class SQSJob(AtomisticGenericJob):
def __init__(self, project, job_name):
super(SQSJob, self).__init__(project, job_name)
self.input = GenericParameters(table_name="input")
self.input['mole_fractions'] = dict()
self.input['weights'] = None
self.input['objective'] = 0.0
self.input['iterations'] = 1e6
self.input['output_structures'] = 1
self._python_only_job = True
self._lst_of_struct = []
@property
def list_of_structures(self):
return self._lst_of_struct
def list_structures(self):
if self.status.finished:
return self._lst_of_struct
else:
return []
# This function is executed
def run_static(self):
self._lst_of_struct, decmp, iterations, cycle_time = get_sqs_structures(
structure=self.structure,
mole_fractions=self.input['mole_fractions'],
weights=self.input['weights'],
objective=self.input['objective'],
iterations=self.input['iterations'],
output_structures=self.input['output_structures'],
num_threads=self.server.cores)
for i, structure in enumerate(self._lst_of_struct):
with self.project_hdf5.open("output/structures/structure_" +
str(i)) as h5:
structure.to_hdf(h5)
with self.project_hdf5.open("output") as h5:
h5["decmp"] = decmp
h5["cycle_time"] = cycle_time
h5["iterations"] = iterations
self.status.finished = True
self.project.db.item_update(self._runtime(), self.job_id)
def to_hdf(self, hdf=None, group_name=None):
super().to_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as h5in:
self.input.to_hdf(h5in)
def from_hdf(self, hdf=None, group_name=None):
super().from_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as h5in:
self.input.from_hdf(h5in)
with self.project_hdf5.open("output/structures") as hdf5_output:
structure_names = hdf5_output.list_groups()
for group in structure_names:
with self.project_hdf5.open("output/structures/" +
group) as hdf5_output:
self._lst_of_struct.append(Atoms().from_hdf(hdf5_output))
class MetadynInput(Input):
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 write(self, structure, modified_elements, directory=None):
"""
Writes all the input files to a specified directory
Args:
structure (atomistics.structure.atoms.Atoms instance): Structure to be written
directory (str): The working directory for the VASP run
"""
# Writing the constraints, increments, and penalty potentials
super(MetadynInput, self).write(structure, modified_elements,
directory)
self.iconst.write_file(file_name="ICONST", cwd=directory)
self.penaltypot.write_file(file_name="PENALTYPOT", cwd=directory)
def to_hdf(self, hdf):
super(MetadynInput, self).to_hdf(hdf)
with hdf.open("input") as hdf5_input:
self.iconst.to_hdf(hdf5_input)
self.penaltypot.to_hdf(hdf5_input)
hdf5_input["constraint_dict"] = self._constraint_dict
hdf5_input["complex_constraint_dict"] = self._complex_constraints
def from_hdf(self, hdf):
super(MetadynInput, self).from_hdf(hdf)
with hdf.open("input") as hdf5_input:
self.iconst.from_hdf(hdf5_input)
self.penaltypot.from_hdf(hdf5_input)
if "constraint_dict" in hdf5_input.list_nodes():
self._constraint_dict = hdf5_input["constraint_dict"]
if "complex_constraint_dict" in hdf5_input.list_nodes():
self._complex_constraints = hdf5_input[
"complex_constraint_dict"]
def _backwards_compatible_input_from_hdf(self):
if "HDF_VERSION" in self.project_hdf5.list_nodes():
version = self.project_hdf5["HDF_VERSION"]
else:
version = "0.1.0"
if version == "0.1.0":
with self.project_hdf5.open("input") as hdf5_input:
gp = GenericParameters(table_name="custom_dict")
gp.from_hdf(hdf5_input)
for k in gp.keys():
self.input[k] = gp[k]
elif version == "0.2.0":
with self.project_hdf5.open("input") as hdf5_input:
self.input.from_hdf(hdf5_input)
else:
raise ValueError("Cannot handle hdf version: {}".format(version))
class SxHarmPotTst(AtomisticGenericJob):
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
@property
def md_job(self):
if self._md_job is None and self._md_job_id is not None:
self._md_job = self.project.load(self._md_job_id)
return self._md_job
@md_job.setter
def md_job(self, job):
if job.status == "finished":
self._md_job_id = job.job_id
self._md_job = job
self._positions_lst = job["output/generic/positions"]
self._forces_lst = job["output/generic/forces"]
else:
raise ValueError("Job not finished!")
def set_input_to_read_only(self):
"""
This function enforces read-only mode for the input classes, but it has to be implement in the individual
classes.
"""
super(SxHarmPotTst, self).set_input_to_read_only()
self.input.read_only = True
def write_harmpot(self, cwd, file_name="harmpot.sx"):
harm_pot_str = (
"format harmpot;\n\n"
+ "valenceCharge=0;\n"
+ "harmonicPotential {\n"
+ ' //include "refSym.sx";\n'
+ ' //include "equivalence.sx";\n'
+ " maxDist="
+ str(float(self.input["maximum_noise"]) / BOHR_TO_ANGSTROM)
+ ";\n"
+ ' include "shells.sx";\n'
+ "}\n"
+ 'include "structure_wrapper.sx";'
)
if cwd is not None:
file_name = os.path.join(cwd, file_name)
with open(file_name, "w") as f:
f.write(harm_pot_str)
def write_structure(self, cwd, file_name="structure_wrapper.sx"):
structure_file_name = "structure.sx"
iw = InputWriter()
iw.structure = self._md_job.structure
iw.write_structure(file_name=structure_file_name, cwd=cwd)
with open(os.path.join(cwd, file_name), "w") as f:
f.writelines(["structure { include <" + structure_file_name + ">; }"])
def validate_ready_to_run(self):
if len(self._positions_lst) == 0 or len(self._forces_lst) == 0:
raise ValueError()
def write_input(self):
self.write_structure(
cwd=self.working_directory, file_name="structure_wrapper.sx"
)
self.write_harmpot(cwd=self.working_directory, file_name="harmpot.sx")
pos_force_mat = np.concatenate((self._positions_lst, self._forces_lst), axis=2)
cont_pos_force_mat = pos_force_mat.reshape(-1, pos_force_mat.shape[-1])
np.savetxt(
os.path.join(self.working_directory, "POSITIONs"), cont_pos_force_mat
)
lines = [
"#!/bin/bash\n",
"sxstructparam -i structure_wrapper.sx -c "
+ str(float(self.input["interaction_radius"]) / BOHR_TO_ANGSTROM)
+ " --printReduced=shells.sx --log\n",
"sxharmpottst --param=POSITIONs --vasp --printHesse HesseMatrix_sphinx -i harmpot.sx --log --svd\n",
]
with open(os.path.join(self.working_directory, "sxharmpottst.sh"), "w") as f:
f.writelines(lines)
def get_hesse_matrix(self):
if "output" in self.project_hdf5.list_groups():
return self.project_hdf5["output/hesse"]
def collect_output(self):
with self.project_hdf5.open("output") as hdf_out:
hdf_out["hesse"] = np.loadtxt(
os.path.join(self.working_directory, "HesseMatrix_sphinx")
)
def to_hdf(self, hdf=None, group_name=None):
"""
Store the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(SxHarmPotTst, self).to_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.to_hdf(hdf5_input)
if len(self._positions_lst) != 0:
hdf5_input["positions"] = self._positions_lst
if len(self._forces_lst) != 0:
hdf5_input["forces"] = self._forces_lst
if self._md_job_id is not None:
hdf5_input["md_job_id"] = self._md_job_id
def from_hdf(self, hdf=None, group_name=None):
"""
Restore the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(SxHarmPotTst, self).from_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.from_hdf(hdf5_input)
if "positions" in hdf5_input.list_nodes():
self._positions_lst = hdf5_input["positions"]
if "forces" in hdf5_input.list_nodes():
self._forces_lst = hdf5_input["forces"]
if "md_job_id" in hdf5_input.list_nodes():
self._md_job_id = hdf5_input["md_job_id"]
class SxUniqDispl(AtomisticGenericJob):
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 = []
self._id_pyi_to_spx = []
self._id_spx_to_pyi = []
@property
def id_spx_to_pyi(self):
if self.structure is None:
return None
if len(self._id_spx_to_pyi) == 0:
self._initialize_order()
return self._id_spx_to_pyi
@property
def id_pyi_to_spx(self):
if self.structure is None:
return None
if len(self._id_pyi_to_spx) == 0:
self._initialize_order()
return self._id_pyi_to_spx
def _initialize_order(self):
for elm_species in self.structure.get_species_objects():
self._id_pyi_to_spx.append(
np.arange(len(self.structure))[
self.structure.get_chemical_symbols() == elm_species.Abbreviation
]
)
self._id_pyi_to_spx = np.array(
[ooo for oo in self._id_pyi_to_spx for ooo in oo]
)
self._id_spx_to_pyi = np.array([0] * len(self._id_pyi_to_spx))
for i, p in enumerate(self._id_pyi_to_spx):
self._id_spx_to_pyi[p] = i
def set_input_to_read_only(self):
"""
This function enforces read-only mode for the input classes, but it has to be implement in the individual
classes.
"""
super(SxUniqDispl, self).set_input_to_read_only()
self.input.read_only = True
def list_structures(self):
if self.status.finished:
return self.structure_lst
else:
return []
def write_structure(self, cwd, file_name="structure_wrapper.sx"):
structure_file_name = "structure.sx"
iw = InputWriter()
iw.structure = self.structure
iw.write_structure(file_name=structure_file_name, cwd=cwd)
with open(os.path.join(cwd, file_name), "w") as f:
f.writelines(["structure { include <" + structure_file_name + ">; }"])
def extract_structure(self, working_directory):
structure_lst = [self.structure]
parser = Output(self)
for f in os.listdir(working_directory):
if "input-disp" in f:
structure_template = self.structure.copy()
parser.collect_relaxed_hist(file_name=f, cwd=working_directory)
structure_template.cell = parser._parse_dict["cell"][0]
structure_template.positions = parser._parse_dict["positions"][0]
structure_lst.append(structure_template)
return structure_lst
def write_input(self):
self.write_structure(
cwd=self.working_directory, file_name="structure_wrapper.sx"
)
lines = [
"#!/bin/bash\n",
"sxuniqdispl --log -d "
+ str(float(self.input["displacement"]) / BOHR_TO_ANGSTROM)
+ " -i structure_wrapper.sx\n",
]
with open(os.path.join(self.working_directory, "sxuniqdispl.sh"), "w") as f:
f.writelines(lines)
def collect_output(self):
self.structure_lst = self.extract_structure(
working_directory=self.working_directory
)
with self.project_hdf5.open("output") as hdf_out:
for ind, struct in enumerate(self.structure_lst):
struct.to_hdf(hdf=hdf_out, group_name="structure_" + str(ind))
def to_hdf(self, hdf=None, group_name=None):
"""
Store the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(SxUniqDispl, self).to_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.to_hdf(hdf5_input)
def from_hdf(self, hdf=None, group_name=None):
"""
Restore the ExampleJob object in the HDF5 File
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(SxUniqDispl, self).from_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.from_hdf(hdf5_input)
if "output" in self.project_hdf5.list_groups():
with self.project_hdf5.open("output") as hdf5_output:
self.structure_lst = [
Atoms().from_hdf(hdf5_output, group_name)
for group_name in hdf5_output.list_groups()
]
class InteractiveWrapper(GenericMaster):
def __init__(self, project, job_name):
super(InteractiveWrapper, self).__init__(project, job_name)
self._ref_job = None
self.input = GenericParameters("parameters")
@property
def structure(self):
if self.ref_job:
return self._ref_job.structure
else:
return None
@structure.setter
def structure(self, basis):
if self.ref_job:
self._ref_job.structure = basis
else:
raise ValueError(
"A structure can only be set after a start job has been assinged."
)
@property
def ref_job(self):
"""
Get the reference job template from which all jobs within the ParallelMaster are generated.
Returns:
GenericJob: reference job
"""
if self._ref_job is not None:
return self._ref_job
try:
if isinstance(self[0], GenericJob):
self._ref_job = self[0]
return self._ref_job
else:
return None
except IndexError:
return None
@ref_job.setter
def ref_job(self, ref_job):
"""
Set the reference job template from which all jobs within the ParallelMaster are generated.
Args:
ref_job (GenericJob): reference job
"""
if not ref_job.server.run_mode.interactive:
warnings.warn(
"Run mode of the reference job not set to interactive")
self.append(ref_job)
def set_input_to_read_only(self):
"""
This function enforces read-only mode for the input classes, but it has to be implement in the individual
classes.
"""
self.input.read_only = True
def validate_ready_to_run(self):
"""
Validate that the calculation is ready to be executed. By default no generic checks are performed, but one could
check that the input information is complete or validate the consistency of the input at this point.
"""
self.ref_job.validate_ready_to_run()
def check_setup(self):
"""
Checks whether certain parameters (such as plane wave cutoff radius in DFT) are changed from the pyiron standard
values to allow for a physically meaningful results. This function is called manually or only when the job is
submitted to the queueing system.
"""
try:
self.ref_job.check_setup()
except AttributeError:
pass
def ref_job_initialize(self):
"""
"""
if len(self._job_name_lst) > 0:
self._ref_job = self.pop(-1)
if self._job_id is not None and self._ref_job._master_id is None:
self._ref_job.master_id = self.job_id
self._ref_job.server.cores = self.server.cores
def get_final_structure(self):
"""
Returns:
"""
warnings.warn(
"get_final_structure() is deprecated - please use get_structure() instead.",
DeprecationWarning,
)
if self.ref_job:
return self._ref_job.get_structure(iteration_step=-1)
else:
return None
def to_hdf(self, hdf=None, group_name=None):
"""
Store the InteractiveWrapper in an HDF5 file
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
if self._ref_job is not None and self._ref_job.job_id is None:
self.append(self._ref_job)
super(InteractiveWrapper, self).to_hdf(hdf=hdf, group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.to_hdf(hdf5_input)
def from_hdf(self, hdf=None, group_name=None):
"""
Restore the InteractiveWrapper from an HDF5 file
Args:
hdf (ProjectHDFio): HDF5 group object - optional
group_name (str): HDF5 subgroup name - optional
"""
super(InteractiveWrapper, self).from_hdf(hdf=hdf,
group_name=group_name)
with self.project_hdf5.open("input") as hdf5_input:
self.input.from_hdf(hdf5_input)
def collect_output(self):
pass
def collect_logfiles(self):
pass
def db_entry(self):
"""
Generate the initial database entry
Returns:
(dict): db_dict
"""
db_dict = super(InteractiveWrapper, self).db_entry()
if self.structure:
if isinstance(self.structure, PAtoms):
parent_structure = self.structure.get_parent_basis()
else:
parent_structure = ase_to_pyiron(
self.structure).get_parent_basis()
db_dict["ChemicalFormula"] = parent_structure.get_chemical_formula(
)
return db_dict
def _db_entry_update_run_time(self):
"""
Returns:
"""
job_id = self.get_job_id()
db_dict = {}
start_time = self.project.db.get_item_by_id(job_id)["timestart"]
db_dict["timestop"] = datetime.now()
db_dict["totalcputime"] = (db_dict["timestop"] - start_time).seconds
self.project.db.item_update(db_dict, job_id)
def _finish_job(self):
"""
Returns:
"""
self.status.finished = True
self._db_entry_update_run_time()
self._logger.info("{}, status: {}, monte carlo master".format(
self.job_info_str, self.status))
self._calculate_successor()
self.send_to_database()
self.update_master()
def __getitem__(self, item):
"""
Get/ read data from the GenericMaster
Args:
item (str, slice): path to the data or key of the data object
Returns:
dict, list, float, int: data or data object
"""
child_id_lst = self.child_ids
child_name_lst = [
self.project.db.get_item_by_id(child_id)["job"]
for child_id in self.child_ids
]
if isinstance(item, int):
total_lst = child_name_lst + self._job_name_lst
item = total_lst[item]
return self._get_item_when_str(item=item,
child_id_lst=child_id_lst,
child_name_lst=child_name_lst)