def tearDownClass(cls):
file_location = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(file_location, 'testing_copyto'))
sub_project = project.open('sub_project_ex')
sub_project.remove(enable=True)
sub_project = project.open('sub_project')
sub_project.remove(enable=True)
def __init__(self, working_directory, job_id, debug=False):
self.working_directory = working_directory
pr = Project(path=working_directory)
self.job = pr.load(int(job_id))
# setup logger
self._logger = self.setup_logger(debug=debug)
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 = CrystalStructure(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 setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location, "wrapper_testing"))
cls.job = cls.project.create_job("ExampleJob", "job_test_run")
cls.job.input["count"] = 12
cls.job.server.run_mode.manual = True
cls.job.run()
def __init__(self, db, job_id=None, db_entry=None, user=None):
if not db_entry:
db_entry = db.get_item_by_id(job_id)
if db_entry is None:
raise ValueError("job ID {0} does not exist!".format(job_id))
job_name = db_entry["job"]
h5_path = None
sub_job = db_entry["subjob"]
if sub_job is not None:
if len(sub_job.strip()) > 0:
h5_path = '/'.join(sub_job.split('/')[:-1])
hdf5_file = sub_job.split('/')[1] + '.h5'
gp = GenericPath(root_path=db_entry["projectpath"],
project_path=db_entry["project"])
hdf_project = ProjectHDFio(project=Project(path=gp, user=user),
file_name=hdf5_file,
h5_path=h5_path,
mode="r")
super(JobPath, self).__init__(hdf_project, job_name)
self.__name__ = db_entry["hamilton"]
self.__version__ = db_entry["hamversion"]
if 'id' in db_entry:
self._job_id = db_entry["id"]
self._status = db_entry["status"]
self._master_id = db_entry["masterid"]
self._parent_id = db_entry["parentid"]
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_non_modal'))
cls.project.remove_jobs(recursive=True)
cls.project.set_logging_level('INFO')
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 = CrystalStructure(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 setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "lammps"))
structure = Atoms(
symbols="Fe2",
positions=np.outer(np.arange(2), np.ones(3)),
cell=2 * np.eye(3),
)
cls.job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="lammps",
)
cls.job.server.run_mode.interactive = True
cls.job.structure = structure
cls.minimize_job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="minimize_lammps",
)
cls.minimize_control_job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="minimize_control_lammps",
)
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "lammps"))
cls.job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="lammps",
)
cls.job_water = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_water"),
job_name="lammps_water",
)
cls.job_water_dump = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_water_dump"),
job_name="lammps_water_dump",
)
cls.job_dump = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_dump_static"),
job_name="lammps_dump_static",
)
cls.job_vcsgc_input = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_vcsgc_input"),
job_name="lammps_vcsgc_input",
)
cls.minimize_job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="minimize_lammps",
)
cls.minimize_control_job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="minimize_control_lammps",
)
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.job = cls.project.create_job("ExampleJob", "job_test_run")
cls.job.input['count'] = cls.count
cls.job.run()
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_quickff"))
cls.job = cls.project.create_job("QuickFF", "trial")
cls.job_complete = QuickFF(
project=ProjectHDFio(project=cls.project, file_name="quickff_complete"),
job_name="quickff_complete",
)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.file_location,
'test_murnaghan'))
cls.basis = CrystalStructure(element="Fe",
bravais_basis='fcc',
lattice_constant=3.5)
cls.project.remove_jobs(recursive=True)
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, "testing_murnaghan_non_modal"))
cls.basis = CrystalStructure(element="Fe",
bravais_basis="bcc",
lattice_constant=2.8)
cls.project.remove_jobs(recursive=True)
def __init__(self,
working_directory,
job_id=None,
hdf5_file=None,
h5_path=None,
submit_on_remote=False,
debug=False):
self.working_directory = working_directory
self._remote_flag = submit_on_remote
pr = Project(path=os.path.join(working_directory, '..', '..'))
if job_id is not None:
self.job = pr.load(int(job_id))
else:
projectpath = s.top_path(hdf5_file)
if projectpath is None:
project = os.path.dirname(hdf5_file)
else:
project = os.path.relpath(os.path.dirname(hdf5_file),
projectpath)
job_name = h5_path[1:]
self.job = pr.load_from_jobpath(
job_id=None,
db_entry={
"job":
job_name,
"subjob":
h5_path,
"projectpath":
projectpath,
"project":
project + '/',
"status":
get_job_status_from_file(hdf5_file=hdf5_file,
job_name=job_name),
"hamilton":
get_hamilton_from_file(hdf5_file=hdf5_file,
job_name=job_name),
"hamversion":
get_hamilton_version_from_file(hdf5_file=hdf5_file,
job_name=job_name)
},
convert_to_object=True)
# setup logger
self._logger = self.setup_logger(debug=debug)
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_atomistic'))
cls.job = cls.project.create_job("AtomisticExampleJob", "job_test_atomistic_run")
cls.job.input['count'] = cls.count
cls.job.structure = Atoms(positions=[[0, 0, 0], [1, 1, 1]], elements=['Fe', 'Fe'], cell=2*np.eye(3))
cls.job.interactive_open()
cls.job.run()
def _create_project_from_hdf5(self):
"""
Internal function to create a pyiron project pointing to the directory where the HDF5 file is located.
Returns:
Project: pyiron project object
"""
from pyiron.base.project.generic import Project
return Project(path=self.file_path)
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "test_vasp"))
cls.job = cls.project.create_job("Vasp", "trial")
cls.job_complete = Vasp(
project=ProjectHDFio(project=cls.project, file_name="vasp_complete"),
job_name="vasp_complete",
)
poscar_file = posixpath.join(
cls.execution_path, "../static/vasp_test_files/full_job_sample/POSCAR"
)
cls.job_complete.structure = read_atoms(poscar_file, species_from_potcar=True)
class TestProject(unittest.TestCase):
def setUp(self):
self.current_dir = os.path.dirname(os.path.abspath(__file__)).replace('\\', '/')
self.project = Project(os.path.join(self.current_dir, 'sub_folder'))
def tearDown(self):
self.project.remove(enable=True)
def test_repr(self):
self.assertEqual([], self.project.list_groups())
pr_down_one = self.project['..']
pr_down_two = self.project['../..']
pr_down_twice = self.project['..']['..']
self.assertEqual(pr_down_two.__repr__(), pr_down_twice.__repr__())
self.assertEqual(sorted([directory for directory in os.listdir(self.current_dir)
if not os.path.isfile(os.path.join(self.current_dir, directory))]),
pr_down_one.list_groups())
self.assertEqual(sorted([directory for directory in os.listdir(os.path.join(self.current_dir, '..'))
if not os.path.isfile(os.path.join(self.current_dir, '..', directory))]),
pr_down_two.list_groups())
self.assertEqual(pr_down_two.list_groups(), pr_down_twice.list_groups())
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 tearDownClass(cls):
project = Project(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"random_testing"))
job = project.load(project.get_job_ids()[0])
job.remove()
project.remove(enable=True)
def tearDownClass(cls):
project = Project(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"hdf5_content"))
ham = project.load(project.get_job_ids()[0])
ham.remove()
project.remove(enable=True)
def setUpClass(cls):
cls.count_run_one = 12
cls.count_run_two = 12
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(
os.path.join(cls.file_location, "random_testing_lib"))
cls.ham = cls.project.create_job("ExampleJob", "job_test_run")
cls.ham.input["count"] = cls.count_run_one
cls.ham.server.run_mode.interactive = True
cls.ham.run()
cls.ham.input["count"] = cls.count_run_two
cls.ham.run()
cls.ham.interactive_close()
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, 'lammps'))
cls.job = Lammps(project=ProjectHDFio(project=cls.project,
file_name='lammps'),
job_name='lammps')
cls.job_water = Lammps(project=ProjectHDFio(project=cls.project,
file_name='lammps_water'),
job_name='lammps_water')
cls.job_water_dump = Lammps(project=ProjectHDFio(
project=cls.project, file_name='lammps_water_dump'),
job_name='lammps_water_dump')
cls.job_dump = Lammps(project=ProjectHDFio(
project=cls.project, file_name='lammps_dump_static'),
job_name='lammps_dump_static')
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, "lammps"))
cls.job = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps"),
job_name="lammps",
)
cls.job_water = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_water"),
job_name="lammps_water",
)
cls.job_water_dump = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_water_dump"),
job_name="lammps_water_dump",
)
cls.job_dump = Lammps(
project=ProjectHDFio(project=cls.project, file_name="lammps_dump_static"),
job_name="lammps_dump_static",
)
def __init__(self, job_path):
job_path_lst = job_path.replace('\\', '/').split('.h5')
if len(job_path_lst) != 2:
raise ValueError
sub_job = job_path_lst[1]
h5_path = None
if sub_job is not None:
if len(sub_job.strip()) > 0:
h5_path = '/'.join(sub_job.split('/')[:-1])
hdf_project = ProjectHDFio(
project=Project(os.path.dirname(job_path_lst[0])),
file_name=job_path_lst[0].split('/')[-1] + '.h5',
h5_path=h5_path,
mode="r")
super(JobPathBase,
self).__init__(project=hdf_project,
job_name=job_path_lst[1].split('/')[-1])
def test_hdf(self):
pr = Project(self.file_location)
file_name = os.path.join(self.file_location, 'genericpara.h5')
hdf = ProjectHDFio(project=pr,
file_name=file_name,
h5_path="/test",
mode="a")
hdf.create_group('test')
self.generic_parameters_str.to_hdf(hdf=hdf, group_name='input')
gp_reload = GenericParameters(table_name='str')
gp_reload.from_hdf(hdf=hdf, group_name='input')
self.assertEqual(gp_reload.get("par___1"), 1)
self.assertEqual(gp_reload.get("par_2"), 'all')
self.assertEqual(gp_reload.get("count"), 0)
self.assertTrue(gp_reload.get("write_restart"))
self.assertFalse(gp_reload.get("read_restart"))
self.assertEqual(gp_reload.get("dict"), {"a": 1, "b": 2})
self.assertEqual(gp_reload.get("list"), [1, "s"])
os.remove(file_name)
def tearDownClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.execution_path, 'lammps'))
project.remove_jobs(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, "hdf5_content"))
cls.ham = cls.project.create_job("ExampleJob", "job_test_run")
cls.ham.run()
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
cls.project = Project(os.path.join(cls.execution_path, 'lammps'))
cls.job = Lammps(project=ProjectHDFio(project=cls.project, file_name='lammps'), job_name='lammps')
cls.job.server.run_mode.interactive = True
cls.job.structure = Atoms(symbols='Fe2', positions=np.outer(np.arange(2), np.ones(3)), cell=2*np.eye(3))
def setUpClass(cls):
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")