def test_siesta(): import numpy as np from ase.calculators.siesta.siesta import Siesta from ase.calculators.siesta.parameters import Species, PAOBasisBlock from ase.calculators.calculator import FileIOCalculator from ase import Atoms # Setup test structures. h = Atoms('H', [(0.0, 0.0, 0.0)]) ch4 = Atoms('CH4', np.array([ [0.000000, 0.000000, 0.000000], [0.682793, 0.682793, 0.682793], [-0.682793, -0.682793, 0.682790], [-0.682793, 0.682793, -0.682793], [0.682793, -0.682793, -0.682793]])) # Test the initialization. siesta = Siesta() assert isinstance(siesta, FileIOCalculator) assert isinstance(siesta.implemented_properties, tuple) assert isinstance(siesta.default_parameters, dict) assert isinstance(siesta.name, str) assert isinstance(siesta.default_parameters, dict) # Test simple fdf-argument case. atoms = h.copy() siesta = Siesta( label='test_label', fdf_arguments={'DM.Tolerance': 1e-3}) atoms.set_calculator(siesta) siesta.write_input(atoms, properties=['energy']) atoms = h.copy() atoms.set_calculator(siesta) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as fd: lines = fd.readlines() assert any([line.split() == ['DM.Tolerance', '0.001'] for line in lines]) # Test (slightly) more complex case of setting fdf-arguments. siesta = Siesta( label='test_label', mesh_cutoff=3000, fdf_arguments={ 'DM.Tolerance': 1e-3, 'ON.eta': (5, 'Ry')}) atoms.set_calculator(siesta) siesta.write_input(atoms, properties=['energy']) atoms = h.copy() atoms.set_calculator(siesta) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() assert 'MeshCutoff\t3000\teV\n' in lines assert 'DM.Tolerance\t0.001\n' in lines assert 'ON.eta\t5\tRy\n' in lines # Test setting fdf-arguments after initiation. siesta.set_fdf_arguments( {'DM.Tolerance': 1e-2, 'ON.eta': (2, 'Ry')}) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() assert 'MeshCutoff\t3000\teV\n' in lines assert 'DM.Tolerance\t0.01\n' in lines assert 'ON.eta\t2\tRy\n' in lines # Test initiation using Species. atoms = ch4.copy() species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Species(symbol='C', tag=1)]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) atoms.set_tags([0, 0, 0, 1, 0]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Species(symbol='H', tag=1, basis_set='SZ')]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 3, 2])) siesta = Siesta(label='test_label', species=species) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() lines = [line.split() for line in lines] assert ['1', '6', 'C.lda.1'] in lines assert ['2', '1', 'H.lda.2'] in lines assert ['3', '1', 'H.lda.3'] in lines assert ['C.lda.1', 'DZP'] in lines assert ['H.lda.2', 'DZP'] in lines assert ['H.lda.3', 'SZ'] in lines # Test if PAO block can be given as species. c_basis = """2 nodes 1.00 0 1 S 0.20 P 1 0.20 6.00 5.00 1.00 1 2 S 0.20 P 1 E 0.20 6.00 6.00 5.00 1.00 0.95""" basis_set = PAOBasisBlock(c_basis) species = Species(symbol='C', basis_set=basis_set) siesta = Siesta(label='test_label', species=[species]) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() lines = [line.split() for line in lines] assert ['%block', 'PAO.Basis'] in lines assert ['%endblock', 'PAO.Basis'] in lines
assert 'ON.eta\t5\tRy\n' in lines # Test setting fdf-arguments after initiation. siesta.set_fdf_arguments( {'DM.Tolerance': 1e-2, 'ON.eta': (2, 'Ry')}) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() assert 'MeshCutoff\t3000\teV\n' in lines assert 'DM.Tolerance\t0.01\n' in lines assert 'ON.eta\t2\tRy\n' in lines # Test initiation using Species. atoms = ch4.copy() species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Species(symbol='C', tag=1)]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) atoms.set_tags([0, 0, 0, 1, 0]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Species(symbol='H', tag=1, basis_set='SZ')]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 3, 2])) siesta = Siesta(label='test_label', species=species) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() lines = [line.split() for line in lines]
assert 'ON.eta 68.02846506 eV\n' in lines # Test setting fdf-arguments after initiation. siesta.set_fdf_arguments( {'DM.Tolerance': 1e-2, 'ON.eta': 2 * Ry}) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() assert 'MeshCutoff 3000.0000 eV\n' in lines assert 'DM.Tolerance 0.01\n' in lines assert 'ON.eta 27.21138602 eV\n' in lines # Test initiation using Species. atoms = ch4.copy() species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Specie(symbol='C', tag=1)]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) atoms.set_tags([0, 0, 0, 1, 0]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 2, 2])) siesta = Siesta(species=[Specie(symbol='H', tag=1, basis_set='SZ')]) species, numbers = siesta.species(atoms) assert all(numbers == np.array([1, 2, 2, 3, 2])) siesta = Siesta(label='test_label', species=species) siesta.write_input(atoms, properties=['energy']) with open('test_label.fdf', 'r') as f: lines = f.readlines() lines = [line.split() for line in lines]