Merge pull request #180 from pyiron/outputkeys

Rename output parameter to output_keys

Author: jan-janssen

atomistics/calculators/ase.py

@@ -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)
@@ -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(
@@ -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(
@@ -169,7 +170,7 @@ def calc_molecular_dynamics_npt_with_ase(
         temperature=temperature,
         run=run,
         thermo=thermo,
-        output=output,
+        output_keys=output_keys,
     )
 
 
@@ -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(
@@ -195,7 +196,7 @@ def calc_molecular_dynamics_langevin_with_ase(
         temperature=temperature,
         run=run,
         thermo=thermo,
-        output=output,
+        output_keys=output_keys,
     )
 
 
@@ -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(
@@ -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,
     )

atomistics/calculators/lammps/calculator.py

@@ -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
@@ -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
 
@@ -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 = (
@@ -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
@@ -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 = (
@@ -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
@@ -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 = (
@@ -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
@@ -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 = (
@@ -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
@@ -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 = (
@@ -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,
     )
 
@@ -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)

atomistics/calculators/lammps/helpers.py

@@ -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(
@@ -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(
@@ -125,7 +125,7 @@ def lammps_thermal_expansion_loop(
         ThermalExpansionProperties(
             temperatures_lst=temperature_md_lst, volumes_lst=volume_md_lst
         ),
-        *output,
+        *output_keys,
     )
 
 

atomistics/calculators/qe.py

@@ -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")
@@ -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
     )
 
 
@@ -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:

atomistics/workflows/elastic/workflow.py

@@ -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:
 
@@ -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
         )

atomistics/workflows/evcurve/debye.py

@@ -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(
@@ -245,5 +245,5 @@ def get_thermal_properties(
             constant_volume=constant_volume,
             num_steps=num_steps,
         ),
-        *output,
+        *output_keys,
     )

atomistics/workflows/evcurve/workflow.py

@@ -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(
@@ -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
 
@@ -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,
@@ -216,5 +218,5 @@ def get_thermal_properties(
             t_step=t_step,
             temperatures=temperatures,
             constant_volume=constant_volume,
-            output=output,
+            output_keys=output_keys,
         )