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Melting: Edit bisection algorithm related files #638

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0e69b42
Rename functions, add type hints
prabhath-c Mar 15, 2026
04f1415
Format black
pyiron-runner Mar 15, 2026
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74 changes: 39 additions & 35 deletions src/atomistics/calculators/lammps/melting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ def _get_repeated_structure(structure: Atoms, target_number_of_atoms: int) -> At
return basis


def _next_calc(
def _run_npt_molecular_dynamics(
structure: Atoms,
potential_dataframe: pd.DataFrame,
temperature: float,
Expand Down Expand Up @@ -167,36 +167,39 @@ def _next_calc(
return structure_md


def _next_step_funct(
number_of_atoms,
key_max,
structure_left,
structure_right,
def _run_next_bisection_iteration(
number_of_atoms: int,
key_max: str,
structure_left: Atoms,
structure_right: Atoms,
potential_dataframe: pd.DataFrame,
temperature_left,
temperature_right,
distribution_initial_half,
structure_after_minimization,
run_time_steps,
diamond_flag,
seed,
):
temperature_left: float,
temperature_right: float,
distribution_initial_half: float,
structure_after_minimization: Atoms,
run_time_steps: int,
diamond_flag: bool,
seed: int,
) -> tuple[Atoms, Atoms, float, float]:
"""
Run the next iteration of the bisection method for estimating the melting temperature.

Args:
number_of_atoms:
key_max:
structure_left:
structure_right:
temperature_left:
temperature_right:
distribution_initial_half:
structure_after_minimization:
run_time_steps:
seed:
number_of_atoms: int
key_max: str
structure_left: Atoms
structure_right: Atoms
temperature_left: float
temperature_right: float
distribution_initial_half: float
structure_after_minimization: Atoms
run_time_steps: int
diamond_flag: bool
seed: int

Returns:

tuple[Atoms, Atoms, float, float]: A tuple containing the updated left and right structures,
and the updated left and right temperatures.
"""
structure_left_dict = _analyse_structure(
structure=structure_left,
Expand All @@ -216,7 +219,7 @@ def _next_step_funct(
structure_left = structure_right.copy()
temperature_left = temperature_right
temperature_right += temperature_diff
structure_right = _next_calc(
structure_right = _run_npt_molecular_dynamics(
structure=structure_after_minimization,
temperature=temperature_right,
potential_dataframe=potential_dataframe,
Expand All @@ -230,7 +233,7 @@ def _next_step_funct(
):
temperature_diff /= 2
temperature_left += temperature_diff
structure_left = _next_calc(
structure_left = _run_npt_molecular_dynamics(
structure=structure_after_minimization,
temperature=temperature_left,
potential_dataframe=potential_dataframe,
Expand All @@ -245,7 +248,7 @@ def _next_step_funct(
temperature_right = temperature_left
temperature_left -= temperature_diff
structure_right = structure_left.copy()
structure_left = _next_calc(
structure_left = _run_npt_molecular_dynamics(
structure=structure_after_minimization,
temperature=temperature_left,
potential_dataframe=potential_dataframe,
Expand All @@ -254,18 +257,19 @@ def _next_step_funct(
)
else:
raise ValueError("We should never reach this point!")

return structure_left, structure_right, temperature_left, temperature_right


def estimate_melting_temperature_using_bisection_CNA(
structure: Atoms,
potential_dataframe: pd.DataFrame,
target_number_of_atoms: int,
strain_run_time_steps=1000,
temperature_left=0,
temperature_right=1000,
number_of_atoms=8000,
seed=None,
strain_run_time_steps: int = 1000,
temperature_left: float = 0,
temperature_right: float = 1000,
number_of_atoms: int = 8000,
seed: int = None,
):

if seed is None:
Expand Down Expand Up @@ -301,7 +305,7 @@ def estimate_melting_temperature_using_bisection_CNA(
)

structure_left = structure_after_minimization
structure_right = _next_calc(
structure_right = _run_npt_molecular_dynamics(
structure=structure_after_minimization,
temperature=temperature_right,
seed=seed,
Expand All @@ -316,7 +320,7 @@ def estimate_melting_temperature_using_bisection_CNA(
structure_right,
temperature_left,
temperature_right,
) = _next_step_funct(
) = _run_next_bisection_iteration(
number_of_atoms=number_of_atoms,
key_max=key_max,
structure_left=structure_left,
Expand Down
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