def testConstruction(self): """ Test the construction of the unitcell """ vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0] vector_c = [0.0, 0.0, 11.8] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]] cell_vectors = [vector_a, vector_b, vector_c] cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Check the vectors stored on the class. ref_vectors = numpy.array(cell_vectors) check_vectors = cell._KMCUnitCell__cell_vectors self.assertAlmostEqual( numpy.linalg.norm(ref_vectors - check_vectors), 0.0, 10) # Check via the query function. ret_vectors = cell.cellVectors() self.assertAlmostEqual( numpy.linalg.norm(ref_vectors - ret_vectors), 0.0, 10) # Check the basis points stored on the class. ref_basis = numpy.array(basis_points) check_basis = cell._KMCUnitCell__basis_points self.assertAlmostEqual( numpy.linalg.norm(ref_basis - check_basis), 0.0, 10)
def testConstructionFailBasis2(self): """ Make sure construction fails if there is a problem with the basis points. """ vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0] vector_c = [0.0, 0.0, 11.8] basis_points = [ [0.0, 0.0, 1.1], # <- too large value [0.5, 0.5, 0.5] ] cell_vectors = [vector_a, vector_b, vector_c] self.assertRaises( Error, lambda: KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points)) vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0] vector_c = [0.0, 0.0, 11.8] basis_points = [ [0.0, 0.0, 1.0], # <- too large value [0.5, 0.5, 0.5] ] cell_vectors = [vector_a, vector_b, vector_c] self.assertRaises( Error, lambda: KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points)) vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0] vector_c = [0.0, 0.0, 11.8] basis_points = [[0.0, 0.0, 0.999999], [0.5, 0.5, -0.01]] # <- too small value cell_vectors = [vector_a, vector_b, vector_c] self.assertRaises( Error, lambda: KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points))
def testConstruction(self): """ Test the construction of the unitcell """ vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0] vector_c = [0.0, 0.0, 11.8] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]] cell_vectors = [vector_a, vector_b, vector_c] cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Check the vectors stored on the class. ref_vectors = numpy.array(cell_vectors) check_vectors = cell._KMCUnitCell__cell_vectors self.assertAlmostEqual(numpy.linalg.norm(ref_vectors - check_vectors), 0.0, 10) # Check via the query function. ret_vectors = cell.cellVectors() self.assertAlmostEqual(numpy.linalg.norm(ref_vectors - ret_vectors), 0.0, 10) # Check the basis points stored on the class. ref_basis = numpy.array(basis_points) check_basis = cell._KMCUnitCell__basis_points self.assertAlmostEqual(numpy.linalg.norm(ref_basis - check_basis), 0.0, 10)
def testTransformToCartesian(self): """ Test the transformation from internal to cartesian coordinates. """ # Setup a simple reference system. a = numpy.array([[1.0, 2.0, 3.0], [1.1, 0.4, 3.7], [1.2, 2.5, 0.8]]) r = numpy.array([[1.2, 2.5, 3.8], [3.2, 4.5, 5.8]]) ref_xyz = numpy.dot(r, a) # Cell vectors. vector_a = [1.0, 2.0, 3.0] vector_b = [1.1, 0.4, 3.7] vector_c = [1.2, 2.5, 0.8] cell_vectors = [vector_a, vector_b, vector_c] cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=[[0.0, 0.0, 0.0]]) # Transform r to cartesian coordinates. xyz = cell.transformToCartesian(r) diff = numpy.linalg.norm(xyz - ref_xyz) self.assertAlmostEqual(diff, 0.0, 10)
def testGlobalIndex(self): """ Test that the global index function returns correct values. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the repetitions. nI = 2 nJ = 12 nK = 3 nB = 2 repetitions = (nI, nJ, nK) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Loop through all indices and check that the globalIndex function computes them correctly. increment = 0 for i in range(nI): for j in range(nJ): for k in range(nK): for b in range(nB): index = lattice._globalIndex(i, j, k, b) self.assertEqual(index, increment) increment += 1
def testConstructionFailPeriodic(self): """ Test that construction of the lattice fails if the periodic parameter is incorrect.""" # Setup a valid unitcell. cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) repetitions = (10, 12, 45) # Fail because of not being a sequence. periodic = True self.assertRaises( Error, lambda: KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic)) # Fail because of wrong length. periodic = (True, True, True, True) self.assertRaises( Error, lambda: KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic)) # Fail because of wrong type. periodic = (True, True, 1) self.assertRaises( Error, lambda: KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic))
def testLatticeQuery(self): """ Test the query function for the lattice. """ # Setup a valid KMCUnitCell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]]), basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) # Setup the lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 4, 1), periodic=(True, True, False)) types = [ 'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a' ] # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, possible_types=['a', 'c', 'b']) # Query for the lattice. ret_lattice = config.lattice() # Check by reference. self.assertTrue(lattice == ret_lattice)
def testLatticeMap(self): """ Check that we can get a valid lattice map out. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the repetitions. nI = 2 nJ = 12 nK = 3 nB = 2 repetitions = (nI, nJ, nK) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Get the lattice map. cpp_lattice_map = lattice._map() # Check the type. self.assertTrue(isinstance(cpp_lattice_map, Backend.LatticeMap)) # Get it again and check that we get the same instance. cpp_lattice_map2 = lattice._map() # Check the instance. self.assertTrue(cpp_lattice_map == cpp_lattice_map2)
def testConstruction(self): """ Test that the XYZTrajectory object can be constructed. """ filename = "abc123.xyz" name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") filename = os.path.join(name, filename) if MPICommons.isMaster(): self.__files_to_remove.append(filename) unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, True, True), repetitions=(4,4,4)) config = KMCConfiguration(lattice=lattice, types=["A","B","C","D"]*16) t = XYZTrajectory(trajectory_filename=filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) # Check that the internal memory buffers have been initiated. self.assertEqual(t._XYZTrajectory__atom_id_types, []) self.assertEqual(t._XYZTrajectory__atom_id_coordinates, []) self.assertEqual(t._XYZTrajectory__time, []) self.assertEqual(t._XYZTrajectory__step, [])
def testLatticeMap(self): """ Make sure the lattice map we get correspond to the lattice we give. """ # Setup a valid KMCUnitCell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]]), basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) # Setup the lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 4, 1), periodic=(True, True, False)) types = [ 'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a' ] # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, possible_types=['a', 'c', 'b']) # Get the lattice map. cpp_lattice_map = config._latticeMap() # Get the map from the lattice. cpp_lattice_map_ref = lattice._map() # Check that these two are references to the same underlying object. self.assertTrue(cpp_lattice_map == cpp_lattice_map_ref)
def notestTypesBucketFormat(self): """ Test that the configuration accepts the bucket input format. """ # Define the unit cell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.1, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]), basis_points=[[0.0, 0.0, 0.0]]) # And a lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(10, 1, 1), periodic=(True, False, False)) # Populate the lattice with types. types = [(2, "A"), "B", ["B", "B", "A"], ["B", (2, "A")], "B", "empty", [(3, "A")], [(1, "B"), "A"], [(2, "A")], "empty"] # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, possible_types=['A', 'B', 'empty']) # Retrieve the types information from the configuration backend. # FXME: NEEDS IMPLEMENTATION print config.types()
def testQueryUnitCell(self): """ Test that the unitcell query function returns correctly. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the repetitions. nI = 2 nJ = 12 nK = 3 nB = 2 repetitions = (nI, nJ, nK) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Query. ret_unit_cell = lattice.unitCell() # Test by reference. self.assertTrue(unit_cell == ret_unit_cell)
def testConstructionLongFormat(self): """ Test that the KMCConfiguration class can be constructed with the long types format. """ # Setup a valid KMCUnitCell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]]), basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) # Setup the lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 3, 2), periodic=(True, True, False)) types = [(0, 0, 0, 0, 'g'), (3, 2, 1, 2, 'h')] default_type = 'a' # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, default_type=default_type) # Get the types information out. ret_types = config.types() ref_types = [ 'g', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'h' ] # Check that they are what we inserted. self.assertEqual(ref_types, ret_types) # Check that the possible types are what we expect. self.assertEqual(set(['a', 'g', 'h', '*']), set(config._KMCConfiguration__possible_types)) # Check that the number of lattice sites corresponds # to the lattice. self.assertEqual(config._KMCConfiguration__n_lattice_sites, len(lattice.sites())) # Construct again, now with a list of possible types. config = KMCConfiguration(lattice=lattice, types=types, default_type=default_type, possible_types=['aa', 'a', 'h', 'g']) # Check that the possible types are what we expect. self.assertEqual(set(['aa', 'a', 'g', 'h', '*']), set(config._KMCConfiguration__possible_types))
def testConstructionFailVectors(self): """ Make sure construction fails if there is a problem with the unitcell vectors. """ vector_a = [2.3, 0.0, 0.0] vector_b = [2.4, 3.0, 0.0, 1.3] # <- wrong shape vector_c = [0.0, 0.0, 11.8] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]] cell_vectors = [vector_a, vector_b, vector_c] self.assertRaises( Error, lambda: KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points))
def testConstructionShortFormat(self): """ Test that the KMCConfiguration class can be constructed. """ # Setup a valid KMCUnitCell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]]), basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) # Setup the lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 4, 1), periodic=(True, True, False)) types = [ 'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a' ] # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, possible_types=['a', 'c', 'b']) # Get the types information out. ret_types = config.types() # Check that they are what we inserted. self.assertEqual(types, ret_types) # Check that the possible types are what we expect. self.assertEqual(set(['a', 'c', 'b', '*']), set(config._KMCConfiguration__possible_types.keys())) # Check that the number of lattice sites corresponds to the lattice. self.assertEqual(config._KMCConfiguration__n_lattice_sites, len(lattice.sites())) # Check that the lattice site can be returned from the configuration. self.assertAlmostEqual( numpy.linalg.norm( numpy.array(config.sites()) - numpy.array(lattice.sites())), 0.0, 10) # Construct without possible types and check that the list is set correctly # from the given types. config = KMCConfiguration(lattice=lattice, types=types) self.assertEqual(set(['a', 'b', '*']), set(config._KMCConfiguration__possible_types.keys()))
def testQueryLatticeSites(self): """ Test that the returned lattice site data is coorect. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the other input. repetitions = (2, 1, 1) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # These are all the sites in the lattice, given in # the fractional coordinates of the original cell. sites = lattice.sites() ref_sites = numpy.array([[0., 0., 0.], [0.5, 0.5, 0.], [1., 0., 0.], [1.5, 0.5, 0.]]) # Check against a hardcoded reference. self.assertAlmostEqual(numpy.linalg.norm(sites - ref_sites), 0.0, 10) # Test with another repetition. repetitions = (2, 3, 4) lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) sites = lattice.sites() ref_sites = numpy.array([[0., 0., 0.], [0.5, 0.5, 0.], [0., 0., 1.], [0.5, 0.5, 1.], [0., 0., 2.], [0.5, 0.5, 2.], [0., 0., 3.], [0.5, 0.5, 3.], [0., 1., 0.], [0.5, 1.5, 0.], [0., 1., 1.], [0.5, 1.5, 1.], [0., 1., 2.], [0.5, 1.5, 2.], [0., 1., 3.], [0.5, 1.5, 3.], [0., 2., 0.], [0.5, 2.5, 0.], [0., 2., 1.], [0.5, 2.5, 1.], [0., 2., 2.], [0.5, 2.5, 2.], [0., 2., 3.], [0.5, 2.5, 3.], [1., 0., 0.], [1.5, 0.5, 0.], [1., 0., 1.], [1.5, 0.5, 1.], [1., 0., 2.], [1.5, 0.5, 2.], [1., 0., 3.], [1.5, 0.5, 3.], [1., 1., 0.], [1.5, 1.5, 0.], [1., 1., 1.], [1.5, 1.5, 1.], [1., 1., 2.], [1.5, 1.5, 2.], [1., 1., 3.], [1.5, 1.5, 3.], [1., 2., 0.], [1.5, 2.5, 0.], [1., 2., 1.], [1.5, 2.5, 1.], [1., 2., 2.], [1.5, 2.5, 2.], [1., 2., 3.], [1.5, 2.5, 3.]]) # Check against a hardcoded reference. self.assertAlmostEqual(numpy.linalg.norm(sites - ref_sites), 0.0, 10)
def testScript(self): """ Test that a valid script can be generated. """ # Setup a valid cell. vector_a = [2.3, 1.0, 0.1] vector_b = [2.4, 3.0, 0.0] vector_c = [0.4, 0.3, 11.8] basis_points = [[0.4, 0.3, 0.2], [0.2, 0.33, 0.11], [0.6, 0.5, 0.1]] cell_vectors = [vector_a, vector_b, vector_c] cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Get the script. script = cell._script() # Check against the known reference script. ref_script = """ # ----------------------------------------------------------------------------- # Unit cell cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01], [ 2.400000e+00, 3.000000e+00, 0.000000e+00], [ 4.000000e-01, 3.000000e-01, 1.180000e+01]] basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01], [ 2.000000e-01, 3.300000e-01, 1.100000e-01], [ 6.000000e-01, 5.000000e-01, 1.000000e-01]] unit_cell = KMCUnitCell( cell_vectors=cell_vectors, basis_points=basis_points) """ self.assertEqual(script, ref_script) # Setup another valid cell. vector_a = [2.3, 1.0, 0.1] vector_b = [2.4, 3.0, 0.0] vector_c = [0.4, 0.3, 11.8] basis_points = [[0.4, 0.3, 0.2]] cell_vectors = [vector_a, vector_b, vector_c] cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) script = cell._script(variable_name="CELL_NAME_HERE") # Check against the known reference. ref_script = """ # ----------------------------------------------------------------------------- # Unit cell cell_vectors = [[ 2.300000e+00, 1.000000e+00, 1.000000e-01], [ 2.400000e+00, 3.000000e+00, 0.000000e+00], [ 4.000000e-01, 3.000000e-01, 1.180000e+01]] basis_points = [[ 4.000000e-01, 3.000000e-01, 2.000000e-01]] CELL_NAME_HERE = KMCUnitCell( cell_vectors=cell_vectors, basis_points=basis_points) """ self.assertEqual(script, ref_script)
def testWriteHeader(self): """ Test the header output. """ # Get a file name. name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") trajectory_filename = os.path.join(name, "tmp_trajectory.xyz") if MPICommons.isMaster(): self.__files_to_remove.append(trajectory_filename) # Setup the trajectory object. unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, True, True), repetitions=(4,2,3)) config = KMCConfiguration(lattice=lattice, types=["A","B","C"]*8) t = XYZTrajectory(trajectory_filename=trajectory_filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) if MPICommons.isMaster(): # Check that the header was written. self.assertTrue(os.path.exists(trajectory_filename)) # Check the content of the header. with open(trajectory_filename, "r") as f: content = f.read() ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15 CELL VECTORS a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 REPETITIONS 4 2 3 PERIODICITY True True True """ self.assertEqual( content, ref_content )
def testQueryRepetitionsAndPeriodic(self): """ Test that the returned repetitions data is coorect. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the repetitions. repetitions = (2, 1, 1) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Check that the repetitions are the same. self.assertEqual(lattice.repetitions()[0], repetitions[0]) self.assertEqual(lattice.repetitions()[1], repetitions[1]) self.assertEqual(lattice.repetitions()[2], repetitions[2]) # Check that the periodic is the same. self.assertTrue(lattice.periodic()[0]) self.assertTrue(lattice.periodic()[1]) self.assertFalse(lattice.periodic()[2]) # Setup again with different periodicity and check. periodic = (True, False, True) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) self.assertTrue(lattice.periodic()[0]) self.assertFalse(lattice.periodic()[1]) self.assertTrue(lattice.periodic()[2]) # And again. periodic = (False, True, True) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) self.assertFalse(lattice.periodic()[0]) self.assertTrue(lattice.periodic()[1]) self.assertTrue(lattice.periodic()[2])
def testGetScriptComponent(self): """ Test the general get script component function. """ # Set the path to the file to read from. module_path = os.path.abspath(os.path.dirname(__file__)) script_file_path = os.path.join(module_path, "..", "TestUtilities", "Scripts") script_file_path = os.path.join(script_file_path, "kmc_configuration_script.py") # Make sure the file exists. self.assertTrue(os.path.exists(script_file_path)) # Get the KMCLattice out of this script. lattice = getScriptComponent(script_file_path, KMCLattice) # Check that it is the correct lattice by cheking its values # against these known references. unit_cell = KMCUnitCell(cell_vectors=[[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]], basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) ref_lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 4, 1), periodic=(True, True, False)) self.assertEqual(lattice.repetitions(), ref_lattice.repetitions()) self.assertEqual(lattice.periodic(), ref_lattice.periodic()) self.assertAlmostEqual( numpy.linalg.norm( numpy.array(lattice.sites()) - numpy.array(ref_lattice.sites())), 0.0, 12) self.assertEqual( numpy.linalg.norm( numpy.array(lattice.basis()) - numpy.array(ref_lattice.basis())), 0.0, 12) # Check that the function returns None if no component of the correct type is found. self.assertTrue( (getScriptComponent(script_file_path, numpy.ndarray) is None)) # Check that we fail in a controlled way if there is a problme with the file. self.assertRaises( Error, lambda: getScriptComponent("THIS IS NOT A VALID PATH", numpy .ndarray))
def testConstruction(self): """ Test the construction of the lattice """ # Setup a valid unitcell. cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the other input. repetitions = (10, 12, 45) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Check that the unitcell object stored on the class # is the same one as constructed here (checked by reference) self.assertTrue(unit_cell == lattice._KMCLattice__unit_cell)
def testQueryBasis(self): """ Test that the returned basis data is coorect. """ cell_vectors = [[2.3, 0.0, 0.0], [2.4, 3.0, 0.0], [0.0, 0.0, 11.8]] basis_points = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]] unit_cell = KMCUnitCell(cell_vectors=cell_vectors, basis_points=basis_points) # Setup the repetitions. repetitions = (2, 1, 1) periodic = (True, True, False) # Construct the KMCLattice object. lattice = KMCLattice(unit_cell=unit_cell, repetitions=repetitions, periodic=periodic) # Check that the basis is the one from the unitcell. self.assertAlmostEqual( numpy.linalg.norm(lattice.basis() - lattice._KMCLattice__unit_cell.basis()), 0.0, 10)
def testBackend(self): """ Make sure the C++ backend is what we expect. """ # Setup a valid KMCUnitCell. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0], [0.0, 3.2, 0.0], [0.0, 0.5, 3.0]]), basis_points=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.25, 0.25, 0.75]]) # Setup the lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(4, 4, 1), periodic=(True, True, False)) types = [ 'a', 'a', 'a', 'a', 'b', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'b', 'a', 'b', 'b', 'b', 'a', 'b', 'a', 'b', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'b', 'a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'a', 'b', 'b', 'a' ] # Setup the configuration. config = KMCConfiguration(lattice=lattice, types=types, possible_types=['a', 'c', 'b']) # Make sure that the backend stored on the config is None. self.assertTrue(config._KMCConfiguration__backend is None) # Query for the backend. cpp_backend = config._backend() # Check that the backend on the class is returned. self.assertTrue(config._KMCConfiguration__backend == cpp_backend) # Check the type of the cpp backend. self.assertTrue(isinstance(cpp_backend, Backend.Configuration))
def testCalculation(self): """ Test a calculation with the on-the-fly MSD analysis. """ # Setup a system, a periodic 10 atoms long 1D chain. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0], [0.0,1.0,0.0], [0.0,0.0,1.0]]), basis_points=[[0.0,0.0,0.0]]) # And a lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(10,10,10), periodic=(True,True,True)) # Setup an initial configuration with one B in a sea of A:s. types = ["A"]*10*10*10 types[5] = "B" config = KMCConfiguration(lattice=lattice, types=types, possible_types=["A","B"]) # Setup a diffusion process to the left. coordinates_p0 = [[0.0, 0.0, 0.0],[-1.0, 0.0, 0.0]] p0 = KMCProcess(coordinates=coordinates_p0, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p1 = [[0.0, 0.0, 0.0],[1.0, 0.0, 0.0]] p1 = KMCProcess(coordinates=coordinates_p1, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p2 = [[0.0, 0.0, 0.0],[0.0,-1.0, 0.0]] p2 = KMCProcess(coordinates=coordinates_p2, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p3 = [[0.0, 0.0, 0.0],[0.0, 1.0, 0.0]] p3 = KMCProcess(coordinates=coordinates_p3, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p4 = [[0.0, 0.0, 0.0],[0.0, 0.0,-1.0]] p4 = KMCProcess(coordinates=coordinates_p4, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p5 = [[0.0, 0.0, 0.0],[0.0, 0.0, 1.0]] p5 = KMCProcess(coordinates=coordinates_p5, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) interactions = KMCInteractions(processes=[p0, p1, p2, p3, p4, p5], implicit_wildcards=True) model = KMCLatticeModel(configuration=config, interactions=interactions) # Setup the analysis. msd = OnTheFlyMSD(history_steps=400, n_bins=10, t_max=25.0, track_type="B") # Setup the control parameters. control_parameters = KMCControlParameters(number_of_steps=4000, dump_interval=100, analysis_interval=1, seed=2013) # Run the model. model.run(control_parameters=control_parameters, analysis=[msd]) # Get the results out. results = msd.results() time_steps = msd.timeSteps() std_dev = msd.stdDev() bin_counters = msd.binCounters() # Compare against references. ref_results = numpy.array([[ 2.77712331 , 8.22333156 , 14.21578638 , 21.11949845 , 27.57598537, 33.81520414, 40.5640313 , 47.35067074, 54.83134718, 63.0006103 ], [ 2.80810946 , 8.48503234 , 13.7997313 , 17.62812205 , 22.37202018, 29.12157221, 35.40750463, 41.44944591, 48.94392653, 56.67111894], [ 2.98786918 , 8.65022668 , 14.01808716 , 18.62678885 , 22.65708384, 26.03107861, 30.03937616, 35.1483 , 40.68319007, 47.21074474], [ 5.58523277 , 16.70836389 , 28.01551768 , 38.74762049 , 49.94800555, 62.93677636, 75.97153593, 88.80011665, 103.77527371, 119.67172924], [ 5.76499249 , 16.87355824 , 28.23387354 , 39.7462873 , 50.23306921, 59.84628275, 70.60340745, 82.49897073, 95.51453725, 110.21135504], [ 5.79597864 , 17.13525902 , 27.81781846 , 36.2549109 , 45.02910402, 55.15265082, 65.44688079, 76.59774591, 89.62711659, 103.88186368], [ 8.57310195 , 25.35859057 , 42.03360484 , 57.37440934 , 72.60508939, 88.96785497, 106.01091209, 123.94841665, 144.45846377, 166.88247398]]) diff = numpy.linalg.norm(ref_results - results) self.assertAlmostEqual(diff, 0.0, 6) ref_time_steps = numpy.array([ 1.25, 3.75, 6.25, 8.75, 11.25, 13.75, 16.25, 18.75, 21.25, 23.75]) diff = numpy.linalg.norm(ref_time_steps - time_steps) self.assertAlmostEqual(diff, 0.0, 8) ref_std_dev = numpy.array( [[ 0.14837207, 0.7305895 , 1.61912818, 2.84016862, 4.19935234, 5.69504607, 7.43238623, 9.31932103, 11.49445671, 13.97165319], [ 0.15002755, 0.75383991, 1.57174096, 2.37064526, 3.40687718, 4.90455993, 6.48757634, 8.15787162, 10.26025939, 12.5679611 ], [ 0.15963149, 0.76851636, 1.59661093, 2.50494685, 3.45028752, 4.38406911, 5.5039955 , 6.91771175, 8.52853689, 10.46993274], [ 0.21100039, 1.04965011, 2.25628521, 3.68460183, 5.37841647, 7.49505328, 9.84289993, 12.35824143, 15.38290727, 18.76634124], [ 0.2177914 , 1.06002792, 2.27387093, 3.77956739, 5.40911222, 7.12701069, 9.14740325, 11.48131598, 14.15839455, 17.28281115], [ 0.218962 , 1.07646844, 2.24036311, 3.44756425, 4.84874766, 6.56805258, 8.47932177, 10.66004723, 13.28568526, 16.29025096], [ 0.26444438, 1.30073885, 2.76405291, 4.45469653, 6.38348309, 8.65082886, 11.21442742, 14.08440462, 17.48404426, 21.36747194]]) diff = numpy.linalg.norm(ref_std_dev - std_dev) self.assertAlmostEqual(diff, 0.0, 6) ref_bin_counters = (59930, 59996, 59545, 59256, 59064, 59076, 58284, 58294, 57817, 57349) self.assertEqual(bin_counters, ref_bin_counters)
def testFlush2(self): """ Test the file output. """ # Get a file name. name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") trajectory_filename = os.path.join(name, "tmp_trajectory.xyz") if MPICommons.isMaster(): self.__files_to_remove.append(trajectory_filename) # Setup the trajectory object. unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, False, True), repetitions=(4,4,4)) config = KMCConfiguration(lattice=lattice, types=["A","B","C","D"]*16) t = XYZTrajectory(trajectory_filename=trajectory_filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) # Set data directly on the class. t._XYZTrajectory__atom_id_types = [("A","B","C","D","E"), ("This","is","the","next","step")] t._XYZTrajectory__atom_id_coordinates = [numpy.zeros((5,3)), numpy.ones((5,3))*1.234] t._XYZTrajectory__step = [0, 12] t._XYZTrajectory__time = [12.123,75.43] # Flush. t.flush() ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15 CELL VECTORS a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 REPETITIONS 4 4 4 PERIODICITY True False True STEP 0 5 TIME 1.2123000000e+01 A 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0 B 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1 C 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 2 D 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 3 E 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 4 STEP 12 5 TIME 7.5430000000e+01 This 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 0 is 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 1 the 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 2 next 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 3 step 1.2340000000e+00 1.2340000000e+00 1.2340000000e+00 4 """ if MPICommons.isMaster(): with open(trajectory_filename, "r") as f: content = f.read() self.assertEqual( content, ref_content ) # Check that the buffers are empty. self.assertEqual(t._XYZTrajectory__atom_id_types, []) self.assertEqual(t._XYZTrajectory__atom_id_coordinates, []) self.assertEqual(t._XYZTrajectory__time, []) self.assertEqual(t._XYZTrajectory__step, [])
def testBufferSize(self): """ Test the buffer size function. """ # Get a file name. name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") trajectory_filename = os.path.join(name, "tmp_trajectory.xyz") if MPICommons.isMaster(): self.__files_to_remove.append(trajectory_filename) # Setup the trajectory object. unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, True, True), repetitions=(4,4,4)) config = KMCConfiguration(lattice=lattice, types=["A","B","C","D"]*16) t = XYZTrajectory(trajectory_filename=trajectory_filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) # Store a bunch of data. simulation_time = 1.234 step = 123 t._storeData(simulation_time, step, config) buffer_size = t._bufferSize() # Check the size again. ref_size = sys.getsizeof(t._XYZTrajectory__atom_id_coordinates) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_coordinates[0])*len(t._XYZTrajectory__atom_id_coordinates) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types[0])*len(t._XYZTrajectory__atom_id_types) ref_size += sys.getsizeof(t._XYZTrajectory__time) ref_size += sys.getsizeof(t._XYZTrajectory__time[0])*len(t._XYZTrajectory__time) ref_size += sys.getsizeof(t._XYZTrajectory__step) ref_size += sys.getsizeof(t._XYZTrajectory__step[0])*len(t._XYZTrajectory__step) self.assertEqual(buffer_size, ref_size) # Store more data. t._storeData(simulation_time, step, config) # Check the size again. t._storeData(simulation_time, step, config) t._storeData(simulation_time, step, config) t._storeData(simulation_time, step, config) t._storeData(simulation_time, step, config) t._storeData(simulation_time, step, config) ref_size = sys.getsizeof(t._XYZTrajectory__atom_id_coordinates) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_coordinates[0])*len(t._XYZTrajectory__atom_id_coordinates) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types) ref_size += sys.getsizeof(t._XYZTrajectory__atom_id_types[0])*len(t._XYZTrajectory__atom_id_types) ref_size += sys.getsizeof(t._XYZTrajectory__time) ref_size += sys.getsizeof(t._XYZTrajectory__time[0])*len(t._XYZTrajectory__time) ref_size += sys.getsizeof(t._XYZTrajectory__step) ref_size += sys.getsizeof(t._XYZTrajectory__step[0])*len(t._XYZTrajectory__step) buffer_size = t._bufferSize() self.assertEqual(buffer_size, ref_size)
def testFlush(self): """ Test the file output. """ # Get a file name. name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") trajectory_filename = os.path.join(name, "tmp_trajectory.xyz") if MPICommons.isMaster(): self.__files_to_remove.append(trajectory_filename) # Setup the trajectory object. unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, False, True), repetitions=(4,4,4)) config = KMCConfiguration(lattice=lattice, types=["A","B","C","D"]*16) t = XYZTrajectory(trajectory_filename=trajectory_filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) # Store data. simulation_time = 1.234 step = 123 t._storeData(simulation_time, step, config) # Flush. t.flush() # Check the file. ref_content = """KMCLib XYZ FORMAT VERSION 2013.10.15 CELL VECTORS a: 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 b: 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 c: 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 REPETITIONS 4 4 4 PERIODICITY True False True STEP 123 64 TIME 1.2340000000e+00 A 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0 B 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 1 C 0.0000000000e+00 0.0000000000e+00 2.0000000000e+00 2 D 0.0000000000e+00 0.0000000000e+00 3.0000000000e+00 3 A 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 4 B 0.0000000000e+00 1.0000000000e+00 1.0000000000e+00 5 C 0.0000000000e+00 1.0000000000e+00 2.0000000000e+00 6 D 0.0000000000e+00 1.0000000000e+00 3.0000000000e+00 7 A 0.0000000000e+00 2.0000000000e+00 0.0000000000e+00 8 B 0.0000000000e+00 2.0000000000e+00 1.0000000000e+00 9 C 0.0000000000e+00 2.0000000000e+00 2.0000000000e+00 10 D 0.0000000000e+00 2.0000000000e+00 3.0000000000e+00 11 A 0.0000000000e+00 3.0000000000e+00 0.0000000000e+00 12 B 0.0000000000e+00 3.0000000000e+00 1.0000000000e+00 13 C 0.0000000000e+00 3.0000000000e+00 2.0000000000e+00 14 D 0.0000000000e+00 3.0000000000e+00 3.0000000000e+00 15 A 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 16 B 1.0000000000e+00 0.0000000000e+00 1.0000000000e+00 17 C 1.0000000000e+00 0.0000000000e+00 2.0000000000e+00 18 D 1.0000000000e+00 0.0000000000e+00 3.0000000000e+00 19 A 1.0000000000e+00 1.0000000000e+00 0.0000000000e+00 20 B 1.0000000000e+00 1.0000000000e+00 1.0000000000e+00 21 C 1.0000000000e+00 1.0000000000e+00 2.0000000000e+00 22 D 1.0000000000e+00 1.0000000000e+00 3.0000000000e+00 23 A 1.0000000000e+00 2.0000000000e+00 0.0000000000e+00 24 B 1.0000000000e+00 2.0000000000e+00 1.0000000000e+00 25 C 1.0000000000e+00 2.0000000000e+00 2.0000000000e+00 26 D 1.0000000000e+00 2.0000000000e+00 3.0000000000e+00 27 A 1.0000000000e+00 3.0000000000e+00 0.0000000000e+00 28 B 1.0000000000e+00 3.0000000000e+00 1.0000000000e+00 29 C 1.0000000000e+00 3.0000000000e+00 2.0000000000e+00 30 D 1.0000000000e+00 3.0000000000e+00 3.0000000000e+00 31 A 2.0000000000e+00 0.0000000000e+00 0.0000000000e+00 32 B 2.0000000000e+00 0.0000000000e+00 1.0000000000e+00 33 C 2.0000000000e+00 0.0000000000e+00 2.0000000000e+00 34 D 2.0000000000e+00 0.0000000000e+00 3.0000000000e+00 35 A 2.0000000000e+00 1.0000000000e+00 0.0000000000e+00 36 B 2.0000000000e+00 1.0000000000e+00 1.0000000000e+00 37 C 2.0000000000e+00 1.0000000000e+00 2.0000000000e+00 38 D 2.0000000000e+00 1.0000000000e+00 3.0000000000e+00 39 A 2.0000000000e+00 2.0000000000e+00 0.0000000000e+00 40 B 2.0000000000e+00 2.0000000000e+00 1.0000000000e+00 41 C 2.0000000000e+00 2.0000000000e+00 2.0000000000e+00 42 D 2.0000000000e+00 2.0000000000e+00 3.0000000000e+00 43 A 2.0000000000e+00 3.0000000000e+00 0.0000000000e+00 44 B 2.0000000000e+00 3.0000000000e+00 1.0000000000e+00 45 C 2.0000000000e+00 3.0000000000e+00 2.0000000000e+00 46 D 2.0000000000e+00 3.0000000000e+00 3.0000000000e+00 47 A 3.0000000000e+00 0.0000000000e+00 0.0000000000e+00 48 B 3.0000000000e+00 0.0000000000e+00 1.0000000000e+00 49 C 3.0000000000e+00 0.0000000000e+00 2.0000000000e+00 50 D 3.0000000000e+00 0.0000000000e+00 3.0000000000e+00 51 A 3.0000000000e+00 1.0000000000e+00 0.0000000000e+00 52 B 3.0000000000e+00 1.0000000000e+00 1.0000000000e+00 53 C 3.0000000000e+00 1.0000000000e+00 2.0000000000e+00 54 D 3.0000000000e+00 1.0000000000e+00 3.0000000000e+00 55 A 3.0000000000e+00 2.0000000000e+00 0.0000000000e+00 56 B 3.0000000000e+00 2.0000000000e+00 1.0000000000e+00 57 C 3.0000000000e+00 2.0000000000e+00 2.0000000000e+00 58 D 3.0000000000e+00 2.0000000000e+00 3.0000000000e+00 59 A 3.0000000000e+00 3.0000000000e+00 0.0000000000e+00 60 B 3.0000000000e+00 3.0000000000e+00 1.0000000000e+00 61 C 3.0000000000e+00 3.0000000000e+00 2.0000000000e+00 62 D 3.0000000000e+00 3.0000000000e+00 3.0000000000e+00 63 """ if MPICommons.isMaster(): with open(trajectory_filename, "r") as f: content = f.read() self.assertEqual( content, ref_content ) # Check that the buffers are empty. self.assertEqual(t._XYZTrajectory__atom_id_types, []) self.assertEqual(t._XYZTrajectory__atom_id_coordinates, []) self.assertEqual(t._XYZTrajectory__time, []) self.assertEqual(t._XYZTrajectory__step, [])
def testStoreData(self): """ Test the data storage function. """ # Get a file name. name = os.path.abspath(os.path.dirname(__file__)) name = os.path.join(name, "..", "..") name = os.path.join(name, "TestUtilities", "Scratch") trajectory_filename = os.path.join(name, "tmp_trajectory.xyz") if MPICommons.isMaster(): self.__files_to_remove.append(trajectory_filename) # Setup the trajectory object. unit_cell = KMCUnitCell(cell_vectors=[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], basis_points=[[0.0, 0.0, 0.0]]) lattice = KMCLattice(unit_cell=unit_cell, periodic=(True, True, True), repetitions=(4,4,4)) config = KMCConfiguration(lattice=lattice, types=["A","B","C","D"]*16) t = XYZTrajectory(trajectory_filename=trajectory_filename, configuration=config, max_buffer_size=12345, max_buffer_time=123.0) # Construct data to store. simulation_time = 1.234 step = 123 configuration = config # Store. t._storeData(simulation_time, step, configuration) # Check that the member data was updated. self.assertEqual(len(t._XYZTrajectory__atom_id_types), 1) self.assertEqual(len(t._XYZTrajectory__atom_id_coordinates), 1) self.assertEqual(len(t._XYZTrajectory__time), 1) self.assertEqual(len(t._XYZTrajectory__step), 1) # store again. simulation_time = 1.999 step = 4444 t._storeData(simulation_time, step, configuration) # Check that the member data was updated. self.assertEqual(len(t._XYZTrajectory__atom_id_types), 2) self.assertEqual(len(t._XYZTrajectory__atom_id_coordinates), 2) self.assertEqual(len(t._XYZTrajectory__time), 2) self.assertEqual(len(t._XYZTrajectory__step), 2) # Check the values of the stored data. self.assertAlmostEqual(t._XYZTrajectory__time[0], 1.234, 10) self.assertAlmostEqual(t._XYZTrajectory__time[1], 1.999, 10) self.assertEqual(t._XYZTrajectory__step[0], 123) self.assertEqual(t._XYZTrajectory__step[1], 4444) diff = numpy.linalg.norm(config.atomIDCoordinates() - t._XYZTrajectory__atom_id_coordinates[0]) self.assertAlmostEqual(diff, 0.0, 10) diff = numpy.linalg.norm(config.atomIDCoordinates() - t._XYZTrajectory__atom_id_coordinates[1]) self.assertAlmostEqual(diff, 0.0, 10) self.assertEqual(t._XYZTrajectory__atom_id_types[0], config.atomIDTypes()) self.assertEqual(t._XYZTrajectory__atom_id_types[1], config.atomIDTypes())
def testFinalizeWithCoordinateTransform(self): """ Test finalization. """ msd = OnTheFlyMSD.__new__(OnTheFlyMSD) # Replace the getBackendResults function. def dummy(): pass msd._OnTheFlyMSD__getBackendResults = dummy # Set a unitcell on the class. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0], [0.0,1.0,0.0], [0.0,0.0,1.0]]), basis_points=[[0.0,0.0,0.0]]) msd._OnTheFlyMSD__unit_cell = unit_cell # Set the values. msd._OnTheFlyMSD__raw_histogram = numpy.array([[ 171144., 173906., 188389.], [ 516721., 497558., 536213.], [ 851961., 810151., 836426.], [ 1195930., 1046238., 1111184.], [ 1507650., 1366678., 1434213.], [ 1780731., 1743443., 1719186.], [ 2155426., 2154562., 1980822.], [ 2554205., 2604757., 2354967.], [ 2954351., 3032799., 2698023.], [ 3372070., 3443433., 3158002.]]) bin_counters = (60283, 60628, 60461, 59779, 59683, 59178, 58856, 58752, 58162, 57881) msd._OnTheFlyMSD__bin_counters = bin_counters msd._OnTheFlyMSD__n_bins = 10 msd._OnTheFlyMSD__binsize = 2.5 hstep_counts = [8919,8918,8917,8916,8915,8914,8913,8912,8911,8910,8099,8908,8907,8906,8905,8904,8903,8902,8901] msd._OnTheFlyMSD__hstep_counts = hstep_counts history_bin_counters = [(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), (0, 0, 0, 0, 0, 1, 87, 58752, 58162, 57881)] msd._OnTheFlyMSD__history_bin_counters = history_bin_counters msd._OnTheFlyMSD__n_eff = [1.12, 2.24, 3.36, 4.48, 5.60, 6.72, 7.84, 8.96, 9.0, 10.12] # Call the finalize function. msd.finalize() # Check a few results. result_0_3 = 1195930. / 59779.0 self.assertAlmostEqual(result_0_3, msd._OnTheFlyMSD__results[0][3], 10) result_1_7 = 2604757.0 / 58752.0 self.assertAlmostEqual(result_1_7, msd._OnTheFlyMSD__results[1][7], 10) result_2_0 = 188389.0 / 60283.0 self.assertAlmostEqual(result_2_0, msd._OnTheFlyMSD__results[2][0], 10) result_3_4 = ( 1507650.0 + 1366678.0) / 59683.0 self.assertAlmostEqual(result_3_4, msd._OnTheFlyMSD__results[3][4], 10) result_4_4 = ( 1507650.0 + 1434213.0) / 59683.0 self.assertAlmostEqual(result_4_4, msd._OnTheFlyMSD__results[4][4], 10) result_5_6 = ( 2154562.0 + 1980822.0) / 58856.0 self.assertAlmostEqual(result_5_6, msd._OnTheFlyMSD__results[5][6], 10) result_6_5 = ( 1780731.0 + 1743443.0 + 1719186.0)/ 59178.0 self.assertAlmostEqual(result_6_5, msd._OnTheFlyMSD__results[6][5], 10) # Check the corresponding standard deviation against hardcoded values. std_0_3 = 42.291401180595834 std_1_7 = 0.813230156401512 std_2_0 = 6.634050132990601 std_3_4 = 71.931090096615776 std_4_4 = 73.621177716983027 std_5_6 = 7.877909031669120 std_6_5 = 62.119638306131414 self.assertAlmostEqual(std_0_3, msd._OnTheFlyMSD__std_dev[0][3], 10) self.assertAlmostEqual(std_1_7, msd._OnTheFlyMSD__std_dev[1][7], 10) self.assertAlmostEqual(std_2_0, msd._OnTheFlyMSD__std_dev[2][0], 10) self.assertAlmostEqual(std_3_4, msd._OnTheFlyMSD__std_dev[3][4], 10) self.assertAlmostEqual(std_4_4, msd._OnTheFlyMSD__std_dev[4][4], 10) self.assertAlmostEqual(std_5_6, msd._OnTheFlyMSD__std_dev[5][6], 10) self.assertAlmostEqual(std_6_5, msd._OnTheFlyMSD__std_dev[6][5], 10)
def testFinalizeNoCoordinateTransform(self): """ Test finalization. """ msd = OnTheFlyMSD.__new__(OnTheFlyMSD) # Replace the getBackendResults function. def dummy(): pass msd._OnTheFlyMSD__getBackendResults = dummy # Set a unitcell on the class. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[1.0,0.0,0.0], [0.0,1.0,0.0], [0.0,0.0,1.0]]), basis_points=[[0.0,0.0,0.0]]) msd._OnTheFlyMSD__unit_cell = unit_cell # Set the values. msd._OnTheFlyMSD__raw_histogram = numpy.array([[ 171144., 173906., 188389.], [ 516721., 497558., 536213.], [ 851961., 810151., 836426.], [ 1195930., 1046238., 1111184.], [ 1507650., 1366678., 1434213.], [ 1780731., 1743443., 1719186.], [ 2155426., 2154562., 1980822.], [ 2554205., 2604757., 2354967.], [ 2954351., 3032799., 2698023.], [ 3372070., 3443433., 3158002.]]) bin_counters = (60283, 60628, 60461, 59779, 59683, 59178, 58856, 58752, 58162, 57881) msd._OnTheFlyMSD__bin_counters = bin_counters msd._OnTheFlyMSD__n_bins = 10 msd._OnTheFlyMSD__binsize = 2.5 hstep_counts = [8919,8918,8917,8916,8915,8914,8913,8912,8911,8910,8099,8908,8907,8906,8905,8904,8903,8902,8901] msd._OnTheFlyMSD__hstep_counts = hstep_counts history_bin_counters = [(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), (0, 0, 0, 0, 0, 1, 87, 58752, 58162, 57881)] msd._OnTheFlyMSD__history_bin_counters = history_bin_counters msd._OnTheFlyMSD__n_eff = [1.12, 2.24, 3.36, 4.48, 5.60, 6.72, 7.84, 8.96, 9.0, 10.12] # Call the finalize function. msd.finalize() # Check a few results. result_0_3 = 1195930. / 59779.0 self.assertAlmostEqual(result_0_3, msd._OnTheFlyMSD__results[0][3], 10) result_1_7 = 2604757.0 / 58752.0 self.assertAlmostEqual(result_1_7, msd._OnTheFlyMSD__results[1][7], 10) result_2_0 = 188389.0 / 60283.0 self.assertAlmostEqual(result_2_0, msd._OnTheFlyMSD__results[2][0], 10) # Check the corresponding standard deviation. n_eff = numpy.zeros(10) for i in range(len(n_eff)): for b in range(len(history_bin_counters)): fraction = float(history_bin_counters[b][i]) / float(bin_counters[i]) n_eff[i] += fraction * (b+1.0) K1 = hstep_counts[int(n_eff[3]+1)] K2 = K1*K1 std_0_3 = result_0_3 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[3]*n_eff[3]*K1 + 2*K1 + n_eff[3] - n_eff[3]*n_eff[3]*n_eff[3])/(n_eff[3]*6*K2)) self.assertAlmostEqual(std_0_3, msd._OnTheFlyMSD__std_dev[0][3], 10) K1 = hstep_counts[int(n_eff[7]+1)] K2 = K1*K1 std_1_7 = result_1_7 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[7]*n_eff[7]*K1 + 2*K1 + n_eff[7] - n_eff[7]*n_eff[7]*n_eff[7])/(n_eff[7]*6*K2)) self.assertAlmostEqual(std_1_7, msd._OnTheFlyMSD__std_dev[1][7], 10) K1 = hstep_counts[int(n_eff[0]+1)] K2 = K1*K1 std_2_0 = result_2_0 * numpy.sqrt(2.0) * numpy.sqrt((4*n_eff[0]*n_eff[0]*K1 + 2*K1 + n_eff[0] - n_eff[0]*n_eff[0]*n_eff[0])/(n_eff[0]*6*K2)) self.assertAlmostEqual(std_2_0, msd._OnTheFlyMSD__std_dev[2][0], 10)
def testCalculationNonOrthogonal(self): """ Test a calculation with the on-the-fly MSD analysis. """ # Setup a system, a periodic 10 atoms long 1D chain. unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.0,1.0,0.0], [0.0,1.0,0.0], [0.0,2.0,1.0]]), basis_points=[[0.0,0.0,0.0]]) # And a lattice. lattice = KMCLattice(unit_cell=unit_cell, repetitions=(10,10,10), periodic=(True,True,True)) # Setup an initial configuration with one B in a sea of A:s. types = ["A"]*10*10*10 types[5] = "B" config = KMCConfiguration(lattice=lattice, types=types, possible_types=["A","B"]) # Setup a diffusion process to the left. coordinates_p0 = [[0.0, 0.0, 0.0],[-1.0, 0.0, 0.0]] p0 = KMCProcess(coordinates=coordinates_p0, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p1 = [[0.0, 0.0, 0.0],[1.0, 0.0, 0.0]] p1 = KMCProcess(coordinates=coordinates_p1, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p2 = [[0.0, 0.0, 0.0],[0.0,-1.0, 0.0]] p2 = KMCProcess(coordinates=coordinates_p2, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p3 = [[0.0, 0.0, 0.0],[0.0, 1.0, 0.0]] p3 = KMCProcess(coordinates=coordinates_p3, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p4 = [[0.0, 0.0, 0.0],[0.0, 0.0,-1.0]] p4 = KMCProcess(coordinates=coordinates_p4, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) coordinates_p5 = [[0.0, 0.0, 0.0],[0.0, 0.0, 1.0]] p5 = KMCProcess(coordinates=coordinates_p5, elements_before=["B","A"], elements_after=["A","B"], move_vectors=None, basis_sites=[0], rate_constant=1.0) interactions = KMCInteractions(processes=[p0, p1, p2, p3, p4, p5], implicit_wildcards=True) model = KMCLatticeModel(configuration=config, interactions=interactions) # Setup the analysis. msd = OnTheFlyMSD(history_steps=400, n_bins=10, t_max=25.0, track_type="B") # Setup the control parameters. control_parameters = KMCControlParameters(number_of_steps=4000, dump_interval=100, analysis_interval=1, seed=2013) # Run the model. model.run(control_parameters=control_parameters, analysis=[msd]) # Get the results out. results = msd.results() time_steps = msd.timeSteps() std_dev = msd.stdDev() bin_counters = msd.binCounters() # Compare against references. ref_results = numpy.array([[ 11.10849324 , 32.89332622 , 56.86314552 , 84.47799379 , 110.30394149, 135.26081658, 162.25612518, 189.40268295, 219.32538873, 252.00244119], [ 17.33153679 , 50.69982999 , 82.74958435 , 111.33382274 , 136.44824258, 164.84499628, 193.94367236, 234.25340515, 272.64453361, 302.94924061], [ 2.98786918 , 8.65022668 , 14.01808716 , 18.62678885 , 22.65708384, 26.03107861, 30.03937616, 35.1483 , 40.68319007, 47.21074474], [ 28.44003004 , 83.59315621 , 139.61272987 , 195.81181652 , 246.75218407, 300.10581285, 356.19979754, 423.65608811, 491.96992234, 554.95168181], [ 14.09636242 , 41.5435529 , 70.88123268 , 103.10478264 , 132.96102533, 161.29189519, 192.29550134, 224.55098295, 260.00857879, 299.21318593], [ 20.31940597 , 59.35005667 , 96.76767151 , 129.96061158 , 159.10532643, 190.87607489, 223.98304852, 269.40170515, 313.32772368, 350.15998535], [ 31.42789922 , 92.24338289 , 153.63081703 , 214.43860537 , 269.40926791, 326.13689146, 386.2391737 , 458.8043881 , 532.65311241, 602.16242655]]) diff = numpy.linalg.norm(ref_results - results) self.assertAlmostEqual(diff, 0.0, 6) ref_time_steps = numpy.array([ 1.25, 3.75, 6.25, 8.75, 11.25, 13.75, 16.25, 18.75, 21.25, 23.75]) diff = numpy.linalg.norm(ref_time_steps - time_steps) self.assertAlmostEqual(diff, 0.0, 8) ref_std_dev = numpy.array([[ 0.59348826 , 2.92235801 , 6.47651272 , 11.36067446 , 16.79740936, 22.78018427, 29.72954492, 37.27728411, 45.97782684, 55.88661276], [ 0.92596389 , 4.50435001 , 9.42488725 , 14.97226982 , 20.7787406, 27.76265504, 35.53552825, 46.10457783, 57.15527613, 67.18509081], [ 0.15963149 , 0.76851636 , 1.59661093 , 2.50494685 , 3.45028752, 4.38406911 , 5.5039955 , 6.91771175 , 8.52853689 , 10.46993274], [ 1.07441492 , 5.2514756 , 11.24398775 , 18.62020347 , 26.57035045, 35.73918442, 46.14937581, 58.95988 , 72.92611647, 87.02483617], [ 0.53253608 , 2.60984229 , 5.70856048 , 9.80447485 , 14.31728377, 19.20802777, 24.91387536, 31.25058126, 38.54181941, 46.9211633 ], [ 0.76763185 , 3.72847956 , 7.7933761 , 12.35825842 , 17.13251009, 22.73116664, 29.01932554, 37.49242051, 46.4454696 , 54.91039375], [ 0.96941939 , 4.731515 , 10.1024813 , 16.6495642 , 23.68662473, 31.71206536, 40.85854085, 52.13448317, 64.46787783, 77.10029967]]) diff = numpy.linalg.norm(ref_std_dev - std_dev) self.assertAlmostEqual(diff, 0.0, 6) ref_bin_counters = (59930, 59996, 59545, 59256, 59064, 59076, 58284, 58294, 57817, 57349) self.assertEqual(bin_counters, ref_bin_counters)