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Rename output parameter to output_keys #180

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merged 6 commits into from
Jan 8, 2024
Merged

Rename output parameter to output_keys #180

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a2ba0b0
Rename output parameter to output_keys
jan-janssen Jan 8, 2024
fe31aef
Merge remote-tracking branch 'origin/main' into outputkeys
jan-janssen Jan 8, 2024
2fce739
Format black
pyiron-runner Jan 8, 2024
bacb132
more fixes
jan-janssen Jan 8, 2024
d31fff8
Merge remote-tracking branch 'origin/outputkeys' into outputkeys
jan-janssen Jan 8, 2024
33bb53b
fix test
jan-janssen Jan 8, 2024
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27 changes: 14 additions & 13 deletions atomistics/calculators/ase.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ def evaluate_with_ase(
return calc_static_with_ase(
structure=structure,
ase_calculator=ase_calculator,
output=get_quantities_from_tasks(tasks=tasks),
output_keys=get_quantities_from_tasks(tasks=tasks),
)
else:
raise ValueError("The ASE calculator does not implement:", tasks)
Expand All @@ -113,28 +113,29 @@ def evaluate_with_ase(
def calc_static_with_ase(
structure,
ase_calculator,
output=OutputStatic.fields(),
output_keys=OutputStatic.fields(),
):
return ASEOutputStatic.get(
ASEExecutor(ase_structure=structure, ase_calculator=ase_calculator), *output
ASEExecutor(ase_structure=structure, ase_calculator=ase_calculator),
*output_keys,
)


def _calc_md_step_with_ase(
dyn, structure, ase_calculator, temperature, run, thermo, output
dyn, structure, ase_calculator, temperature, run, thermo, output_keys
):
structure.calc = ase_calculator
MaxwellBoltzmannDistribution(atoms=structure, temperature_K=temperature)
cache = {q: [] for q in output}
cache = {q: [] for q in output_keys}
for i in range(int(run / thermo)):
dyn.run(thermo)
calc_dict = ASEOutputMolecularDynamics.get(
ASEExecutor(ase_structure=structure, ase_calculator=ase_calculator),
*output,
*output_keys,
)
for k, v in calc_dict.items():
cache[k].append(v)
return {q: np.array(cache[q]) for q in output}
return {q: np.array(cache[q]) for q in output_keys}


def calc_molecular_dynamics_npt_with_ase(
Expand All @@ -147,7 +148,7 @@ def calc_molecular_dynamics_npt_with_ase(
pfactor=2e6 * units.GPa * (units.fs**2),
temperature=100,
externalstress=np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar,
output=ASEOutputMolecularDynamics.fields(),
output_keys=ASEOutputMolecularDynamics.fields(),
):
return _calc_md_step_with_ase(
dyn=NPT(
Expand All @@ -169,7 +170,7 @@ def calc_molecular_dynamics_npt_with_ase(
temperature=temperature,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)


Expand All @@ -181,7 +182,7 @@ def calc_molecular_dynamics_langevin_with_ase(
timestep=1 * units.fs,
temperature=100,
friction=0.002,
output=ASEOutputMolecularDynamics.fields(),
output_keys=ASEOutputMolecularDynamics.fields(),
):
return _calc_md_step_with_ase(
dyn=Langevin(
Expand All @@ -195,7 +196,7 @@ def calc_molecular_dynamics_langevin_with_ase(
temperature=temperature,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)


Expand Down Expand Up @@ -231,7 +232,7 @@ def calc_molecular_dynamics_thermal_expansion_with_ase(
ttime=100 * units.fs,
pfactor=2e6 * units.GPa * (units.fs**2),
externalstress=np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar,
output=OutputThermalExpansionProperties.fields(),
output_keys=OutputThermalExpansionProperties.fields(),
):
structure_current = structure.copy()
temperature_lst = np.arange(
Expand All @@ -257,5 +258,5 @@ def calc_molecular_dynamics_thermal_expansion_with_ase(
ThermalExpansionProperties(
temperatures_lst=temperature_md_lst, volumes_lst=volume_md_lst
),
*output,
*output_keys,
)
26 changes: 13 additions & 13 deletions atomistics/calculators/lammps/calculator.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ def calc_static_with_lammps(
structure,
potential_dataframe,
lmp=None,
output=LammpsOutputStatic.fields(),
output_keys=LammpsOutputStatic.fields(),
**kwargs,
):
template_str = LAMMPS_THERMO_STYLE + "\n" + LAMMPS_THERMO + "\n" + LAMMPS_RUN
Expand All @@ -134,7 +134,7 @@ def calc_static_with_lammps(
lmp=lmp,
**kwargs,
)
result_dict = LammpsOutputStatic.get(lmp_instance, *output)
result_dict = LammpsOutputStatic.get(lmp_instance, *output_keys)
lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
return result_dict

Expand All @@ -151,7 +151,7 @@ def calc_molecular_dynamics_nvt_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
**kwargs,
):
init_str = (
Expand Down Expand Up @@ -187,7 +187,7 @@ def calc_molecular_dynamics_nvt_with_lammps(
run_str=run_str,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)
lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
return result_dict
Expand All @@ -208,7 +208,7 @@ def calc_molecular_dynamics_npt_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
**kwargs,
):
init_str = (
Expand Down Expand Up @@ -247,7 +247,7 @@ def calc_molecular_dynamics_npt_with_lammps(
run_str=run_str,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)
lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
return result_dict
Expand All @@ -266,7 +266,7 @@ def calc_molecular_dynamics_nph_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
**kwargs,
):
init_str = (
Expand Down Expand Up @@ -302,7 +302,7 @@ def calc_molecular_dynamics_nph_with_lammps(
run_str=run_str,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)
lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
return result_dict
Expand All @@ -320,7 +320,7 @@ def calc_molecular_dynamics_langevin_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
**kwargs,
):
init_str = (
Expand Down Expand Up @@ -358,7 +358,7 @@ def calc_molecular_dynamics_langevin_with_lammps(
run_str=run_str,
run=run,
thermo=thermo,
output=output,
output_keys=output_keys,
)
lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
return result_dict
Expand All @@ -380,7 +380,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output=OutputThermalExpansionProperties.fields(),
output_keys=OutputThermalExpansionProperties.fields(),
**kwargs,
):
init_str = (
Expand Down Expand Up @@ -411,7 +411,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammps(
seed=seed,
dist=dist,
lmp=lmp,
output=output,
output_keys=output_keys,
**kwargs,
)

Expand Down Expand Up @@ -457,7 +457,7 @@ def evaluate_with_lammps_library(
structure=structure,
potential_dataframe=potential_dataframe,
lmp=lmp,
output=get_quantities_from_tasks(tasks=tasks),
output_keys=get_quantities_from_tasks(tasks=tasks),
)
else:
raise ValueError("The LAMMPS calculator does not implement:", tasks)
Expand Down
14 changes: 7 additions & 7 deletions atomistics/calculators/lammps/helpers.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -46,30 +46,30 @@ def lammps_calc_md_step(
lmp_instance,
run_str,
run,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
):
run_str_rendered = Template(run_str).render(run=run)
lmp_instance.interactive_lib_command(run_str_rendered)
return LammpsOutputMolecularDynamics.get(lmp_instance, *output)
return LammpsOutputMolecularDynamics.get(lmp_instance, *output_keys)


def lammps_calc_md(
lmp_instance,
run_str,
run,
thermo,
output=LammpsOutputMolecularDynamics.fields(),
output_keys=LammpsOutputMolecularDynamics.fields(),
):
results_lst = [
lammps_calc_md_step(
lmp_instance=lmp_instance,
run_str=run_str,
run=thermo,
output=output,
output_keys=output_keys,
)
for _ in range(run // thermo)
]
return {q: np.array([d[q] for d in results_lst]) for q in output}
return {q: np.array([d[q] for d in results_lst]) for q in output_keys}


def lammps_thermal_expansion_loop(
Expand All @@ -88,7 +88,7 @@ def lammps_thermal_expansion_loop(
seed=4928459,
dist="gaussian",
lmp=None,
output=OutputThermalExpansionProperties.fields(),
output_keys=OutputThermalExpansionProperties.fields(),
**kwargs,
):
lmp_instance = lammps_run(
Expand Down Expand Up @@ -125,7 +125,7 @@ def lammps_thermal_expansion_loop(
ThermalExpansionProperties(
temperatures_lst=temperature_md_lst, volumes_lst=volume_md_lst
),
*output,
*output_keys,
)


Expand Down
6 changes: 3 additions & 3 deletions atomistics/calculators/qe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ def calc_static_with_qe(
pseudopotentials=None,
tstress=True,
tprnfor=True,
output=OutputStatic.fields(),
output_keys=OutputStatic.fields(),
**kwargs,
):
input_file_name = os.path.join(working_directory, calculation_name + ".pwi")
Expand All @@ -213,7 +213,7 @@ def calc_static_with_qe(
calculation_name=calculation_name, working_directory=working_directory
)
return QuantumEspressoOutputStatic.get(
QEStaticParser(filename=output_file_name), *output
QEStaticParser(filename=output_file_name), *output_keys
)


Expand Down Expand Up @@ -252,7 +252,7 @@ def evaluate_with_qe(
pseudopotentials=pseudopotentials,
tstress=tstress,
tprnfor=tprnfor,
output=get_quantities_from_tasks(tasks=tasks),
output_keys=get_quantities_from_tasks(tasks=tasks),
**kwargs,
)
else:
Expand Down
6 changes: 3 additions & 3 deletions atomistics/workflows/elastic/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,12 +44,12 @@ def generate_structures(self):
)
return {"calc_energy": self._structure_dict}

def analyse_structures(self, output_dict, output=OutputElastic.fields()):
def analyse_structures(self, output_dict, output_keys=OutputElastic.fields()):
"""

Args:
output_dict (dict):
output (tuple):
output_keys (tuple):

Returns:

Expand All @@ -67,5 +67,5 @@ def analyse_structures(self, output_dict, output=OutputElastic.fields()):
self._data["e0"] = ene0
self._data["A2"] = A2
return elastic_matrix_output_elastic.get(
ElasticProperties(elastic_matrix=elastic_matrix), *output
ElasticProperties(elastic_matrix=elastic_matrix), *output_keys
)
4 changes: 2 additions & 2 deletions atomistics/workflows/evcurve/debye.py
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ def get_thermal_properties(
temperatures=None,
constant_volume=False,
num_steps=50,
output=OutputThermodynamic.fields(),
output_keys=OutputThermodynamic.fields(),
):
return DebyeOutputThermodynamic.get(
DebyeThermalProperties(
Expand All @@ -245,5 +245,5 @@ def get_thermal_properties(
constant_volume=constant_volume,
num_steps=num_steps,
),
*output,
*output_keys,
)
10 changes: 6 additions & 4 deletions atomistics/workflows/evcurve/workflow.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,9 @@ def generate_structures(self):
self._structure_dict[1 + np.round(strain, 7)] = basis
return {"calc_energy": self._structure_dict}

def analyse_structures(self, output_dict, output=OutputEnergyVolumeCurve.fields()):
def analyse_structures(
self, output_dict, output_keys=OutputEnergyVolumeCurve.fields()
):
self._fit_dict = EnergyVolumeCurveOutputEnergyVolumeCurve.get(
EnergyVolumeCurveProperties(
fit_module=fit_ev_curve_internal(
Expand All @@ -192,7 +194,7 @@ def analyse_structures(self, output_dict, output=OutputEnergyVolumeCurve.fields(
fit_order=self.fit_order,
)
),
*output,
*output_keys,
)
return self.fit_dict

Expand All @@ -206,7 +208,7 @@ def get_thermal_properties(
t_step=50,
temperatures=None,
constant_volume=False,
output=OutputThermodynamic.fields(),
output_keys=OutputThermodynamic.fields(),
):
return get_thermal_properties(
fit_dict=self.fit_dict,
Expand All @@ -216,5 +218,5 @@ def get_thermal_properties(
t_step=t_step,
temperatures=temperatures,
constant_volume=constant_volume,
output=output,
output_keys=output_keys,
)
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