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LAMMPS: Allow user to change the velocity rescaling - default remains 2 #608

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LAMMPS: Allow user to change the velocity rescaling - default remains 2 #608

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2 changes: 1 addition & 1 deletion src/atomistics/calculators/lammps/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
LAMMPS_TIMESTEP = "timestep {{timestep}}"


LAMMPS_VELOCITY = "velocity all create $(2 * {{ temp }}) {{seed}} dist {{dist}}"
LAMMPS_VELOCITY = "velocity all create $({{velocity_rescale_factor}} * {{ temp }}) {{seed}} dist {{dist}}"


LAMMPS_ENSEMBLE_NPT = "fix ensemble all npt temp {{Tstart}} {{Tstop}} {{Tdamp}} iso {{Pstart}} {{Pstop}} {{Pdamp}}"
Expand Down
2 changes: 2 additions & 0 deletions src/atomistics/calculators/lammps/helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,7 @@ def lammps_thermal_expansion_loop(
Pdamp: float = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
velocity_rescale_factor: float = 2.0,
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⚠️ Potential issue | 🟡 Minor

🧩 Analysis chain

🏁 Script executed:

# First, find the function at line 105 and surrounding context
sed -n '90,120p' src/atomistics/calculators/lammps/helpers.py

Repository: pyiron/atomistics

Length of output: 945

🏁 Script executed:

# Find the corresponding function in libcalculator.py
rg -n "velocity_rescale_factor" src/ --type py -B 2 -A 2

Repository: pyiron/atomistics

Length of output: 6183

🏁 Script executed:

# Search for how velocity_rescale_factor is used in the template rendering
rg -n "velocity_rescale_factor" src/atomistics/calculators/lammps/ --type py

Repository: pyiron/atomistics

Length of output: 1705

Type inconsistency with libcalculator.py functions.

lammps_thermal_expansion_loop uses velocity_rescale_factor: float = 2.0, while all MD functions in libcalculator.py use Optional[float] = 2.0 with conditional logic to handle None values. The helpers.py function lacks this guard, so passing None would render "None * temp" in the LAMMPS velocity command, causing an error.

Align the type to Optional[float] and add the same conditional logic used in libcalculator.py (skip velocity initialization when None), or document that this function always requires a numeric value.

🤖 Prompt for AI Agents 
In @src/atomistics/calculators/lammps/helpers.py at line 105, The parameter
velocity_rescale_factor in lammps_thermal_expansion_loop is typed as float and
will produce an invalid LAMMPS command if None is passed; change its type to
Optional[float] and add the same conditional guard used in libcalculator.py:
only emit/compose the LAMMPS velocity initialization/rescale command when
velocity_rescale_factor is not None, otherwise skip velocity initialization
entirely to avoid generating "None * temp" in the command.

lmp=None,
output_keys=OutputThermalExpansion.keys(),
**kwargs,
Expand All @@ -115,6 +116,7 @@ def lammps_thermal_expansion_loop(
timestep=timestep,
seed=seed,
dist=dist,
velocity_rescale_factor=velocity_rescale_factor,
),
lmp=lmp,
**kwargs,
Expand Down
22 changes: 13 additions & 9 deletions src/atomistics/calculators/lammps/libcalculator.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from __future__ import annotations

from typing import TYPE_CHECKING
from typing import TYPE_CHECKING, Optional

import numpy as np
import pandas
Expand Down Expand Up @@ -154,12 +154,12 @@ def calc_molecular_dynamics_nvt_with_lammpslib(
timestep: float = 0.001,
seed: int = 4928459,
dist: str = "gaussian",
disable_initial_velocity: bool = False,
velocity_rescale_factor: Optional[float] = 2.0,
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
) -> dict:
if not disable_initial_velocity:
if velocity_rescale_factor is not None:
init_str = (
LAMMPS_THERMO_STYLE
+ "\n"
Expand All @@ -180,6 +180,7 @@ def calc_molecular_dynamics_nvt_with_lammpslib(
timestep=timestep,
seed=seed,
dist=dist,
velocity_rescale_factor=velocity_rescale_factor,
)
else:
init_str = (
Expand Down Expand Up @@ -232,12 +233,12 @@ def calc_molecular_dynamics_npt_with_lammpslib(
Pdamp: float = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
disable_initial_velocity: bool = False,
velocity_rescale_factor: Optional[float] = 2.0,
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
) -> dict:
if not disable_initial_velocity:
if velocity_rescale_factor is not None:
init_str = (
LAMMPS_THERMO_STYLE
+ "\n"
Expand All @@ -261,6 +262,7 @@ def calc_molecular_dynamics_npt_with_lammpslib(
timestep=timestep,
seed=seed,
dist=dist,
velocity_rescale_factor=velocity_rescale_factor,
)
else:
init_str = (
Expand Down Expand Up @@ -314,12 +316,12 @@ def calc_molecular_dynamics_nph_with_lammpslib(
Pdamp: float = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
disable_initial_velocity: bool = False,
velocity_rescale_factor: Optional[float] = 2.0,
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
) -> dict:
if not disable_initial_velocity:
if velocity_rescale_factor is not None:
init_str = (
LAMMPS_THERMO_STYLE
+ "\n"
Expand All @@ -340,6 +342,7 @@ def calc_molecular_dynamics_nph_with_lammpslib(
timestep=timestep,
seed=seed,
dist=dist,
velocity_rescale_factor=velocity_rescale_factor,
)
else:
init_str = (
Expand Down Expand Up @@ -389,12 +392,12 @@ def calc_molecular_dynamics_langevin_with_lammpslib(
Tdamp: float = 0.1,
seed: int = 4928459,
dist: str = "gaussian",
disable_initial_velocity: bool = False,
velocity_rescale_factor: Optional[float] = 2.0,
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
):
if not disable_initial_velocity:
if velocity_rescale_factor is not None:
init_str = (
LAMMPS_THERMO_STYLE
+ "\n"
Expand All @@ -417,6 +420,7 @@ def calc_molecular_dynamics_langevin_with_lammpslib(
timestep=timestep,
seed=seed,
dist=dist,
velocity_rescale_factor=velocity_rescale_factor,
)
else:
init_str = (
Expand Down
4 changes: 2 additions & 2 deletions tests/test_lammpslib_md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def test_lammps_md_nvt_all_no_velocity(self):
seed=4928459,
dist="gaussian",
lmp=None,
disable_initial_velocity=True,
velocity_rescale_factor=None,
)
self.assertEqual(result_dict["positions"].shape, (10, 32, 3))
self.assertEqual(result_dict["velocities"].shape, (10, 32, 3))
Expand Down Expand Up @@ -163,7 +163,7 @@ def test_lammps_md_npt_all_no_velocity(self):
seed=4928459,
dist="gaussian",
lmp=None,
disable_initial_velocity=True,
velocity_rescale_factor=None,
)
self.assertEqual(result_dict["positions"].shape, (10, 32, 3))
self.assertEqual(result_dict["velocities"].shape, (10, 32, 3))
Expand Down
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