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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
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: 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 <sstream>
#include "BrookBrownianDynamics.h"
#include "BrookPlatform.h"
#include "OpenMMException.h"
#include "BrookStreamImpl.h"
#include "gpu/kshakeh.h"
#include "gpu/kupdatebd.h"
#include "gpu/kcommon.h"
// use random number generator
#include "../../reference/src/SimTKUtilities/SimTKOpenMMUtilities.h"
#include "../../reference/src/SimTKUtilities/SimTKOpenMMRealType.h"
using namespace OpenMM;
using namespace std;
/**
*
* Constructor
*
*/
BrookBrownianDynamics::BrookBrownianDynamics( ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::BrookBrownianDynamics";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
BrookOpenMMFloat oneMinus = (BrookOpenMMFloat) -1.0;
// ---------------------------------------------------------------------------------------
_numberOfParticles = -1;
// mark stream dimension variables as unset
_bdParticleStreamWidth = -1;
_bdParticleStreamHeight = -1;
_bdParticleStreamSize = -1;
for( int ii = 0; ii < LastStreamIndex; ii++ ){
_streams[ii] = NULL;
}
_temperature = oneMinus;
_stepSize = oneMinus;
_tau = oneMinus;
_noiseAmplitude = zero;
_forceScale = zero;
// setup inverse sqrt masses
_inverseSqrtMasses = NULL;
// set randomNumber seed
_randomNumberSeed = 1393;
//_randomNumberSeed = randomNumberSeed ? randomNumberSeed : 1393;
//SimTKOpenMMUtilities::setRandomNumberSeed( randomNumberSeed );
}
/**
* Destructor
*
*/
BrookBrownianDynamics::~BrookBrownianDynamics( ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::~BrookBrownianDynamics";
// ---------------------------------------------------------------------------------------
for( int ii = 0; ii < LastStreamIndex; ii++ ){
delete _streams[ii];
}
delete[] _inverseSqrtMasses;
}
/**
* Get tau
*
* @return tau
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getTau( void ) const {
return _tau;
}
/**
* Get friction
*
* @return friction
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getFriction( void ) const {
static const BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
static const BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
return ( (_tau == zero) ? zero : (one/_tau) );
}
/**
* Get temperature
*
* @return temperature
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getTemperature( void ) const {
return _temperature;
}
/**
* Get stepSize
*
* @return stepSize
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getStepSize( void ) const {
return _stepSize;
}
/**
* Get force scale
*
* @return force scale
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getForceScale( void ) const {
return _forceScale;
}
/**
* Get noise amplitude
*
* @return noise amplitude
*
*/
BrookOpenMMFloat BrookBrownianDynamics::getNoiseAmplitude( void ) const {
return _noiseAmplitude;
}
/**
* Set tau
*
* @param tau new tau value
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::_setTau( BrookOpenMMFloat tau ){
_tau = tau;
_setNoiseAmplitude();
_setForceScale();
return DefaultReturnValue;
}
/**
* Set friction = 1/tau
*
* @param friction new friction value
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::_setFriction( BrookOpenMMFloat friction ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_setFriction";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
// ---------------------------------------------------------------------------------------
_tau = (BrookOpenMMFloat) ( (friction != zero) ? one/friction : zero);
_setNoiseAmplitude();
_setForceScale();
return DefaultReturnValue;
}
/**
* Set temperature
*
* @parameter temperature
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::_setTemperature( BrookOpenMMFloat temperature ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_setTemperature";
// ---------------------------------------------------------------------------------------
_temperature = temperature;
_setNoiseAmplitude();
return DefaultReturnValue;
}
/**
* Set stepSize
*
* @param stepSize
*
* @return DefaultReturnValue
*
* @throw OpenMMException, if stepSize <= 0
*
*/
int BrookBrownianDynamics::_setStepSize( BrookOpenMMFloat stepSize ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBrownianDynamics::_setStepSize";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat two = (BrookOpenMMFloat) 2.0;
// ---------------------------------------------------------------------------------------
if( stepSize <= zero ){
std::stringstream message;
message << methodName << " step size=" << stepSize << " is invalid.";
throw OpenMMException( message.str() );
}
_stepSize = stepSize;
_setNoiseAmplitude();
_setForceScale();
return DefaultReturnValue;
}
/**
* Set noise amplitude
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::_setNoiseAmplitude( void ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_setNoiseAmplitude";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat two = (BrookOpenMMFloat) 2.0;
// ---------------------------------------------------------------------------------------
_noiseAmplitude = _temperature*_stepSize*_tau;
// skip sqrt if value is negative -- presumably not all values updated
if( _noiseAmplitude > zero ){
RealOpenMM intermediate = (RealOpenMM) BOLTZ*( (RealOpenMM) (two*_noiseAmplitude) );
_noiseAmplitude = (BrookOpenMMFloat) SQRT( intermediate );
}
return DefaultReturnValue;
}
/**
* Set force scale
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::_setForceScale( void ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_setForceScale";
// ---------------------------------------------------------------------------------------
_forceScale = _stepSize*_tau;
return DefaultReturnValue;
}
/**
* Update parameters -- only way parameters can be set
*
* @param temperature temperature
* @param friction friction
* @param step size step size
*
* @return solute dielectric
*
*/
int BrookBrownianDynamics::updateParameters( double temperature, double friction, double stepSize ){
// ---------------------------------------------------------------------------------------
static int showUpdate = 1;
static int maxShowUpdate = 3;
static const std::string methodName = "\nBrookBrownianDynamics::updateParameters";
// ---------------------------------------------------------------------------------------
_setStepSize( (BrookOpenMMFloat) stepSize );
_setFriction( (BrookOpenMMFloat) friction );
//_setTau( (BrookOpenMMFloat) friction );
_setTemperature( (BrookOpenMMFloat) temperature );
_updateStreams( );
// show update
if( showUpdate && getLog() && (showUpdate++ < maxShowUpdate) ){
std::string contents = getContentsString( );
(void) fprintf( getLog(), "%s contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
return DefaultReturnValue;
};
/**
* Update
*
* @param positions particle positions
* @param velocities particle velocities
* @param forces particle forces
* @param brookShakeAlgorithm BrookShakeAlgorithm reference
* @param brookRandomNumberGenerator BrookRandomNumberGenerator reference
*
* @return DefaultReturnValue
*
*/
int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
const Stream& forces,
BrookShakeAlgorithm& brookShakeAlgorithm,
BrookRandomNumberGenerator& brookRandomNumberGenerator ){
// ---------------------------------------------------------------------------------------
float omega = 1.0f;
float one = 1.0f;
static const std::string methodName = "\nBrookBrownianDynamics::update";
static const int PrintOn = 0;
// ---------------------------------------------------------------------------------------
BrookStreamImpl& positionStream = dynamic_cast<BrookStreamImpl&> (positions.getImpl());
BrookStreamImpl& velocityStream = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
const BrookStreamImpl& forceStreamC = dynamic_cast<const BrookStreamImpl&> (forces.getImpl());
BrookStreamImpl& forceStream = const_cast<BrookStreamImpl&> (forceStreamC);
if( (1 || PrintOn) && getLog() ){
static int showAux = 1;
if( showAux ){
(void) fprintf( getLog(), "%s shake=%d\n", methodName, brookShakeAlgorithm.getNumberOfConstraints() );
(void) fflush( getLog() );
}
// show update
if( showAux ){
showAux = 0;
std::string contents = brookRandomNumberGenerator.getContentsString( );
(void) fprintf( getLog(), "%s RNG contents\n%s", methodName, contents.c_str() );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
contents = brookShakeAlgorithm.getContentsString( );
(void) fprintf( getLog(), "%s Shake contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
}
// diagnostics
if( (1 || PrintOn) ){
(void) fprintf( getLog(), "\nPre kintegrate_bd: %d rngStrW=%3d rngOff=%5d "
"ForceScale=%12.5e NoiseAmplitude=%12.5e\n",
getBrownianDynamicsParticleStreamWidth(),
brookRandomNumberGenerator.getRandomNumberStreamWidth(),
brookRandomNumberGenerator.getRvStreamOffset(),
getForceScale(), getNoiseAmplitude() );
// (void) fprintf( getLog(), "\nInverseMassStream\n" );
//getInverseMassStream()->printToFile( getLog() );
//StreamImpl& positionStreamImpl = positionStream.getImpl();
//const BrookStreamImpl brookPositions = dynamic_cast<BrookStreamImpl&> (positionStreamImpl);
/*
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
*/
double forceSum[3];
BrookStreamInternal* brookStreamInternalFF = forceStream.getBrookStreamInternal();
BrookFloatStreamInternal* brookStreamInternalF = dynamic_cast<BrookFloatStreamInternal*> (brookStreamInternalFF);
brookStreamInternalF->sumByDimension( getNumberOfParticles(), forceSum );
(void) fprintf( getLog(), "\nForceStream [%18.10e %18.10e %18.10e]\n", forceSum[0], forceSum[1], forceSum[2] );
brookStreamInternalF->printToFile( getLog() );
/*
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nRvStreamIndex=%d\n", brookRandomNumberGenerator.getRvStreamIndex() );
*/
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
}
// integration step -- deltas returned in XPrime
kintegrate_bd(
(float) getBrownianDynamicsParticleStreamWidth(),
(float) brookRandomNumberGenerator.getRandomNumberStreamWidth(),
(float) brookRandomNumberGenerator.getRvStreamOffset(),
getForceScale(), getNoiseAmplitude(),
brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->getBrookStream(),
positionStream.getBrookStream(), forceStream.getBrookStream(),
getXPrimeStream()->getBrookStream() );
// diagnostics
if( PrintOn ){
(void) fprintf( getLog(), "\nPost kintegrate_bd: %d rngStrW=%3d rngOff=%5d "
"ForceScale=%12.5e NoiseAmplitude=%12.5e\n",
getBrownianDynamicsParticleStreamWidth(),
brookRandomNumberGenerator.getRandomNumberStreamWidth(),
brookRandomNumberGenerator.getRvStreamOffset(),
getForceScale(), getNoiseAmplitude() );
// (void) fprintf( getLog(), "\nInverseMassStream\n" );
//getInverseMassStream()->printToFile( getLog() );
//StreamImpl& positionStreamImpl = positionStream.getImpl();
//const BrookStreamImpl brookPositions = dynamic_cast<BrookStreamImpl&> (positionStreamImpl);
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nForceStream\n" );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nRvStreamIndex=%d\n", brookRandomNumberGenerator.getRvStreamIndex() );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
}
// advance random number cursor
brookRandomNumberGenerator.advanceGVCursor( getNumberOfParticles() );
// Shake
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
/*
kshakeh_fix1(
(float) brookShakeAlgorithm.getMaxIterations(),
(float) getBrownianDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
brookShakeAlgorithm.getShakeTolerance(),
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
brookShakeAlgorithm.getShakeParticleParameterStream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons0Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons1Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons2Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream() );
// second Shake gather
kshakeh_update2_fix1(
(float) getBrownianDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getShakeInverseMapStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons0Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons1Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons2Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream(),
positionStream.getBrookStream() );
*/
fprintf( stderr, "\nBrownian shake off!!\n" );
// diagnostics
if( PrintOn ){
(void) fprintf( getLog(), "\nPost kupdate_bd:\n" );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
}
} else {
// update step
float velocityScale = (float) (one/getStepSize());
kupdate_bd2( velocityScale, getXPrimeStream()->getBrookStream(),
positionStream.getBrookStream(), velocityStream.getBrookStream(), positionStream.getBrookStream() );
// diagnostics
if( (1 || PrintOn) ){
(void) fprintf( getLog(), "\nPost kupdate_bd2: velocityScale=%12.5e\n", velocityScale );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
}
}
return DefaultReturnValue;
};
/**
* Get Particle stream size
*
* @return Particle stream size
*
*/
int BrookBrownianDynamics::getBrownianDynamicsParticleStreamSize( void ) const {
return _bdParticleStreamSize;
}
/**
* Get particle stream width
*
* @return particle stream width
*
*/
int BrookBrownianDynamics::getBrownianDynamicsParticleStreamWidth( void ) const {
return _bdParticleStreamWidth;
}
/**
* Get particle stream height
*
* @return particle stream height
*/
int BrookBrownianDynamics::getBrownianDynamicsParticleStreamHeight( void ) const {
return _bdParticleStreamHeight;
}
/**
* Get XPrime stream
*
* @return Xprime stream
*
*/
BrookFloatStreamInternal* BrookBrownianDynamics::getXPrimeStream( void ) const {
return _streams[XPrimeStream];
}
/**
* Get InverseMass stream
*
* @return inverse mass stream
*
*/
BrookFloatStreamInternal* BrookBrownianDynamics::getInverseMassStream( void ) const {
return _streams[InverseMassStream];
}
/**
* Initialize stream dimensions
*
* @param numberOfParticles number of particles
* @param platform platform
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
*/
int BrookBrownianDynamics::_initializeStreamSizes( int numberOfParticles, const Platform& platform ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_initializeStreamSizes";
// ---------------------------------------------------------------------------------------
_bdParticleStreamSize = getParticleStreamSize( platform );
_bdParticleStreamWidth = getParticleStreamWidth( platform );
_bdParticleStreamHeight = getParticleStreamHeight( platform );
return DefaultReturnValue;
}
/**
* Initialize streams
*
* @param platform platform
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
*/
int BrookBrownianDynamics::_initializeStreams( const Platform& platform ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_initializeStreams";
BrookOpenMMFloat dangleValue = (BrookOpenMMFloat) 0.0;
// ---------------------------------------------------------------------------------------
int sdParticleStreamSize = getBrownianDynamicsParticleStreamSize();
int sdParticleStreamWidth = getBrownianDynamicsParticleStreamWidth();
_streams[VPrimeStream] = new BrookFloatStreamInternal( BrookCommon::VPrimeStream,
sdParticleStreamSize, sdParticleStreamWidth,
BrookStreamInternal::Float3, dangleValue );
_streams[XPrimeStream] = new BrookFloatStreamInternal( BrookCommon::XPrimeStream,
sdParticleStreamSize, sdParticleStreamWidth,
BrookStreamInternal::Float3, dangleValue );
_streams[InverseMassStream] = new BrookFloatStreamInternal( BrookCommon::InverseMassStream,
sdParticleStreamSize, sdParticleStreamWidth,
BrookStreamInternal::Float, dangleValue );
return DefaultReturnValue;
}
/**
* Update streams -- called after parameters change
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
*/
int BrookBrownianDynamics::_updateStreams( void ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_updateStreams";
// ---------------------------------------------------------------------------------------
//int particleStreamSize = getBrownianDynamicsParticleStreamSize();
return DefaultReturnValue;
}
/**
* Set masses
*
* @param masses particle masses
*
*/
int BrookBrownianDynamics::_setInverseSqrtMasses( const std::vector<double>& masses ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookBrownianDynamics::_setInverseSqrtMasses";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
// ---------------------------------------------------------------------------------------
// setup inverse sqrt masses
_inverseSqrtMasses = new BrookOpenMMFloat[masses.size()];
int index = 0;
for( std::vector<double>::const_iterator ii = masses.begin(); ii != masses.end(); ii++, index++ ){
if( *ii != 0.0 ){
BrookOpenMMFloat value = static_cast<BrookOpenMMFloat>(*ii);
_inverseSqrtMasses[index] = ( SQRT( one/value ) );
} else {
_inverseSqrtMasses[index] = zero;
}
}
return DefaultReturnValue;
}
/*
* Setup of BrownianDynamics parameters
*
* @param masses masses
* @param platform Brook platform
*
* @return nonzero value if error
*
* */
int BrookBrownianDynamics::setup( const std::vector<double>& masses, const Platform& platform ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBrownianDynamics::setup";
// ---------------------------------------------------------------------------------------
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
setLog( brookPlatform.getLog() );
int numberOfParticles = (int) masses.size();
setNumberOfParticles( numberOfParticles );
// set stream sizes and then create streams
_initializeStreamSizes( numberOfParticles, platform );
_initializeStreams( platform );
_setInverseSqrtMasses( masses );
return DefaultReturnValue;
}
/*
* Get contents of object
*
* @param level level of dump
*
* @return string containing contents
*
* */
std::string BrookBrownianDynamics::getContentsString( int level ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBrownianDynamics::getContentsString";
static const unsigned int MAX_LINE_CHARS = 256;
char value[MAX_LINE_CHARS];
static const char* Set = "Set";
static const char* NotSet = "Not set";
// ---------------------------------------------------------------------------------------
std::stringstream message;
std::string tab = " ";
#ifdef WIN32
#define LOCAL_SPRINTF(a,b,c) sprintf_s( (a), MAX_LINE_CHARS, (b), (c) );
#else
#define LOCAL_SPRINTF(a,b,c) sprintf( (a), (b), (c) );
#endif
(void) LOCAL_SPRINTF( value, "%d", getNumberOfParticles() );
message << _getLine( tab, "Number of particles:", value );
(void) LOCAL_SPRINTF( value, "%d", getParticleStreamWidth() );
message << _getLine( tab, "Particle stream width:", value );
(void) LOCAL_SPRINTF( value, "%d", getParticleStreamHeight() );
message << _getLine( tab, "Particle stream height:", value );
(void) LOCAL_SPRINTF( value, "%d", getParticleStreamSize() );
message << _getLine( tab, "Particle stream size:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getTau() );
message << _getLine( tab, "Tau:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getTemperature() );
message << _getLine( tab, "Temperature:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getStepSize() );
message << _getLine( tab, "Step size:", value );
(void) LOCAL_SPRINTF( value, "%.5e", getForceScale() );
message << _getLine( tab, "Force scale:", value );
(void) LOCAL_SPRINTF( value, "%.5e", getNoiseAmplitude() );
message << _getLine( tab, "Noise amplitude:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getTemperature() );
message << _getLine( tab, "Temperature:", value );
message << _getLine( tab, "Log:", (getLog() ? Set : NotSet) );
for( int ii = 0; ii < LastStreamIndex; ii++ ){
message << std::endl;
if( _streams[ii] ){
message << _streams[ii]->getContentsString( );
}
}
#undef LOCAL_SPRINTF
return message.str();
}
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 ...@@ -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 // nonbonded forces
......
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