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Commit 56755055 authored by Mark Friedrichs's avatar Mark Friedrichs
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Remove Brownian dynamics files -- not ready yet

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platforms/brook/src/BrookBrownianDynamics.cpp deleted 100644 → 0
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platforms/brook/src/BrookBrownianDynamics.h deleted 100644 → 0
View file @ aff802d9
#ifndef OPENMM_BROOK_BROWNIAN_DYNAMCIS_H_
#define OPENMM_BROOK_BROWNIAN_DYNAMCIS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include <vector>
#include <set>
#include "BrookFloatStreamInternal.h"
#include "BrookShakeAlgorithm.h"
#include "BrookRandomNumberGenerator.h"
#include "BrookPlatform.h"
#include "BrookCommon.h"
namespace OpenMM {
/**
*
* Encapsulates stochastic dynamics algorithm
*
*/
class BrookBrownianDynamics : public BrookCommon {
public:
/**
* Constructor
*
*/
BrookBrownianDynamics( );
/**
* Destructor
*
*/
~BrookBrownianDynamics();
/**
* Get tau
*
* @return tau
*/
BrookOpenMMFloat getTau( void ) const;
/**
* Get friction
*
* @return friction
*/
BrookOpenMMFloat getFriction( void ) const;
/**
* Get temperature
*
* @return temperature
*/
BrookOpenMMFloat getTemperature( void ) const;
/**
* Get step size
*
* @return step size
*/
BrookOpenMMFloat getStepSize( void ) const;
/**
* Get noise amplitude
*
* @return noise amplitude
*/
BrookOpenMMFloat getNoiseAmplitude( void ) const;
/**
* Get force scale
*
* @return force scale
*/
BrookOpenMMFloat getForceScale( void ) const;
/**
* Get BrownianDynamics particle stream width
*
* @return particle stream width
*/
int getBrownianDynamicsParticleStreamWidth( void ) const;
/**
* Get BrownianDynamics particle stream height
*
* @return particle stream height
*/
int getBrownianDynamicsParticleStreamHeight( void ) const;
/**
* Get BrownianDynamics particle stream size
*
* @return particle stream size
*/
int getBrownianDynamicsParticleStreamSize( void ) const;
/**
* Update parameters
*
* @param temperature temperature
* @param friction friction
* @param step size step size
*
* @return DefaultReturnValue
*
*/
int updateParameters( double temperature, double friction, double stepSize );
/**
* Update
*
* @param positions particle positions
* @param velocities particle velocities
* @param forces particle forces
* @param brookShakeAlgorithm BrookShakeAlgorithm reference
* @param brookRandomNumberGenerator BrookRandomNumberGenerator reference
*
* @return DefaultReturnValue
*
*/
int update( Stream& positions, Stream& velocities,
const Stream& forces, BrookShakeAlgorithm& brookShakeAlgorithm,
BrookRandomNumberGenerator& brookRandomNumberGenerator );
/**
* Get array of BrownianDynamics streams
*
* @return array ofstreams
*
*/
BrookFloatStreamInternal** getStreams( void );
/*
* Setup of BrownianDynamics parameters
*
* @param masses particle masses
* @param platform Brook platform
*
* @return ErrorReturnValue value if error, else DefaultReturnValue
*
* */
int setup( const std::vector<double>& masses, const Platform& platform );
/*
* Get contents of object
*
* @param level of dump
*
* @return string containing contents
*
* */
std::string getContentsString( int level = 0 ) const;
/**
* Get X-prime stream
*
* @return X-prime stream
*
*/
BrookFloatStreamInternal* getXPrimeStream( void ) const;
/**
* Get inverse sqrt masses
*
* @return inverse sqrt masses stream
*
*/
BrookFloatStreamInternal* getInverseMassStream( void ) const;
private:
// streams indices
enum BrookBrownianDynamicsStreams {
VPrimeStream,
XPrimeStream,
InverseMassStream,
LastStreamIndex
};
// randomNumberSeed
unsigned int _randomNumberSeed;
BrookOpenMMFloat _tau;
BrookOpenMMFloat _temperature;
BrookOpenMMFloat _stepSize;
BrookOpenMMFloat _forceScale;
BrookOpenMMFloat _noiseAmplitude;
// Particle stream dimensions
int _bdParticleStreamWidth;
int _bdParticleStreamHeight;
int _bdParticleStreamSize;
/*
* Update streams
*
* @return DefaultReturn
*
*/
int _updateStreams( void );
// inverse sqrt masses
BrookOpenMMFloat* _inverseSqrtMasses;
// internal streams
BrookFloatStreamInternal* _streams[LastStreamIndex];
/**
* Set tau
*
* @param tau new tau value
*
* @return DefaultReturn
*
*/
int _setTau( BrookOpenMMFloat tau );
/**
* Set friction = 1/tau
*
* @param friction new friction value
*
* @return DefaultReturn
*
*/
int _setFriction( BrookOpenMMFloat friction );
/**
* Set temperature
*
* @parameter temperature
*
* @return DefaultReturn
*
*/
int _setTemperature( BrookOpenMMFloat temperature );
/**
* Set stepSize
*
* @param stepSize
*
* @return DefaultReturn
*
*/
int _setStepSize( BrookOpenMMFloat stepSize );
/**
* Set force scale
*
* @return DefaultReturn
*
*/
int _setForceScale( void );
/**
* Set noise amplitude
*
* @return DefaultReturn
*
*/
int _setNoiseAmplitude( void );
/*
* Setup of stream dimensions
*
* @param particleStreamSize particle stream size
* @param particleStreamWidth particle stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* */
int _initializeStreamSizes( int particleStreamSize, int particleStreamWidth );
/**
* Initialize stream dimensions
*
* @param numberOfParticles number of particles
* @param platform platform
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
*/
int _initializeStreamSizes( int numberOfParticles, const Platform& platform );
/**
* Initialize stream dimensions and streams
*
* @param platform platform
*
* @return nonzero value if error
*
*/
int _initializeStreams( const Platform& platform );
/**
* Set masses
*
* @param masses particleic masses
*
*/
int _setInverseSqrtMasses( const std::vector<double>& masses );
};
} // namespace OpenMM
#endif /* OPENMM_BROOK_BROWNIAN_DYNAMCIS_H_ */
platforms/brook/src/BrookIntegrateBrownianStepKernel.cpp deleted 100644 → 0
View file @ aff802d9
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "BrookIntegrateBrownianStepKernel.h"
#include "BrookStreamInternal.h"
using namespace OpenMM;
using namespace std;
/**
* BrookIntegrateBrownianStepKernel constructor
*
* @param name name of the stream to create
* @param platform platform
*
*/
BrookIntegrateBrownianStepKernel::BrookIntegrateBrownianStepKernel( std::string name, const Platform& platform ) :
IntegrateBrownianStepKernel( name, platform ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "BrookIntegrateBrownianStepKernel::BrookIntegrateBrownianStepKernel";
// ---------------------------------------------------------------------------------------
_brookBrownianDynamics = NULL;
_brookShakeAlgorithm = NULL;
_brookRandomNumberGenerator = NULL;
}
/**
* BrookIntegrateVerletStepKernel destructor
*
*/
BrookIntegrateBrownianStepKernel::~BrookIntegrateBrownianStepKernel( ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "BrookIntegrateBrownianStepKernel::~BrookIntegrateBrownianStepKernel";
// ---------------------------------------------------------------------------------------
delete _brookBrownianDynamics;
delete _brookShakeAlgorithm;
delete _brookRandomNumberGenerator;
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses the mass of each particle
* @param constraintIndices each element contains the indices of two particles whose distance should be constrained
* @param constraintLengths the required distance between each pair of constrained particles
*
*/
void BrookIntegrateBrownianStepKernel::initialize( const vector<double>& masses,
const vector<vector<int> >& constraintIndices,
const vector<double>& constraintLengths ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "BrookIntegrateBrownianStepKernel::initialize";
// ---------------------------------------------------------------------------------------
_brookBrownianDynamics = new BrookBrownianDynamics( );
_brookBrownianDynamics->setup( masses, getPlatform() );
_brookShakeAlgorithm = new BrookShakeAlgorithm( );
_brookShakeAlgorithm->setup( masses, constraintIndices, constraintLengths, getPlatform() );
// assert( (_brookShakeAlgorithm->getNumberOfConstraints() > 0) );
_brookRandomNumberGenerator = new BrookRandomNumberGenerator( );
_brookRandomNumberGenerator->setup( (int) masses.size(), getPlatform() );
// _brookRandomNumberGenerator->setVerbosity( 1 );
}
/**
* Execute kernel
*
* @param positions particle coordinates
* @param velocities particle velocities
* @param forces particle forces
* @param temperature heat bath temperature
* @param friction friction coefficient coupling the system to the heat bath
* @param stepSize integration step size
*
*/
void BrookIntegrateBrownianStepKernel::execute( Stream& positions, Stream& velocities,
const Stream& forces, double temperature,
double friction, double stepSize ){
// ---------------------------------------------------------------------------------------
double epsilon = 1.0e-04;
static const std::string methodName = "BrookIntegrateBrownianStepKernel::execute";
// ---------------------------------------------------------------------------------------
// first time through initialize _brookBrownianDynamics
// for each subsequent call, check if parameters need to be updated due to a change
// in T, gamma, or the step size
// take step
double differences[3];
differences[0] = temperature - (double) _brookBrownianDynamics->getTemperature();
differences[1] = friction - (double) _brookBrownianDynamics->getFriction();
differences[2] = stepSize - (double) _brookBrownianDynamics->getStepSize();
if( fabs( differences[0] ) > epsilon || fabs( differences[1] ) > epsilon || fabs( differences[2] ) > epsilon ){
//printf( "%s calling updateParameters\n", methodName.c_str() );
_brookBrownianDynamics->updateParameters( temperature, friction, stepSize );
} else {
//printf( "%s NOT calling updateParameters\n", methodName.c_str() );
}
_brookBrownianDynamics->update( positions, velocities, forces, *_brookShakeAlgorithm, *_brookRandomNumberGenerator );
}
platforms/brook/src/BrookIntegrateBrownianStepKernel.h deleted 100644 → 0
View file @ aff802d9
#ifndef OPENMM_BROOK_INTEGRATE_BROWNIAN_STEP_KERNEL_H_
#define OPENMM_BROOK_INTEGRATE_BROWNIAN_STEP_KERNEL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright ( c ) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files ( the "Software" ), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "kernels.h"
#include "BrookBrownianDynamics.h"
#include "BrookShakeAlgorithm.h"
#include "BrookRandomNumberGenerator.h"
namespace OpenMM {
/**
* This is the base class of Float and Double streams in the Brook Platform.
*/
class BrookIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
// return values
static const int DefaultReturnValue = 0;
static const int ErrorReturnValue = -1;
/**
* BrookIntegrateBrownianStepKernel constructor
*
* @param name name of the stream to create
* @param platform platform
*
*/
BrookIntegrateBrownianStepKernel( std::string name, const Platform& platform );
/**
* BrookIntegrateBrownianStepKernel destructor
*
*/
~BrookIntegrateBrownianStepKernel();
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses particle masses
* @param constraintIndices each element contains the indices of two particles whose distance should be constrained
* @param constraintLengths required distance between each pair of constrained particles
*/
void initialize( const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths );
/**
* Execute kernel
*
* @param positions coordinates
* @param velocities velocities
* @param forces forces
* @param temperature heat bath temperature
* @param friction friction coefficient coupling the system to the heat bath
* @param stepSize step size
*
*/
void execute( Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize );
protected:
BrookBrownianDynamics* _brookBrownianDynamics;
BrookShakeAlgorithm* _brookShakeAlgorithm;
BrookRandomNumberGenerator* _brookRandomNumberGenerator;
};
} // namespace OpenMM
#endif /* OPENMM_BROOK_INTEGRATE_BROWNIAN_STEP_KERNEL_H_ */
platforms/brook/src/BrookNonBonded.cpp
View file @ 56755055
......@@ -1287,7 +1287,11 @@ void BrookNonBonded::computeForces( BrookStreamImpl& positionStream, BrookStream
// ---------------------------------------------------------------------------------------
printOn = (printOn && getLog()) ? printOn : 0;
if( printOn && getLog() ){
log = getLog();
} else {
printOn = 0;
}
// nonbonded forces
......
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