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Introduce get_thermal_expansion_output() function #183

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merged 3 commits into from
Jan 8, 2024
Merged

Introduce get_thermal_expansion_output() function #183

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68e9f3d
Introduce get_thermal_expansion_output() function
jan-janssen Jan 8, 2024
c662ce4
Format black
pyiron-runner Jan 8, 2024
6203b0f
Merge remote-tracking branch 'origin/main' into get_thermal_expansion…
jan-janssen Jan 8, 2024
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17 changes: 7 additions & 10 deletions atomistics/calculators/ase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,8 @@
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.thermal_expansion import get_thermal_expansion_output
from atomistics.shared.output import OutputThermalExpansion
from atomistics.shared.tqdm_iterator import get_tqdm_iterator

if TYPE_CHECKING:
Expand Down Expand Up @@ -232,7 +230,7 @@ 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_keys=OutputThermalExpansionProperties.keys(),
output_keys=OutputThermalExpansion.keys(),
):
structure_current = structure.copy()
temperature_lst = np.arange(
Expand All @@ -254,9 +252,8 @@ 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_keys,
return get_thermal_expansion_output(
temperatures_lst=temperature_md_lst,
volumes_lst=volume_md_lst,
output_keys=output_keys,
)
4 changes: 2 additions & 2 deletions atomistics/calculators/lammps/calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
LammpsOutputStatic,
)
from atomistics.calculators.wrapper import as_task_dict_evaluator
from atomistics.shared.thermal_expansion import OutputThermalExpansionProperties
from atomistics.shared.output import OutputThermalExpansion

if TYPE_CHECKING:
from ase import Atoms
Expand Down Expand Up @@ -380,7 +380,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammps(
seed=4928459,
dist="gaussian",
lmp=None,
output_keys=OutputThermalExpansionProperties.keys(),
output_keys=OutputThermalExpansion.keys(),
**kwargs,
):
init_str = (
Expand Down
17 changes: 7 additions & 10 deletions atomistics/calculators/lammps/helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,8 @@

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.shared.thermal_expansion import get_thermal_expansion_output
from atomistics.shared.output import OutputThermalExpansion
from atomistics.shared.tqdm_iterator import get_tqdm_iterator


Expand Down Expand Up @@ -88,7 +86,7 @@ def lammps_thermal_expansion_loop(
seed=4928459,
dist="gaussian",
lmp=None,
output_keys=OutputThermalExpansionProperties.keys(),
output_keys=OutputThermalExpansion.keys(),
**kwargs,
):
lmp_instance = lammps_run(
Expand Down Expand Up @@ -121,11 +119,10 @@ 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_keys,
return get_thermal_expansion_output(
temperatures_lst=temperature_md_lst,
volumes_lst=volume_md_lst,
output_keys=output_keys,
)


Expand Down
15 changes: 12 additions & 3 deletions atomistics/shared/thermal_expansion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,15 @@ def temperatures(self):
return self._temperatures_lst


OutputThermalExpansionProperties = OutputThermalExpansion(
**{k: getattr(ThermalExpansionProperties, k) for k in OutputThermalExpansion.keys()}
)
def get_thermal_expansion_output(temperatures_lst, volumes_lst, output_keys):
return OutputThermalExpansion(
**{
k: getattr(ThermalExpansionProperties, k)
for k in OutputThermalExpansion.keys()
}
).get(
ThermalExpansionProperties(
temperatures_lst=temperatures_lst, volumes_lst=volumes_lst
),
*output_keys,
)
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