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LAMMPS: Add option to couple xyz for npt #609

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LAMMPS: Add option to couple xyz for npt #609

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16 changes: 13 additions & 3 deletions src/atomistics/calculators/lammps/libcalculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,10 +233,15 @@ def calc_molecular_dynamics_npt_with_lammpslib(
seed: int = 4928459,
dist: str = "gaussian",
disable_initial_velocity: bool = False,
couple_xyz: bool = False,
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
) -> dict:
if couple_xyz:
LAMMPS_ENSEMBLE_NPT_XYZ = LAMMPS_ENSEMBLE_NPT + " couple xyz"
else:
LAMMPS_ENSEMBLE_NPT_XYZ = LAMMPS_ENSEMBLE_NPT
if not disable_initial_velocity:
init_str = (
LAMMPS_THERMO_STYLE
Expand All @@ -247,7 +252,7 @@ def calc_molecular_dynamics_npt_with_lammpslib(
+ "\n"
+ LAMMPS_VELOCITY
+ "\n"
+ LAMMPS_ENSEMBLE_NPT
+ LAMMPS_ENSEMBLE_NPT_XYZ
)
input_template = Template(init_str).render(
thermo=thermo,
Expand All @@ -270,7 +275,7 @@ def calc_molecular_dynamics_npt_with_lammpslib(
+ "\n"
+ LAMMPS_THERMO
+ "\n"
+ LAMMPS_ENSEMBLE_NPT
+ LAMMPS_ENSEMBLE_NPT_XYZ
)
input_template = Template(init_str).render(
thermo=thermo,
Expand Down Expand Up @@ -473,6 +478,7 @@ def calc_molecular_dynamics_thermal_expansion_with_lammpslib(
Pdamp: float = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
couple_xyz: bool = False,
lmp=None,
output_keys=OutputThermalExpansion.keys(),
**kwargs,
Expand All @@ -487,7 +493,11 @@ def calc_molecular_dynamics_thermal_expansion_with_lammpslib(
+ LAMMPS_VELOCITY
+ "\n"
)
run_str = LAMMPS_ENSEMBLE_NPT + "\n" + LAMMPS_RUN
if couple_xyz:
LAMMPS_ENSEMBLE_NPT_XYZ = LAMMPS_ENSEMBLE_NPT + " couple xyz"
else:
LAMMPS_ENSEMBLE_NPT_XYZ = LAMMPS_ENSEMBLE_NPT
run_str = LAMMPS_ENSEMBLE_NPT_XYZ + "\n" + LAMMPS_RUN
temperature_lst = np.arange(Tstart, Tstop + Tstep, Tstep).tolist()
return lammps_thermal_expansion_loop(
structure=structure,
Expand Down
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