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Add explicit compressibility arg (instead of calculating it) to wrapped MD #319

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Jun 14, 2024
Merged

Add explicit compressibility arg (instead of calculating it) to wrapped MD #319

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11 changes: 6 additions & 5 deletions wfl/generate/md/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@


def _sample_autopara_wrappable(atoms, calculator, steps, dt, integrator="NVTBerendsen", temperature=None, temperature_tau=None,
pressure=None, pressure_tau=None, compressibility_fd_displ=0.01,
pressure=None, pressure_tau=None, compressibility_au=None, compressibility_fd_displ=0.01,
traj_step_interval=1, skip_failures=True, results_prefix='last_op__md_', verbose=False, update_config_type="append",
traj_select_during_func=lambda at: True, traj_select_after_func=None, abort_check=None, rng=None,
_autopara_per_item_info=None):
Expand Down Expand Up @@ -53,6 +53,8 @@ def _sample_autopara_wrappable(atoms, calculator, steps, dt, integrator="NVTBere
pressure_tau: float, default None
time scale for Berendsen constant P volume rescaling (fs)
ignored if pressure is None, defaults to 3*temperature_tau
compressibility_au: float, default None
compressibility, if available, for NPTBerendsen
compressibility_fd_displ: float, default 0.01
finite difference in strain to use when computing compressibility for NPTBerendsen
traj_step_interval: int, default 1
Expand Down Expand Up @@ -128,8 +130,7 @@ def _sample_autopara_wrappable(atoms, calculator, steps, dt, integrator="NVTBere
rng = _autopara_per_item_info[at_i].get("rng")

at.calc = calculator
compressibility = None
if pressure is not None:
if pressure is not None and compressibility_au is None:
pressure = sample_pressure(pressure, at, rng=rng)
at.info['MD_pressure_GPa'] = pressure
# convert to ASE internal units
Expand All @@ -143,7 +144,7 @@ def _sample_autopara_wrappable(atoms, calculator, steps, dt, integrator="NVTBere
Em = at.get_potential_energy()
at.set_cell(c0, scale_atoms=True)
d2E_dF2 = (Ep + Em - 2.0 * E0) / (compressibility_fd_displ ** 2)
compressibility = at.get_volume() / d2E_dF2
compressibility_au = at.get_volume() / d2E_dF2

if temperature is not None:
# set initial temperature
Expand All @@ -170,7 +171,7 @@ def _sample_autopara_wrappable(atoms, calculator, steps, dt, integrator="NVTBere
if pressure is not None:
md_constructor = NPTBerendsen
stage_kwargs['pressure_au'] = pressure
stage_kwargs['compressibility_au'] = compressibility
stage_kwargs['compressibility_au'] = compressibility_au
stage_kwargs['taut'] = temperature_tau * fs
stage_kwargs['taup'] = pressure_tau * fs if pressure_tau is not None else temperature_tau * fs * 3
else:
Expand Down
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