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BerendsenThermostatOptimizerState.h
Go to the documentation of this file.
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/**
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* \file IMP/atom/BerendsenThermostatOptimizerState.h
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* \brief Maintains temperature during molecular dynamics using a
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* Berendsen thermostat.
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*
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* Copyright 2007-2013 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPATOM_BERENDSEN_THERMOSTAT_OPTIMIZER_STATE_H
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#define IMPATOM_BERENDSEN_THERMOSTAT_OPTIMIZER_STATE_H
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#include <IMP/atom/atom_config.h>
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#include <
IMP/Particle.h
>
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#include <
IMP/base_types.h
>
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#include <
IMP/OptimizerState.h
>
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#include <
IMP/optimizer_state_macros.h
>
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IMPATOM_BEGIN_NAMESPACE
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//! Maintains temperature during molecular dynamics.
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/** The thermostat scales velocities using the algorithm described
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in H. J. C. Berendsen, J. P. M. Postma,
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W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics
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with coupling to an external bath", Journal of Chemical Physics 81
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pp. 3684-3690 (1984).
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At each update, velocities are rescaled by \f[
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\lambda = \left[1 + \frac{\Delta t}{\tau_T}
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\left( \frac{T}{T_k} -1\right)\right]^{1/2}
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\f]
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where \f$\Delta t\f$ is the molecular dynamics timestep, \f$\tau_T\f$
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is the coupling constant (in fs) of the thermostat, \f$T\f$ is the
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thermostat temperature, and \f$T_k\f$ is the instantaneous (kinetic)
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temperature of the dynamics. (This is equation 11 from the reference above.)
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*/
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class
IMPATOMEXPORT
BerendsenThermostatOptimizerState
:
public
OptimizerState
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{
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public
:
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BerendsenThermostatOptimizerState
(
const
Particles &pis,
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double
temperature,
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double
tau);
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//! Set the particles to use.
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void
set_particles
(
const
Particles &pis) {
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pis_=pis;
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}
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double
get_temperature() {
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return
temperature_;
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}
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double
get_tau() {
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return
tau_;
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}
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void
set_temperature(
double
temperature) {
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temperature_ = temperature;
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}
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void
set_tau(
double
tau) {
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tau_ = tau;
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}
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//! Rescale the velocities now
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void
rescale_velocities()
const
;
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IMP_OPTIMIZER_STATE
(BerendsenThermostatOptimizerState);
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private
:
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Particles pis_;
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double
temperature_;
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double
tau_;
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//! Keys of the xyz velocities
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FloatKey
vs_[3];
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};
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IMP_OBJECTS
(BerendsenThermostatOptimizerState,
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BerendsenThermostatOptimizerStates
);
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IMPATOM_END_NAMESPACE
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#endif
/* IMPATOM_BERENDSEN_THERMOSTAT_OPTIMIZER_STATE_H */