IMLCV.implementations.energy

IMLCV.implementations.energy#

Classes#

OpenMmEnergy

AseEnergy

Conversion to ASE energy

Cp2kEnergy

Conversion to ASE energy

MACEASE

Conversion to ASE energy

Module Contents#

class IMLCV.implementations.energy.OpenMmEnergy#

Bases: IMLCV.base.bias.Energy

pdb: pathlib.Path#
forcefield_name: str = 'amber14-all.xml'#
_simul: openmm.app.Simulation | None = None#
static to_jax_vec(thing)#
get_info()#
_compute_coor(sp: IMLCV.base.CV.SystemParams, nl: IMLCV.base.CV.NeighbourList, gpos=False, vir=False) → IMLCV.base.bias.EnergyResult#
_get_simul()#
__getstate__()#
__setstate__(state)#
class IMLCV.implementations.energy.AseEnergy(atoms: ase.Atoms, calculator=None)#

Bases: IMLCV.base.bias.Energy

Conversion to ASE energy

atoms#
property cell#
property coordinates#
_compute_coor(sp, nl, gpos=False, vir=False) → IMLCV.base.bias.EnergyResult#

use unit conventions of ASE

abstract _calculator()#
_handle_exception(e=None)#
__getstate__()#
__setstate__(state)#
class IMLCV.implementations.energy.Cp2kEnergy(atoms, input_file, input_kwargs: dict, cp2k_path: pathlib.Path | None = None, **kwargs)#

Bases: AseEnergy

Conversion to ASE energy

default_parameters#
atoms#
cp2k_inp#
input_kwargs#
kwargs#
rp = None#
static _relative(target: pathlib.Path, origin: pathlib.Path)#

return path of target relative to origin

_calculator()#
_handle_exception(e=None)#
__getstate__()#
__setstate__(state)#
class IMLCV.implementations.energy.MACEASE(atoms: ase.Atoms, calculator=None)#

Bases: AseEnergy

Conversion to ASE energy

_calculator()#
__getstate__()#
__setstate__(state)#
Contents