def test_position_output():
"""
Test that the hybrid returns the correct positions for the new and old systems after construction
"""
from perses.annihilation.relative import HybridTopologyFactory
import numpy as np
#generate topology proposal
topology_proposal, old_positions, new_positions = utils.generate_solvated_hybrid_test_topology(
)
factory = HybridTopologyFactory(topology_proposal, old_positions,
new_positions)
old_positions_factory = factory.old_positions(factory.hybrid_positions)
new_positions_factory = factory.new_positions(factory.hybrid_positions)
assert np.all(
np.isclose(old_positions.in_units_of(unit.nanometers),
old_positions_factory.in_units_of(unit.nanometers)))
assert np.all(
np.isclose(new_positions.in_units_of(unit.nanometers),
new_positions_factory.in_units_of(unit.nanometers)))
def compute_nonalchemical_perturbation(
alchemical_thermodynamic_state: states.ThermodynamicState,
growth_thermodynamic_state: states.ThermodynamicState,
hybrid_sampler_state: states.SamplerState,
hybrid_factory: HybridTopologyFactory,
nonalchemical_thermodynamic_state: states.ThermodynamicState,
lambda_state: int) -> tuple:
"""
Compute the perturbation of transforming the given hybrid equilibrium result into the system for the given nonalchemical_thermodynamic_state
Parameters
----------
alchemical_thermodynamic_state: states.ThermodynamicState
alchemical thermostate
growth_thermodynamic_state : states.ThermodynamicState
hybrid_sampler_state: states.SamplerState
sampler state for the alchemical thermodynamic_state
hybrid_factory : HybridTopologyFactory
Hybrid factory necessary for getting the positions of the nonalchemical system
nonalchemical_thermodynamic_state : states.ThermodynamicState
ThermodynamicState of the nonalchemical system
lambda_state : int
Whether this is lambda 0 or 1
Returns
-------
valence_energy: float
reduced potential energy of the valence contribution of the alternate endstate
nonalchemical_reduced_potential : float
reduced potential energy of the nonalchemical endstate
hybrid_reduced_potential: float
reduced potential energy of the alchemical endstate
"""
#get the objects we need to begin
hybrid_reduced_potential = compute_reduced_potential(
alchemical_thermodynamic_state, hybrid_sampler_state)
hybrid_positions = hybrid_sampler_state.positions
#get the positions for the nonalchemical system
if lambda_state == 0:
nonalchemical_positions = hybrid_factory.old_positions(
hybrid_positions)
nonalchemical_alternate_positions = hybrid_factory.new_positions(
hybrid_positions)
elif lambda_state == 1:
nonalchemical_positions = hybrid_factory.new_positions(
hybrid_positions)
nonalchemical_alternate_positions = hybrid_factory.old_positions(
hybrid_positions)
else:
raise ValueError("lambda_state must be 0 or 1")
nonalchemical_sampler_state = states.SamplerState(
nonalchemical_positions, box_vectors=hybrid_sampler_state.box_vectors)
nonalchemical_alternate_sampler_state = states.SamplerState(
nonalchemical_alternate_positions,
box_vectors=hybrid_sampler_state.box_vectors)
nonalchemical_reduced_potential = compute_reduced_potential(
nonalchemical_thermodynamic_state, nonalchemical_sampler_state)
#now for the growth system (set at lambda 0 or 1) so we can get the valence energy
if growth_thermodynamic_state:
valence_energy = compute_reduced_potential(
growth_thermodynamic_state, nonalchemical_alternate_sampler_state)
else:
valence_energy = 0.0
#now, the corrected energy of the system (for dispersion correction) is the nonalchemical_reduced_potential + valence_energy
return (valence_energy, nonalchemical_reduced_potential,
hybrid_reduced_potential)