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atom/MolecularDynamics.h
Go to the documentation of this file.
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/**
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* \file IMP/atom/MolecularDynamics.h
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* \brief Simple molecular dynamics optimizer.
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*
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* Copyright 2007-2014 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPATOM_MOLECULAR_DYNAMICS_H
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#define IMPATOM_MOLECULAR_DYNAMICS_H
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#include <IMP/atom/atom_config.h>
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#include "
Simulator.h
"
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#include "
atom_macros.h
"
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#include <
IMP/kernel/Particle.h
>
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#include <
IMP/Optimizer.h
>
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IMPATOM_BEGIN_NAMESPACE
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//! Simple molecular dynamics optimizer.
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/** The particles to be optimized must have optimizable x,y,z attributes
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and a non-optimizable mass attribute; this optimizer assumes the score
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to be energy in kcal/mol, the xyz coordinates to be in angstroms, and
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the mass to be in AMU (g/mol).
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\note RigidBody particles are not handled properly.
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kernel::Particles without optimized x,y,z and nonoptimized mass are skipped.
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\see VelocityScalingOptimizerState
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\see LangevinThermostatOptimizerState
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\see BerendsenThermostatOptimizerState
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\see RemoveRigidMotionOptimizerState
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*/
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class
IMPATOMEXPORT
MolecularDynamics
:
public
Simulator
{
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public
:
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/** Score based on the provided model */
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MolecularDynamics
(
kernel::Model
*m);
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//! Return the current kinetic energy of the system, in kcal/mol
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virtual
Float
get_kinetic_energy()
const
;
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//! Return the current kinetic temperature of the system
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/** \param[in] ekinetic kinetic energy, e.g. from get_kinetic_energy()
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*/
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Float
get_kinetic_temperature(
Float
ekinetic)
const
;
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//! Set maximum velocity in A/fs
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/** At each dynamics time step, the absolute value of each velocity
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component is capped at this value. This prevents spurious strong forces
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(occasionally encountered with frustrated conformations) from causing
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large oscillations in the system.
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By default, velocities are not capped.
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\note The actual velocities that are capped are the half-step velocities
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in the velocity Verlet algorithm.
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*/
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void
set_velocity_cap
(
Float
velocity_cap) { velocity_cap_ = velocity_cap; }
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//! Assign velocities representative of the given temperature
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virtual
void
assign_velocities(
Float
temperature);
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virtual
void
setup
(
const
kernel::ParticleIndexes
&ps)
IMP_OVERRIDE
;
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virtual
double
do_step
(
const
kernel::ParticleIndexes
&sc,
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double
dt)
IMP_OVERRIDE
;
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virtual
bool
get_is_simulation_particle
(
kernel::ParticleIndex
p)
const
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IMP_OVERRIDE
;
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IMP_OBJECT_METHODS
(
MolecularDynamics
);
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protected
:
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void
initialize();
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virtual
void
setup_degrees_of_freedom(
const
kernel::ParticleIndexes
&ps);
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//! First part of velocity Verlet (update coordinates and half-step velocity)
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virtual
void
propagate_coordinates(
const
kernel::ParticleIndexes
&ps,
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double
step_size);
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//! Second part of velocity Verlet (update velocity)
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virtual
void
propagate_velocities(
const
kernel::ParticleIndexes
&ps,
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double
step_size);
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//! Cap a velocity component to the maximum value.
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inline
void
cap_velocity_component
(
Float
&vel) {
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if
(vel >= 0.0) {
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vel = std::min(vel, velocity_cap_);
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}
else
{
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vel = std::max(vel, -velocity_cap_);
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}
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}
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//! Keys of the xyz velocities
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FloatKey
vs_[3];
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//! Number of degrees of freedom in the system
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int
degrees_of_freedom_
;
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//! Maximum absolute value of a single velocity component
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Float
velocity_cap_
;
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};
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IMPATOM_END_NAMESPACE
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#endif
/* IMPATOM_MOLECULAR_DYNAMICS_H */
IMP::atom::Simulator
The base class for simulators.
Definition:
Simulator.h:34
IMP::kernel::Key< 0, true >
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
IMP::base::Vector< ParticleIndex >
Optimizer.h
Import IMP/kernel/Optimizer.h in the namespace.
IMP::atom::MolecularDynamics::set_velocity_cap
void set_velocity_cap(Float velocity_cap)
Set maximum velocity in A/fs.
Definition:
atom/MolecularDynamics.h:57
IMP::atom::MolecularDynamics
Simple molecular dynamics optimizer.
Definition:
atom/MolecularDynamics.h:34
IMP::atom::MolecularDynamics::degrees_of_freedom_
int degrees_of_freedom_
Number of degrees of freedom in the system.
Definition:
atom/MolecularDynamics.h:95
Simulator.h
Simple molecular dynamics optimizer.
IMP::base::Index< ParticleIndexTag >
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions in in int...
IMP::atom::Simulator::get_is_simulation_particle
virtual bool get_is_simulation_particle(kernel::ParticleIndex p) const =0
Return true if the passed particle is appropriate for the simulation.
IMP::atom::MolecularDynamics::cap_velocity_component
void cap_velocity_component(Float &vel)
Cap a velocity component to the maximum value.
Definition:
atom/MolecularDynamics.h:83
atom_macros.h
Various important macros for implementing decorators.
IMP::atom::MolecularDynamics::velocity_cap_
Float velocity_cap_
Maximum absolute value of a single velocity component.
Definition:
atom/MolecularDynamics.h:98
IMP::atom::Simulator::setup
virtual void setup(const kernel::ParticleIndexes &)
Definition:
Simulator.h:157
IMP::Float
double Float
Basic floating-point value (could be float, double...)
Definition:
types.h:20
IMP::atom::Simulator::do_step
virtual double do_step(const kernel::ParticleIndexes &sc, double dt)=0
Perform a single time step.
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:75
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
kernel/Model.h:73