class PhononAbinitInput(AbinitBasicInputMixin, EmbeddedDocument):
gs_input = MSONField(
help_text="The last input used to calculate the wafunctions.")
ddk_input = MSONField(
help_text="The last input used to calculate one of the ddk.")
dde_input = MSONField(
help_text="The last input used to calculate one of the dde.")
wfq_input = MSONField(
help_text="The last input used to calculate one of the wfq.")
phonon_input = MSONField(
help_text="The last input used to calculate one of the phonons.")
kppa = IntField()
ngqpt = ListField(IntField())
qpoints = DictField()
qppa = IntField()
class DteAbinitInput(AbinitBasicInputMixin, EmbeddedDocument):
"""
EmbeddedDocument containing the typical inputs for a DTE workflow.
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: DteAbinitInput
"""
gs_input = MSONField(help_text="The last input used to calculate the wafunctions.")
ddk_input = MSONField(help_text="The last input used to calculate one of the ddk.")
dde_input = MSONField(help_text="The last input used to calculate one of the dde.")
dte_input = MSONField(help_text="The last input used to calculate one of the dte.")
phonon_input = MSONField(help_text="The last input used to calculate one of the phonons.")
kppa = IntField()
with_phonons = BooleanField(help_text="Whether the phonon perturbations have been included or not")
class AbinitBasicInputMixin(object):
"""
Mixin providing some basic fields that are required to run a calculation.
"""
#TODO add more variables
structure = MSONField()
ecut = FloatField()
nshiftk = IntField()
shiftk = ListField(ListField(FloatField()))
ngkpt = ListField(IntField())
kptrlatt = ListField(ListField(IntField()))
dilatmx = FloatField(default=1)
occopt = IntField()
tsmear = FloatField()
pseudopotentials = EmbeddedDocumentField(AbinitPseudoData,
default=AbinitPseudoData)
def set_abinit_basic_from_abinit_input(self, abinit_input):
"""
create the object from an AbinitInput object
"""
self.structure = abinit_input.structure.as_dict()
self.ecut = abinit_input['ecut']
# kpoints may be defined in different ways
self.nshiftk = abinit_input.get('nshiftk', None)
self.shiftk = abinit_input.get('shiftk', None)
self.ngkpt = abinit_input.get('ngkpt', None)
self.kptrlatt = abinit_input.get('kptrlatt', None)
self.dilatmx = abinit_input.get('dilatmx', 1)
self.occopt = abinit_input.get('occopt', 1)
self.tsmear = abinit_input.get('tsmear', None)
class DteResult(MaterialMixin, DateMixin, DirectoryMixin, CustomFieldMixin, Document):
"""
Document containing the results for a dte workflow.
Includes information from the various steps of the workflow (scf, ddk, dde, ph, dte, anaddb)
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: DteResult
"""
mp_id = StringField()
relax_db = MSONField()
relax_id = StringField()
time_report = MSONField()
fw_id = IntField()
abinit_input = EmbeddedDocumentField(DteAbinitInput, default=DteAbinitInput)
abinit_output = EmbeddedDocumentField(DteAbinitOutput, default=DteAbinitOutput)
class PhononResult(MaterialMixin, DateMixin, DirectoryMixin, Document):
"""
Document containing the results for a phonon workflow.
Includes information from the various steps of the workflow (scf, nscf, ddk, dde, ph, anaddb)
"""
mp_id = StringField()
# relax_result = ReferenceField(RelaxationResult)
relax_db = MSONField()
relax_id = StringField()
time_report = MSONField()
fw_id = IntField()
abinit_input = EmbeddedDocumentField(PhononAbinitInput,
default=PhononAbinitInput)
abinit_output = EmbeddedDocumentField(PhononAbinitOutput,
default=PhononAbinitOutput)
class PhononAbinitInput(AbinitBasicInputMixin, EmbeddedDocument):
"""
EmbeddedDocument containing the typical inputs for a phonon workflow.
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: PhononAbinitInput
"""
gs_input = MSONField(help_text="The last input used to calculate the wafunctions.")
ddk_input = MSONField(help_text="The last input used to calculate one of the ddk.")
dde_input = MSONField(help_text="The last input used to calculate one of the dde.")
wfq_input = MSONField(help_text="The last input used to calculate one of the wfq.")
phonon_input = MSONField(help_text="The last input used to calculate one of the phonons.")
kppa = IntField()
ngqpt = ListField(IntField())
qpoints = ListField()
qppa = IntField()
class AbinitDftpOutputMixin(object):
"""
Mixin providing generic fiels for dfpt calculation
"""
ddb = AbiFileField(abiext="DDB", abiform="t", help_text="DDB file produced by a dfpt falculation",
db_field='ddb_id', collection_name='ddb_fs')
structure = MSONField(required=True, help_text="The structure used for the calculation.")
class RelaxAbinitInput(AbinitBasicInputMixin, EmbeddedDocument):
"""
EmbeddedDocument containing the typical inputs for a relaxation workflow.
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: RelaxAbinitInput
"""
last_input = MSONField(help_text="The last input used for the calculation.")
kppa = IntField()
class DfptResult(MaterialMixin, DateMixin, DirectoryMixin, CustomFieldMixin, Document):
"""
Document containing the results for a dfpt workflow.
Includes information from the various steps of the workflow (scf, nscf, ddk, dde, ph, strain, dte, anaddb)
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: DfptResult
"""
mp_id = StringField()
relax_db = MSONField()
relax_id = StringField()
time_report = MSONField()
fw_id = IntField()
abinit_input = EmbeddedDocumentField(DfptAbinitInput, default=DfptAbinitInput)
abinit_output = EmbeddedDocumentField(DfptAbinitOutput, default=DfptAbinitOutput)
has_phonons = BooleanField(help_text="Whether the phonon perturbations have been included or not", default=False)
has_ddk = BooleanField(help_text="Whether the ddk perturbations have been included or not", default=False)
has_dde = BooleanField(help_text="Whether the dde perturbations have been included or not", default=False)
has_strain = BooleanField(help_text="Whether the strain perturbations have been included or not", default=False)
has_dte = BooleanField(help_text="Whether the dte perturbations have been included or not", default=False)
class RelaxResult(MaterialMixin, DateMixin, DirectoryMixin, Document):
"""
Document containing the results for a relaxation workflow consisting of an ion followed by ioncell relaxations.
"""
history = DictField()
mp_id = StringField()
abinit_input = EmbeddedDocumentField(RelaxAbinitInput,
default=RelaxAbinitInput)
abinit_output = EmbeddedDocumentField(RelaxAbinitOutput,
default=RelaxAbinitOutput)
time_report = MSONField()
fw_id = IntField()
class GroundStateOutputMixin(object):
"""
Mixin providing generic fiels for ground state calculation
"""
#TODO would it be convenient to make these FloatWithUnitField?
final_energy = FloatField(help_text="Final energy obtained computed in eV")
efermi = FloatField(help_text="Computed Fermi energy in eV")
total_magnetization = FloatField(
help_text="Total magnetization computed"
) # does pymatgen have a default unit for this?
structure = MSONField(
required=True,
help_text=
"The structure used for the calculation. If a relaxation the final structure."
)
class RelaxAbinitInput(AbinitBasicInputMixin, EmbeddedDocument):
last_input = MSONField(
help_text="The last input used for the calculation.")
kppa = IntField()