Replace dataclass by abstract class

atomistics/calculators/ase.py

@@ -10,11 +10,12 @@
 
 from atomistics.calculators.interface import get_quantities_from_tasks
 from atomistics.calculators.wrapper import as_task_dict_evaluator
-from atomistics.shared.output import OutputStatic, OutputMolecularDynamics
-from atomistics.shared.thermal_expansion import (
-    OutputThermalExpansionProperties,
-    ThermalExpansionProperties,
+from atomistics.shared.output import (
+    OutputStatic,
+    OutputMolecularDynamics,
+    OutputThermalExpansion,
 )
+from atomistics.shared.thermal_expansion import get_thermal_expansion_output
 from atomistics.shared.tqdm_iterator import get_tqdm_iterator
 
 if TYPE_CHECKING:
@@ -24,7 +25,7 @@
     from atomistics.calculators.interface import TaskName
 
 
-class ASEExecutor(object):
+class ASEExecutor(OutputStatic, OutputMolecularDynamics):
     def __init__(self, ase_structure, ase_calculator):
         self.structure = ase_structure
         self.structure.calc = ase_calculator
@@ -65,15 +66,6 @@ def volume(self):
         return self.structure.get_volume()
 
 
-ASEOutputStatic = OutputStatic(
-    **{k: getattr(ASEExecutor, k) for k in OutputStatic.fields()}
-)
-
-ASEOutputMolecularDynamics = OutputMolecularDynamics(
-    **{k: getattr(ASEExecutor, k) for k in OutputMolecularDynamics.fields()}
-)
-
-
 @as_task_dict_evaluator
 def evaluate_with_ase(
     structure: Atoms,
@@ -103,7 +95,7 @@ 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 +105,27 @@ def evaluate_with_ase(
 def calc_static_with_ase(
     structure,
     ase_calculator,
-    output=OutputStatic.fields(),
+    output_keys=OutputStatic.keys(),
 ):
-    return ASEOutputStatic.get(
-        ASEExecutor(ase_structure=structure, ase_calculator=ase_calculator), *output
-    )
+    return ASEExecutor(
+        ase_structure=structure, ase_calculator=ase_calculator
+    ).get_output(output_keys=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,
-        )
+        calc_dict = ASEExecutor(
+            ase_structure=structure, ase_calculator=ase_calculator
+        ).get_output(output_keys=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 +138,7 @@ 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=OutputMolecularDynamics.keys(),
 ):
     return _calc_md_step_with_ase(
         dyn=NPT(
@@ -169,7 +160,7 @@ def calc_molecular_dynamics_npt_with_ase(
         temperature=temperature,
         run=run,
         thermo=thermo,
-        output=output,
+        output_keys=output_keys,
     )
 
 
@@ -181,7 +172,7 @@ def calc_molecular_dynamics_langevin_with_ase(
     timestep=1 * units.fs,
     temperature=100,
     friction=0.002,
-    output=ASEOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
 ):
     return _calc_md_step_with_ase(
         dyn=Langevin(
@@ -195,7 +186,7 @@ def calc_molecular_dynamics_langevin_with_ase(
         temperature=temperature,
         run=run,
         thermo=thermo,
-        output=output,
+        output_keys=output_keys,
     )
 
 
@@ -231,7 +222,7 @@ 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=OutputThermalExpansion.keys(),
 ):
     structure_current = structure.copy()
     temperature_lst = np.arange(
@@ -253,9 +244,8 @@ def calc_molecular_dynamics_thermal_expansion_with_ase(
         structure_current.set_cell(cell=result_dict["cell"][-1], scale_atoms=True)
         temperature_md_lst.append(result_dict["temperature"][-1])
         volume_md_lst.append(result_dict["volume"][-1])
-    return OutputThermalExpansionProperties.get(
-        ThermalExpansionProperties(
-            temperatures_lst=temperature_md_lst, volumes_lst=volume_md_lst
-        ),
-        *output,
+    return get_thermal_expansion_output(
+        temperatures_lst=temperature_md_lst,
+        volumes_lst=volume_md_lst,
+        output_keys=output_keys,
     )

atomistics/calculators/lammps/calculator.py

@@ -7,6 +7,7 @@
 from pylammpsmpi import LammpsASELibrary
 
 from atomistics.calculators.interface import get_quantities_from_tasks
+from atomistics.calculators.lammps.output import LammpsOutput
 from atomistics.calculators.lammps.helpers import (
     lammps_calc_md,
     lammps_run,
@@ -27,12 +28,12 @@
     LAMMPS_RUN,
     LAMMPS_MINIMIZE_VOLUME,
 )
-from atomistics.calculators.lammps.output import (
-    LammpsOutputMolecularDynamics,
-    LammpsOutputStatic,
-)
 from atomistics.calculators.wrapper import as_task_dict_evaluator
-from atomistics.shared.thermal_expansion import OutputThermalExpansionProperties
+from atomistics.shared.output import (
+    OutputStatic,
+    OutputMolecularDynamics,
+    OutputThermalExpansion,
+)
 
 if TYPE_CHECKING:
     from ase import Atoms
@@ -120,7 +121,7 @@ def calc_static_with_lammps(
     structure,
     potential_dataframe,
     lmp=None,
-    output=LammpsOutputStatic.fields(),
+    output_keys=OutputStatic.keys(),
     **kwargs,
 ):
     template_str = LAMMPS_THERMO_STYLE + "\n" + LAMMPS_THERMO + "\n" + LAMMPS_RUN
@@ -134,7 +135,7 @@ def calc_static_with_lammps(
         lmp=lmp,
         **kwargs,
     )
-    result_dict = LammpsOutputStatic.get(lmp_instance, *output)
+    result_dict = LammpsOutput(lmp=lmp_instance).get_output(output_keys=output_keys)
     lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
     return result_dict
 
@@ -151,7 +152,7 @@ def calc_molecular_dynamics_nvt_with_lammps(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
     **kwargs,
 ):
     init_str = (
@@ -187,7 +188,7 @@ 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 +209,7 @@ def calc_molecular_dynamics_npt_with_lammps(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
     **kwargs,
 ):
     init_str = (
@@ -247,7 +248,7 @@ 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 +267,7 @@ def calc_molecular_dynamics_nph_with_lammps(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
     **kwargs,
 ):
     init_str = (
@@ -302,7 +303,7 @@ 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 +321,7 @@ def calc_molecular_dynamics_langevin_with_lammps(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
     **kwargs,
 ):
     init_str = (
@@ -358,7 +359,7 @@ 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 +381,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammps(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=OutputThermalExpansionProperties.fields(),
+    output_keys=OutputThermalExpansion.keys(),
     **kwargs,
 ):
     init_str = (
@@ -411,7 +412,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammps(
         seed=seed,
         dist=dist,
         lmp=lmp,
-        output=output,
+        output_keys=output_keys,
         **kwargs,
     )
 
@@ -457,7 +458,7 @@ 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

@@ -5,11 +5,12 @@
 from pylammpsmpi import LammpsASELibrary
 
 from atomistics.calculators.lammps.potential import validate_potential_dataframe
-from atomistics.calculators.lammps.output import LammpsOutputMolecularDynamics
-from atomistics.shared.thermal_expansion import (
-    OutputThermalExpansionProperties,
-    ThermalExpansionProperties,
+from atomistics.calculators.lammps.output import LammpsOutput
+from atomistics.shared.output import (
+    OutputMolecularDynamics,
+    OutputThermalExpansion,
 )
+from atomistics.shared.thermal_expansion import get_thermal_expansion_output
 from atomistics.shared.tqdm_iterator import get_tqdm_iterator
 
 
@@ -46,30 +47,30 @@ def lammps_calc_md_step(
     lmp_instance,
     run_str,
     run,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
 ):
     run_str_rendered = Template(run_str).render(run=run)
     lmp_instance.interactive_lib_command(run_str_rendered)
-    return LammpsOutputMolecularDynamics.get(lmp_instance, *output)
+    return LammpsOutput(lmp=lmp_instance).get_output(output_keys=output_keys)
 
 
 def lammps_calc_md(
     lmp_instance,
     run_str,
     run,
     thermo,
-    output=LammpsOutputMolecularDynamics.fields(),
+    output_keys=OutputMolecularDynamics.keys(),
 ):
     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 +89,7 @@ def lammps_thermal_expansion_loop(
     seed=4928459,
     dist="gaussian",
     lmp=None,
-    output=OutputThermalExpansionProperties.fields(),
+    output_keys=OutputThermalExpansion.keys(),
     **kwargs,
 ):
     lmp_instance = lammps_run(
@@ -121,11 +122,10 @@ def lammps_thermal_expansion_loop(
         volume_md_lst.append(lmp_instance.interactive_volume_getter())
         temperature_md_lst.append(lmp_instance.interactive_temperatures_getter())
     lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)
-    return OutputThermalExpansionProperties.get(
-        ThermalExpansionProperties(
-            temperatures_lst=temperature_md_lst, volumes_lst=volume_md_lst
-        ),
-        *output,
+    return get_thermal_expansion_output(
+        temperatures_lst=temperature_md_lst,
+        volumes_lst=volume_md_lst,
+        output_keys=output_keys,
     )