class TestStructureContainer(unittest.TestCase):
def setUp(self):
self.lattice_constant = 3.5
self.project = Project('structure_testing')
self.basis = self.project.create_structure(
element="Fe",
bravais_basis='fcc',
lattice_constant=self.lattice_constant)
self.structure_container = self.project.create_job(
"StructureContainer", "structure_container")
self.structure_container.structure = self.basis
@classmethod
def tearDownClass(cls):
project = Project('structure_testing')
ham = project.load(1)
ham.remove()
project.remove(enable=True)
s.close_connection()
os.remove('container.db')
def test_container(self):
structure_container = self.project.load(1)
self.assertEqual(structure_container.job_id, 1)
self.assertEqual(structure_container.job_name, 'structure_container')
self.assertEqual(structure_container.project_hdf5.project_path,
'structure_testing/')
self.assertTrue(structure_container.status.finished)
self.assertEqual(structure_container.structure, self.basis)
class TestStructureContainer(unittest.TestCase):
def setUp(self):
self.lattice_constant = 3.5
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(
os.path.join(self.file_location, 'structure_testing'))
self.basis = self.project.create_structure(
element="Fe",
bravais_basis='fcc',
lattice_constant=self.lattice_constant)
self.structure_container = self.project.create_job(
self.project.job_type.StructureContainer, "structure_container")
self.structure_container.structure = self.basis
@classmethod
def tearDownClass(cls):
file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(file_location, 'structure_testing'))
ham = project.load(project.get_job_ids()[0])
ham.remove()
project.remove(enable=True)
def test_container(self):
structure_container = self.project.load(self.project.get_job_ids()[0])
self.assertEqual(structure_container.job_id,
self.project.get_job_ids()[0])
self.assertEqual(structure_container.job_name, 'structure_container')
self.assertTrue('atomistics/job/structure_testing/' in
structure_container.project_hdf5.project_path)
self.assertTrue(structure_container.status.finished)
self.assertEqual(structure_container.structure, self.basis)
def tearDownClass(cls):
project = Project('structure_testing')
ham = project.load(1)
ham.remove()
project.remove(enable=True)
s.close_connection()
os.remove('container.db')
def setUp(self):
self.lattice_constant = 3.5
self.project = Project('structure_testing')
self.basis = self.project.create_structure(
element="Fe",
bravais_basis='fcc',
lattice_constant=self.lattice_constant)
self.structure_container = self.project.create_job(
"StructureContainer", "structure_container")
self.structure_container.structure = self.basis
def test_Chemical_Element_to_and_from_hdf_with_None_Parent(self):
pr = Project(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'test_periodic_table'))
basis = pr.create_structure(element='Ni', bravais_basis='fcc', lattice_constant=3.7)
ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_2')
test_ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_2')
ham.structure = basis
ham.to_hdf()
test_ham.from_hdf()
self.assertEqual(test_ham['input/structure/species'][0], ham['input/structure/species'][0])
ham.remove()
def test_Chemical_Element_to_and_from_hdf(self):
ni_up = self.pse.add_element("Ni", "Ni_up", spin="up")
pr = Project(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'test_periodic_table'))
basis = pr.create_structure(element=ni_up, bravais_basis='fcc', lattice_constant=3.7)
ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_1')
test_ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_1')
ham.structure = basis
ham.to_hdf()
test_ham.from_hdf()
self.assertEqual(test_ham['input/structure/species'][0], ham['input/structure/species'][0])
ham.remove()
def setUp(self):
self.lattice_constant = 3.5
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(
os.path.join(self.file_location, 'structure_testing'))
self.basis = self.project.create_structure(
element="Fe",
bravais_basis='fcc',
lattice_constant=self.lattice_constant)
self.structure_container = self.project.create_job(
self.project.job_type.StructureContainer, "structure_container")
self.structure_container.structure = self.basis
def setUp(self):
self.count_run_one = 12
self.count_run_two = 12
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(os.path.join(self.file_location, 'random_testing_lib'))
self.ham = self.project.create_job("ExampleJob", "job_test_run")
self.ham.input['count'] = self.count_run_one
self.ham.server.run_mode.interactive = True
self.ham.run()
self.ham.input['count'] = self.count_run_two
self.ham.run()
self.ham.interactive_close()
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "../static/sphinx"))
pt = PeriodicTable()
pt.add_element(parent_element="Fe", new_element="Fe_up", spin="0.5")
Fe_up = pt.element("Fe_up")
cls.basis = Atoms(
elements=[Fe_up, Fe_up],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.6 * np.eye(3),
)
cls.sphinx = cls.project.create_job("Sphinx", "job_sphinx")
cls.sphinx_2_3 = cls.project.create_job("Sphinx", "sphinx_test_2_3")
cls.sphinx_2_5 = cls.project.create_job("Sphinx", "sphinx_test_2_5")
cls.sphinx.structure = cls.basis
cls.sphinx_2_3.structure = Atoms(
elements=["Fe", "Fe"],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.6 * np.eye(3),
)
cls.sphinx_2_5.structure = Atoms(
elements=["Fe", "Ni"],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.83 * np.eye(3),
)
cls.current_dir = os.path.abspath(os.getcwd())
cls.sphinx._create_working_directory()
cls.sphinx_2_3._create_working_directory()
cls.sphinx.write_input()
cls.sphinx.version = "2.6"
cls.sphinx_2_3.to_hdf()
cls.sphinx_2_3.decompress()
cls.sphinx_2_5.decompress()
class TestExampleJob(unittest.TestCase):
def setUp(self):
self.count_run_one = 12
self.count_run_two = 12
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(os.path.join(self.file_location, 'random_testing_lib'))
self.ham = self.project.create_job("ExampleJob", "job_test_run")
self.ham.input['count'] = self.count_run_one
self.ham.server.run_mode.interactive = True
self.ham.run()
self.ham.input['count'] = self.count_run_two
self.ham.run()
self.ham.interactive_close()
@classmethod
def tearDownClass(cls):
file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(file_location, 'random_testing_lib'))
ham = project.load(project.get_job_ids()[0])
ham.remove()
project.remove(enable=True)
def test_output(self):
count = self.ham.get("output/generic/count")
energy = self.ham.get("output/generic/energy")
self.assertEqual(self.count_run_one, count[0])
self.assertEqual(self.count_run_two, count[1])
self.assertEqual(count[0], len(energy[0]))
self.assertEqual(count[0], len(energy[1]))
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, 'testing_murnaghan'))
cls.basis = cls.project.create_structure(element="Fe",
bravais_basis='fcc',
lattice_constant=3.5)
cls.project.remove_jobs(recursive=True)
def setUpClass(cls):
cls.count = 12
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location,
'random_testing'))
cls.ham = cls.project.create_job("ExampleJob", "job_test_run")
cls.ham.input['count'] = cls.count
cls.ham.run()
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, "../static/sphinx"))
pt = PeriodicTable()
pt.add_element(parent_element="Fe", new_element="Fe_up", spin="0.5")
Fe_up = pt.element("Fe_up")
cls.basis = Atoms(
elements=[Fe_up, Fe_up],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.6 * np.eye(3),
)
cls.sphinx = cls.project.create_job("Sphinx", "job_sphinx")
cls.sphinx_band_structure = cls.project.create_job(
"Sphinx", "sphinx_test_bs")
cls.sphinx_2_3 = cls.project.create_job("Sphinx", "sphinx_test_2_3")
cls.sphinx_2_5 = cls.project.create_job("Sphinx", "sphinx_test_2_5")
cls.sphinx_aborted = cls.project.create_job("Sphinx",
"sphinx_test_aborted")
cls.sphinx.structure = cls.basis
cls.sphinx.fix_spin_constraint = True
cls.sphinx_band_structure.structure = cls.project.create_structure(
"Fe", "bcc", 2.81)
cls.sphinx_band_structure.structure = cls.sphinx_band_structure.structure.create_line_mode_structure(
)
cls.sphinx_2_3.structure = Atoms(
elements=["Fe", "Fe"],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.6 * np.eye(3),
)
cls.sphinx_2_5.structure = Atoms(
elements=["Fe", "Ni"],
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
cell=2.83 * np.eye(3),
)
cls.sphinx_aborted.structure = Atoms(
elements=32 * ["Fe"],
scaled_positions=np.arange(32 * 3).reshape(-1, 3) / (32 * 3),
cell=3.5 * np.eye(3),
)
cls.sphinx_aborted.status.aborted = True
cls.current_dir = os.path.abspath(os.getcwd())
cls.sphinx._create_working_directory()
cls.sphinx_2_3._create_working_directory()
cls.sphinx.input["VaspPot"] = False
cls.sphinx.structure.add_tag(selective_dynamics=(True, True, True))
cls.sphinx.structure.selective_dynamics[1] = (False, False, False)
cls.sphinx.load_default_groups()
cls.sphinx.fix_symmetry = False
cls.sphinx.write_input()
try:
cls.sphinx.version = "2.6"
except ValueError:
cls.sphinx.version = "2.6.2_default"
cls.sphinx_2_3.to_hdf()
cls.sphinx_2_3.decompress()
cls.sphinx_2_5.decompress()
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_job"))
cls.job = AtomisticGenericJob(
project=ProjectHDFio(project=cls.project, file_name="test_job"),
job_name="test_job",
)
cls.job.structure = CrystalStructure(
element="Al", bravais_basis="fcc", lattice_constants=4
).repeat(4)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "../static/sxextopt"))
cls.basis = cls.project.create_structure("Fe", "bcc", 2.8)
job = cls.project.create_job(
cls.project.job_type.AtomisticExampleJob, "job_single"
)
job.server.run_mode.interactive = True
job.structure = cls.basis
cls.sxextoptint = cls.project.create_job("SxExtOptInteractive", "job_sxextopt")
cls.sxextoptint.ref_job = job
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "../static/minim"))
cls.basis = cls.project.create_structure("Fe", "bcc", 2.8)
job = cls.project.create_job(
cls.project.job_type.AtomisticExampleJob, "job_single"
)
job.server.run_mode.interactive = True
job.structure = cls.basis
cls.minim = cls.project.create_job("ScipyMinimizer", "job_scipy")
cls.minim.ref_job = job
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "../static/sphinx"))
cls.sphinx = cls.project.create_job("Sphinx", "job_sphinx")
cls.sphinx.structure = Atoms(elements=['Fe']*2, scaled_positions=[3*[0.0], 3*[0.5]], cell=2.6*np.eye(3))
cls.sphinx.structure.set_initial_magnetic_moments(np.ones(2))
cls.current_dir = os.path.abspath(os.getcwd())
cls.sphinx._create_working_directory()
cls.sphinx.write_input()
cls.sphinx.version = "2.6"
cls.sphinx.server.run_mode.interactive = True
def setUpClass(cls):
cls.lattice_constant = 3.5
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, 'structure_testing'))
cls.basis = cls.project.create_structure(
element="Fe",
bravais_basis='fcc',
lattice_constant=cls.lattice_constant)
cls.structure_container = cls.project.create_job(
cls.project.job_type.StructureContainer, "structure_container")
cls.structure_container.structure = cls.basis
def tearDownClass(cls):
project = Project(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'random_testing'))
ham = project.load(project.get_job_ids()[0])
ham.remove()
project.remove(enable=True)
class TestExampleJob(unittest.TestCase):
def setUp(self):
self.count = 12
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(os.path.join(self.file_location, 'random_testing_non_modal'))
self.project.remove_jobs(recursive=True)
self.project.set_logging_level('INFO')
@classmethod
def tearDownClass(cls):
# print('tear down')
file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(file_location, 'random_testing_non_modal'))
project.remove_jobs()
project.remove(enable=True)
def test_non_modal_run(self):
ham_non_modal = self.project.create_job(self.project.job_type.ExampleJob, "job_non_modal")
ham_non_modal.input['count'] = self.count
ham_non_modal.server.run_mode.non_modal = True
ham_non_modal.run()
self.assertFalse(ham_non_modal.status.finished)
self.project.wait_for_job(ham_non_modal, interval_in_s=5, max_iterations=50)
self.assertTrue(ham_non_modal.status.finished)
lines = self.project['job_non_modal/input.inp']
input_lst = ["alat 3.2 #lattice constant (would be in a more realistic example in the structure file)\n",
"alpha 0.1 #noise amplitude\n",
"a_0 3 #equilibrium lattice constant\n",
"a_1 0\n",
"a_2 1. #2nd order in energy (corresponds to bulk modulus)\n",
"a_3 0. #3rd order\n",
"a_4 0. #4th order\n",
"count " + str(self.count) + " #number of calls (dummy)\n",
"write_restart True\n",
"read_restart False\n"]
self.assertEqual(input_lst, lines)
lines = self.project['job_non_modal/restart.out']
restart_lst = ["count " + str(self.count) + " \n"]
self.assertEqual(restart_lst, lines)
energy_lst = ham_non_modal.get("output/generic/energy_tot")
self.assertEqual(len(energy_lst), self.count)
lines = self.project['job_non_modal/output.log']
output_lst = ["exampleExecutable logFile \n",
"alat 3.2 \n",
"count " + str(self.count) + " \n"]
self.assertEqual(output_lst, lines[0:3])
energy_output_lst = np.array([float(line.split(' ')[1]) for line in lines[3:]])
for e_1, e_2 in zip(energy_lst, energy_output_lst):
self.assertTrue(1 > e_1 > 0)
self.assertEqual(e_1, e_2)
ham_non_modal.remove()
class TestVasp(unittest.TestCase):
"""
Tests the pyiron.objects.hamilton.dft.vasp.Vasp class
"""
def setUp(self):
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.project = Project(os.path.join(self.file_location, 'test_vasp'))
self.job = self.project.create_job("Vasp", "trial")
@classmethod
def tearDownClass(cls):
pass
def test_init(self):
self.assertEqual(self.job.__name__, "Vasp")
self.assertEqual(self.job._sorted_indices, None)
self.assertIsInstance(self.job.input, Input)
self.assertIsInstance(self.job._output_parser, Output)
def test_calc_static(self):
self.job.calc_static(electronic_steps=90,
retain_charge_density=True,
retain_electrostatic_potential=True)
self.assertEqual(self.job.input.incar["IBRION"], -1)
self.assertEqual(self.job.input.incar["NELM"], 90)
self.assertEqual(self.job.input.incar["LVTOT"], True)
self.assertEqual(self.job.input.incar["LCHARG"], True)
def test_set_structure(self):
self.assertEqual(self.job.structure, None)
atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
self.job.structure = None
self.assertEqual(self.job.structure, None)
self.job.structure = atoms
self.assertEqual(self.job.structure, atoms)
def test_list_potenitals(self):
self.assertRaises(ValueError, self.job.list_potentials)
def tearDown(self):
pass
def tearDownClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.execution_path, "table"))
project.remove_jobs(recursive=True)
project.remove(enable=True)
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "table"))
def tearDownClass(cls):
file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(file_location, "testing_serial_non_modal"))
project.remove(enable=True, enforce=True)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, "testing_serial_non_modal")
)
cls.project.remove_jobs_silently(recursive=True)
def tearDownClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.file_location, "vasp_import_testing"))
project.remove_jobs_silently(recursive=True)
project.remove(enable=True)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "vasp_import_testing"))
def tearDownClass(cls):
project = Project('testing_murnaghan_non_modal')
project.remove_jobs(recursive=True)
project.remove(enable=True, enforce=True)
def setUpClass(cls):
cls.project = Project('testing_murnaghan_non_modal')
cls.basis = cls.project.create_structure(element="Fe", bravais_basis='bcc', lattice_constant=2.8)
cls.project.remove_jobs(recursive=True)
def tearDownClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.file_location, 'testing_murnaghan'))
project.remove(enable=True, enforce=True)
