def setUp(self):
self.generic_parameters_empty = GenericParameters()
self.generic_parameters_str = GenericParameters()
my_str = '''\
par_1 1
par_2 ab
count 0
write_restart True
read_restart False'''
self.generic_parameters_str.load_string(my_str)
def __init__(self):
super(MetadynInput, self).__init__()
self.iconst = GenericParameters(input_file_name=None,
table_name="iconst",
val_only=True,
comment_char="!")
self.penaltypot = GenericParameters(input_file_name=None,
table_name="penaltypot",
val_only=True,
comment_char="!")
self._constraint_dict = dict()
self._complex_constraints = dict()
def setUpClass(cls):
cls.generic_parameters_empty = GenericParameters(table_name='empty')
cls.generic_parameters_str = GenericParameters(table_name='str')
my_str = '''\
par___1 1
par_2 all
count 0
write_restart True
dict {"a": 1, "b": 2}
list [1, "s"]
read_restart False'''
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.generic_parameters_str.load_string(my_str)
def __init__(self, project, job_name):
super(SxUniqDispl, self).__init__(project, job_name)
self.__version__ = "0.1"
self.__name__ = "SxUniqDispl"
self.input = GenericParameters(table_name="displacement")
self.input["displacement"] = 0.01
self.structure_lst = []
def __init__(self, project, job_name):
self._input = GenericParameters("parameters")
super(ListMaster, self).__init__(project, job_name=job_name)
self.__name__ = "ListMaster"
self.__version__ = "0.1"
self._input["mode"] = "parallel"
self.submission_status = SubmissionStatus(db=project.db, job_id=self.job_id)
self.refresh_submission_status()
def __init__(self, project, job_name):
self.input = GenericParameters("parameters")
super(ParallelMaster, self).__init__(project, job_name=job_name)
self.__name__ = "ParallelMaster"
self.__version__ = "0.3"
self._ref_job = None
self._output = GenericOutput()
self._job_generator = None
self.submission_status = SubmissionStatus(db=project.db, job_id=self.job_id)
self.refresh_submission_status()
def __init__(self, project, job_name):
super(SxHarmPotTst, self).__init__(project, job_name)
self.__version__ = "0.1"
self.__name__ = "SxHarmPotTst"
self.input = GenericParameters(table_name="interaction")
self.input["interaction_radius"] = 4.0
self.input["maximum_noise"] = 0.26
self._positions_lst = []
self._forces_lst = []
self._md_job_id = None
self._md_job = None
def get_custom_dict():
folder = Path('.').cwd().parts[-1]
hdf_file = Path('.').cwd().parents[1]/folder
hdf_file = str(hdf_file)+'.h5'
if Path(hdf_file).exists():
hdf = FileHDFio(hdf_file)
custom_dict = GenericParameters()
for k, v in zip(hdf[folder+'/input/custom_dict/data_dict']['Parameter'],
hdf[folder+'/input/custom_dict/data_dict']['Value']):
custom_dict[k] = v
return custom_dict
else:
print(hdf_file, 'not found')
return None
def __init__(self, project, job_name):
self._input = GenericParameters("parameters") # e.g. convergence goal
super(SerialMasterBase, self).__init__(project, job_name=job_name)
self.__name__ = "SerialMaster"
self.__version__ = "0.3"
self._output = GenericOutput()
self._max_iterations = 100
self._start_job = None
self._run_fast = False
self._logger.debug("run_fast: {}".format(self._run_fast))
self._convergence_goal = None
self._convergence_goal_qwargs = {}
self._convergence_goal_str = None
def get_custom_dict():
folder = Path(".").cwd().parts[-1]
hdf_file = Path(".").cwd().parents[1] / folder
hdf_file = str(hdf_file) + ".h5"
if Path(hdf_file).exists():
hdf = FileHDFio(hdf_file)
custom_dict = GenericParameters()
for k, v in zip(
hdf[folder + "/input/custom_dict/data_dict"]["Parameter"],
hdf[folder + "/input/custom_dict/data_dict"]["Value"],
):
custom_dict[k] = v
return custom_dict
else:
print(hdf_file, "not found")
return None
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 __init__(self, project, job_name):
super().__init__(project, job_name)
self.input = GenericParameters(table_name="input")
def __init__(self, project, job_name):
super(InteractiveWrapper, self).__init__(project, job_name)
self._ref_job = None
self.input = GenericParameters("parameters")
def __init__(self, project, job_name):
super(ScriptJob, self).__init__(project, job_name)
self.__version__ = "0.1"
self.__name__ = "Script"
self._script_path = None
self.input = GenericParameters(table_name="custom_dict")