_INSTALLED = True except ImportError: NUMPY_INSTALLED = False @unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available") class PythonNumpy(unittest.TestCase): def setUp(self): machine = None if 'LAMMPS_MACHINE_NAME' in os.environ: machine=os.environ['LAMMPS_MACHINE_NAME'] self.lmp = lammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo','screen']) def tearDown(self): del self.lmp def testLammpsPointer(self): self.assertEqual(type(self.lmp.lmp), c_void_p) def testExtractComputeGlobalScalar(self): # TODO pass def testExtractComputeGlobalVector(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("compute coordsum all reduce sum x y z") natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) values = self.lmp.numpy.extract_compute("coordsum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR) self.assertEqual(len(values), 3) self.assertEqual(values[0], 2.0) self.assertEqual(values[1], 2.0) self.assertEqual(values[2], 2.5) def testExtractComputeGlobalArray(self): # TODO pass def testExtractComputePerAtomVector(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("compute ke all ke/atom") natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) values = self.lmp.numpy.extract_compute("ke", LMP_STYLE_ATOM, LMP_TYPE_VECTOR) self.assertEqual(len(values), 2) self.assertEqual(values[0], 0.0) self.assertEqual(values[1], 0.0) def testExtractComputePerAtomArray(self): # TODO pass def testExtractComputeLocalScalar(self): # TODO pass def testExtractComputeLocalVector(self): # TODO pass def testExtractComputeLocalArray(self): # TODO pass def testExtractAtomDeprecated(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) self.assertEqual(nlocal, 2) ident = self.lmp.numpy.extract_atom_iarray("id", nlocal, dim=1) self.assertEqual(len(ident), 2) ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT) self.assertEqual(ntypes, 1) x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3) v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) self.assertEqual(len(x), 2) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) def testExtractAtom(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) ident = self.lmp.numpy.extract_atom("id") self.assertEqual(len(ident), 2) ntypes = self.lmp.extract_global("ntypes") self.assertEqual(ntypes, 1) x = self.lmp.numpy.extract_atom("x") v = self.lmp.numpy.extract_atom("v") self.assertEqual(len(x), 2) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) def testNeighborList(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("boundary f f f") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) self.lmp.command("mass 1 1.0") self.lmp.command("velocity all create 3.0 87287") self.lmp.command("pair_style lj/cut 2.5") self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5") self.lmp.command("neighbor 0.1 bin") self.lmp.command("neigh_modify every 20 delay 0 check no") self.lmp.command("run 0") self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0) nlist = self.lmp.numpy.get_neighlist(0) self.assertEqual(len(nlist), 2) atom_i, neighbors_i = nlist[0] atom_j, neighbors_j = nlist[1] self.assertEqual(atom_i, 0) self.assertEqual(atom_j, 1) self.assertEqual(len(neighbors_i), 1) self.assertEqual(len(neighbors_j), 0) self.assertIn(1, neighbors_i) self.assertNotIn(0, neighbors_j) def test_extract_variable_equalstyle(self): self.lmp.command("variable a equal 100") a = self.lmp.numpy.extract_variable("a") self.assertEqual(a, 100) self.lmp.command("variable a equal 3.14") a = self.lmp.numpy.extract_variable("a") self.assertEqual(a, 3.14) def test_extract_variable_atomstyle(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("boundary f f f") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) self.lmp.command("variable a atom x*x+y*y+z*z") a = self.lmp.numpy.extract_variable("a", "all", LMP_VAR_ATOM) self.assertIs(type(a), numpy.ndarray) self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2]) self.assertEqual(a[1], x[3]*x[3]+x[4]*x[4]+x[5]*x[5]) if __name__ == "__main__": unittest.main()