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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
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include
IMP
atom
version 2.20.2
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 2007-2022 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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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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public
:
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BerendsenThermostatOptimizerState
(
const
Particles
&pis,
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double
temperature,
double
tau);
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//! Set the particles to use.
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void
set_particles
(
const
Particles
&pis) { pis_ = pis; }
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double
get_temperature() {
return
temperature_; }
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double
get_tau() {
return
tau_; }
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void
set_temperature(
double
temperature) { temperature_ = temperature; }
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void
set_tau(
double
tau) { tau_ = tau; }
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//! Rescale the velocities now
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void
rescale_velocities()
const
;
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IMP_OBJECT_METHODS
(
BerendsenThermostatOptimizerState
);
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protected
:
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virtual
void
do_update
(
unsigned
int
)
override
;
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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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};
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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 */
base_types.h
Basic types used by IMP.
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
IMP::OptimizerState::do_update
virtual void do_update(unsigned int)
Definition:
OptimizerState.h:133
IMP::Vector< Pointer< Particle > >
IMP::atom::BerendsenThermostatOptimizerState::set_particles
void set_particles(const Particles &pis)
Set the particles to use.
Definition:
BerendsenThermostatOptimizerState.h:42
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
IMP_OBJECTS
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
Definition:
object_macros.h:44
IMP::OptimizerState
Shared optimizer state that is invoked upon commitment of new coordinates.
Definition:
OptimizerState.h:45
OptimizerState.h
Shared optimizer state.
IMP::atom::BerendsenThermostatOptimizerState
Maintains temperature during molecular dynamics.
Definition:
BerendsenThermostatOptimizerState.h:36