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Commit 4ed00931 authored by Mark Friedrichs's avatar Mark Friedrichs
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platforms/brook/src/BrookCommon.cpp
View file @ 4ed00931
......@@ -30,7 +30,10 @@
* -------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <sstream>
#include "BrookCommon.h"
#include "BrookPlatform.h"
#include "BrookStreamFactory.h"
......@@ -73,6 +76,16 @@ const std::string BrookCommon::SDPC2Stream
const std::string BrookCommon::SD2XStream = "SD2XStream";
const std::string BrookCommon::SD1VStream = "SD1VStream";
// Shake streams
const std::string BrookCommon::ShakeAtomIndicesStream = "ShakeAtomIndicesStream";
const std::string BrookCommon::ShakeAtomParameterStream = "ShakeAtomParameterStream";
const std::string BrookCommon::ShakeXCons0Stream = "ShakeXCons0Stream";
const std::string BrookCommon::ShakeXCons1Stream = "ShakeXCons1Stream";
const std::string BrookCommon::ShakeXCons2Stream = "ShakeXCons2Stream";
const std::string BrookCommon::ShakeXCons3Stream = "ShakeXCons3Stream";
const std::string BrookCommon::ShakeInverseMapStream = "ShakeInverseMapStream";
/**
* Constructor
*
......@@ -354,3 +367,90 @@ std::string BrookCommon::_getLine( const std::string& tab, const std::string& de
return message.str();
}
/*
* Given number of stream elements and width, returns the appropriate
* height of the stream
*
* @param streamSize stream size
* @param width stream width
*
* @return stream height
*
*/
int BrookCommon::getStreamHeight( int streamSize, int streamWidth ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookCommon::getStreamHeight";
// ---------------------------------------------------------------------------------------
int streamHeight = streamSize/streamWidth;
if( streamSize % streamWidth ){
streamHeight++;
}
return streamHeight;
}
/*
* Given number of stream elements, get stream width & height
*
* @param streamSize stream size
* @param streamWidth output stream width
* @param streamHeight output stream height
*
* @return stream height
*
*/
void BrookCommon::getStreamDimensions( int streamSize, int *streamWidth, int *streamHeight ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookCommon::getStreamDimensions";
// ---------------------------------------------------------------------------------------
// There are two conditions - stream should be as square
// as possible, but should also be multiple of 16 along
// one dimension
float s = sqrtf( (float) streamSize );
// find nearest multiple of 16 to the perfect square size
int low = ( (int) floor( s/16.0f ) ) * 16;
if ( !low ) {
*streamWidth = 16;
*streamHeight = getStreamHeight( streamSize, *streamWidth );
} else {
int high = low + 1;
// I'm not sure 48 is such a good stream width. Things seem
// to be faster with 32 or 64. Can make this a special
// case later.
// Choose low or high depending on which one is
// more square
int htlow = getStreamHeight( streamSize, low );
int hthigh = getStreamHeight( streamSize, high );
if ( abs( htlow - low ) < abs( hthigh - high ) ) {
*streamWidth = low;
*streamHeight = htlow;
} else {
*streamWidth = high;
*streamHeight = hthigh;
}
}
return;
}
platforms/brook/src/BrookCommon.h
View file @ 4ed00931
......@@ -84,6 +84,23 @@ class BrookCommon {
static const std::string ObcIntermediateForceStream;
static const std::string ObcChainStream;
// Stochastic Dynamics streams
static const std::string SDPC1Stream;
static const std::string SDPC2Stream;
static const std::string SD2XStream;
static const std::string SD1VStream;
// Shake streams
static const std::string ShakeAtomIndicesStream;
static const std::string ShakeAtomParameterStream;
static const std::string ShakeXCons0Stream;
static const std::string ShakeXCons1Stream;
static const std::string ShakeXCons2Stream;
static const std::string ShakeXCons3Stream;
static const std::string ShakeInverseMapStream;
// ---------------------------------------------------------------------------------------
/**
......@@ -203,6 +220,32 @@ class BrookCommon {
FILE* getLog( void ) const;
/*
* Given number of stream elements and width, returns the appropriate
* height of the stream
*
* @param streamSize stream size
* @param width stream width
*
* @return stream height
*
*/
static int getStreamHeight( int streamSize, int streamWidth );
/*
* Given number of stream elements, get stream width & height
*
* @param streamSize stream size
* @param streamWidth output stream width
* @param streamHeight output stream height
*
* @return stream height
*
*/
static void getStreamDimensions( int streamSize, int *streamWidth, int *streamHeight );
protected:
// number of atoms
......
platforms/brook/src/BrookGbsa.cpp
View file @ 4ed00931
......@@ -65,6 +65,7 @@ BrookGbsa::BrookGbsa( ){
_duplicationFactor = 4;
_includeAce = 1;
_solventDielectric = 78.3;
_soluteDielectric = 1.0;
_dielectricOffset = 0.09;
......@@ -117,6 +118,18 @@ int BrookGbsa::getNumberOfForceStreams( void ) const {
return NumberOfForceStreams;
}
/**
* Include ACE approximation in calculation of force
*
* @return true if ACE approximation is to be included in calculation of force
*
*/
int BrookGbsa::includeAce( void ) const {
return _includeAce;
}
/**
* Get inner loop unroll
*
......
platforms/brook/src/BrookGbsa.h
View file @ 4ed00931
......@@ -369,6 +369,10 @@ class BrookGbsa : public BrookCommon {
int _duplicationFactor;
// include ACE approximation
int _includeAce;
// force stream width
int _partialForceStreamWidth;
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp
View file @ 4ed00931
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "BrookIntegrateKernals.h"
#include "BrookIntegrateLangevinStepKernel.h"
#include "BrookStreamInternal.h"
using namespace OpenMM;
......@@ -44,14 +44,8 @@ BrookIntegrateLangevinStepKernel::BrookIntegrateLangevinStepKernel( std::string
// ---------------------------------------------------------------------------------------
_numberOfConstraints = -1;
_brookStochasticDynamics = NULL;
_brookShakeAlgorithm = NULL;
_atomMasses = NULL;
_shakeParameters = NULL;
_constraintIndices = NULL;
_shakeParameters = NULL;
}
......@@ -63,12 +57,8 @@ BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel( ){
// ---------------------------------------------------------------------------------------
delete _brookkStochasticDynamics;
delete _brookStochasticDynamics;
delete _brookShakeAlgorithm;
delete _atomMasses;
delete _shakeParameters;
delete _constraintIndices;
delete _shakeParameters;
}
......@@ -82,25 +72,11 @@ void BrookIntegrateLangevinStepKernel::initialize( const vector<double>& masses,
// ---------------------------------------------------------------------------------------
_brookkStochasticDynamics = new BrookStochasticDynamics( masses );
_brookkStochasticDynamics->setup( masses, getPlatform() );
_brookShakeAlgorithm = new BrookShakeAlgorithm( masses, constraintIndices, constraintLengths );
/*
this->masses = new RealOpenMM[masses.size()];
for (size_t i = 0; i < masses.size(); ++i)
this->masses[i] = static_cast<RealOpenMM>( masses[i] );
numConstraints = constraintIndices.size();
this->constraintIndices = allocateIntArray(numConstraints, 2);
for (int i = 0; i < numConstraints; ++i) {
this->constraintIndices[i][0] = constraintIndices[i][0];
this->constraintIndices[i][1] = constraintIndices[i][1];
}
shakeParameters = allocateRealArray(constraintLengths.size(), 1);
for (size_t i = 0; i < constraintLengths.size(); ++i)
shakeParameters[i][0] = static_cast<RealOpenMM>( constraintLengths[i] );
_brookStochasticDynamics = new BrookStochasticDynamics( );
_brookStochasticDynamics->setup( masses, getPlatform() );
*/
_brookShakeAlgorithm = new BrookShakeAlgorithm( );
_brookShakeAlgorithm->setup( masses, constraintIndices, constraintLengths, getPlatform() );
}
/**
......@@ -121,6 +97,7 @@ void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& veloc
// ---------------------------------------------------------------------------------------
double epsilon = 1.0e-04;
//static const std::string methodName = "BrookIntegrateLangevinStepKernel::execute";
// ---------------------------------------------------------------------------------------
......@@ -132,12 +109,13 @@ void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& veloc
// take step
if( _brookStochasticDynamics == NULL ){
_brookStochasticDynamics = new BrookStochasticDynamics( getNumberOfAtoms(), static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(temperature) );
} else if( temperature != _brookStochasticDynamics->getTemperatur() || friction != _brookStochasticDynamics->getFriction() ){
_brookStochasticDynamics->updateParameters( temperature, friction );
double differences[3];
differences[0] = temperature - (double) _brookStochasticDynamics->getTemperature();
differences[1] = friction - (double) _brookStochasticDynamics->getFriction();
differences[2] = stepSize - (double) _brookStochasticDynamics->getStepSize();
if( fabs( differences[0] ) < epsilon || fabs( differences[1] ) < epsilon || fabs( differences[2] ) < epsilon ){
_brookStochasticDynamics->updateParameters( temperature, friction, stepSize );
}
_brookStochasticDynamics->update( positions, velocities, forces );
_brookStochasticDynamics->update( positions, velocities, forces, *_brookShakeAlgorithm );
}
platforms/brook/src/BrookIntegrateLangevinStepKernel.h
View file @ 4ed00931
......@@ -85,18 +85,12 @@ class BrookIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
*
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
void execute( Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
protected:
BrookStochasticDynamics* _brookStochasticDynamics;
BrookShakeAlgorithm* _brookShakeAlgorithm;
RealOpenMM* _atomMasses;
RealOpenMM** _shakeParameters;
int** _constraintIndices;
int _numberOfConstraints;
double prevTemp, prevFriction, prevStepSize;
};
......
platforms/brook/src/BrookIntegrateVerletStepKernel.cpp
View file @ 4ed00931
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "BrookIntegrateKernals.h"
#include "BrookIntegrateVerletStepKernel.h"
#include "BrookStreamInternal.h"
using namespace OpenMM;
......
platforms/brook/src/BrookKernelFactory.cpp
View file @ 4ed00931
......@@ -31,8 +31,9 @@
#include "BrookKernelFactory.h"
#include "BrookCalcStandardMMForceFieldKernel.h"
#include "BrookIntegrateKernals.h"
#include "BrookIntegrateLangevinStepKernel.h"
#include "BrookCalcKineticEnergyKernel.h"
#include "BrookCalcGBSAOBCForceFieldKernel.h"
using namespace OpenMM;
......@@ -44,27 +45,41 @@ KernelImpl* BrookKernelFactory::createKernelImpl( std::string name, const Platfo
// ---------------------------------------------------------------------------------------
// StandardMM
if( name == CalcStandardMMForceFieldKernel::Name() ){
return new BrookCalcStandardMMForceFieldKernel( name, platform );
// GBSA OBC
} else if( name == CalcGBSAOBCForceFieldKernel::Name() ){
(void) fprintf( stderr, "CalcGBSAOBCForceFieldKernel not set BrookKernelFactory::createKernelImpl\n" );
(void) fflush( stderr );
//return new BrookCalcGBSAOBCForceFieldKernel(name, platform);
return new BrookCalcGBSAOBCForceFieldKernel(name, platform);
// Verlet integrator
} else if( name == IntegrateVerletStepKernel::Name() ){
(void) fprintf( stderr, "IntegrateVerletStepKernel created BrookKernelFactory::createKernelImpl\n" );
(void) fflush( stderr );
return new BrookIntegrateVerletStepKernel( name, platform );
// return new BrookIntegrateVerletStepKernel( name, platform );
// Brownian integrator
} else if( name == IntegrateBrownianStepKernel::Name() ){
// return new BrookIntegrateBrownianStepKernel( name, platform );
// Andersen integrator
} else if( name == ApplyAndersenThermostatKernel::Name() ){
// return new BrookIntegrateAndersenThermostatKernel( name, platform );
// Langevin integrator
} else if( name == IntegrateLangevinStepKernel::Name() ){
return new BrookIntegrateLangevinStepKernel( name, platform );
// KE calculator
......@@ -75,13 +90,5 @@ KernelImpl* BrookKernelFactory::createKernelImpl( std::string name, const Platfo
(void) fprintf( stderr, "createKernelImpl: name=<%s> not found.", methodName.c_str(), name.c_str() );
(void) fflush( stderr );
/*
if (name == IntegrateLangevinStepKernel::Name())
//return new BrookIntegrateLangevinStepKernel(name, platform);
//if (name == IntegrateBrownianStepKernel::Name())
//return new BrookIntegrateBrownianStepKernel(name, platform);
if (name == ApplyAndersenThermostatKernel::Name())
//return new BrookApplyAndersenThermostatKernel(name, platform);
*/
return NULL;
}
platforms/brook/src/BrookShakeAlgorithm.cpp 0 → 100644
View file @ 4ed00931
This diff is collapsed.
platforms/brook/src/BrookShakeAlgorithm.h 0 → 100644
View file @ 4ed00931
#ifndef OPENMM_BROOK_SHAKE_H_
#define OPENMM_BROOK_SHAKE_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 "BrookPlatform.h"
#include "BrookCommon.h"
namespace OpenMM {
/**
*
* Encapsulates stochastic dynamics algorithm
*
*/
class BrookShakeAlgorithm : public BrookCommon {
public:
/**
* Constructor
*
*/
BrookShakeAlgorithm( );
/**
* Destructor
*
*/
~BrookShakeAlgorithm();
/**
* Get number of constraints
*
* @return number of constraints
*
*/
int getNumberOfConstraints( void ) const;
/**
* Get inverse of hydrogen mass
*
* @return inverse of hydrogen mass
*/
BrookOpenMMFloat getInverseHydrogenMass( void ) const;
/**
* Get Shake atom stream width
*
* @return atom stream width
*/
int getShakeAtomStreamWidth( void ) const;
/**
* Get Shake atom stream height
*
* @return atom stream height
*/
int getShakeAtomStreamHeight( void ) const;
/**
* Get Shake atom stream size
*
* @return atom stream size
*/
int getShakeAtomStreamSize( void ) const;
/**
* Get Shake constraint stream width
*
* @return constraint stream width
*/
int getShakeConstraintStreamWidth( void ) const;
/**
* Get Shake constraint stream height
*
* @return constraint stream height
*/
int getShakeConstraintStreamHeight( void ) const;
/**
* Get Shake constraint stream size
*
* @return constraint stream size
*/
int getShakeConstraintStreamSize( void ) const;
/**
* Get array of Shake streams
*
* @return array ofstreams
*
*/
BrookFloatStreamInternal** getStreams( void );
/*
* Setup of Shake parameters
*
* @param masses masses
* @param constraintIndices constraint atom indices
* @param constraintLengths constraint lengths
* @param platform Brook platform
*
* @return ErrorReturnValue if error
*
*/
int setup( const std::vector<double>& masses, const std::vector< std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths, const Platform& platform );
/*
* Get contents of object
*
* @param level of dump
*
* @return string containing contents
*
* */
std::string getContentsString( int level = 0 ) const;
/**
* Get Shake atom indices stream
*
* @return Shake atom indices stream
*
*/
BrookFloatStreamInternal* getShakeAtomIndicesStream( void ) const;
/**
* Get Shake atom parameter stream
*
* @return Shake atom parameter stream
*
*/
BrookFloatStreamInternal* getShakeAtomParameterStream( void ) const;
/**
* Get XCons0 stream
*
* @return XCons0 stream
*
*/
BrookFloatStreamInternal* getShakeXCons0Stream( void ) const;
/**
* Get XCons1 stream
*
* @return XCons1 stream
*
*/
BrookFloatStreamInternal* getShakeXCons1Stream( void ) const;
/**
* Get XCons2 stream
*
* @return XCons2 stream
*
*/
BrookFloatStreamInternal* getShakeXCons2Stream( void ) const;
/**
* Get XCons3 stream
*
* @return XCons3 stream
*
*/
BrookFloatStreamInternal* getShakeXCons3Stream( void ) const;
/**
* Get Shake inverse map stream
*
* @return Shake inverse map stream
*
*/
BrookFloatStreamInternal* getShakeInverseMapStream( void ) const;
private:
// streams indices
enum BrookShakeAlgorithmStreams {
ShakeAtomIndicesStream,
ShakeAtomParameterStream,
ShakeXCons0Stream,
ShakeXCons1Stream,
ShakeXCons2Stream,
ShakeXCons3Stream,
ShakeInverseMapStream,
LastStreamIndex
};
// number of constraints
int _numberOfConstraints;
// inverse of H mass
BrookOpenMMFloat _inverseHydrogenMass;
// atom stream dimensions
int _shakeAtomStreamWidth;
int _shakeAtomStreamHeight;
int _shakeAtomStreamSize;
// constraint stream dimensions
int _shakeConstraintStreamSize;
int _shakeConstraintStreamWidth;
int _shakeConstraintStreamHeight;
// inverse sqrt masses
BrookOpenMMFloat* _inverseSqrtMasses;
// internal streams
BrookFloatStreamInternal* _shakeStreams[LastStreamIndex];
/*
* Setup of stream dimensions
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValueValue
*
* */
int _initializeStreamSizes( int atomStreamSize, int atomStreamWidth );
/**
* Initialize stream dimensions
*
* @param numberOfAtoms number of atoms
* @param numberOfConstraints number of constraints
* @param platform platform
*
* @return ErrorReturnValue if error, else DefaultReturnValueValue
*
*/
int _initializeStreamSizes( int numberOfAtoms, int numberOfConstraints, const Platform& platform );
/**
* Initialize stream dimensions and streams
*
* @param platform platform
*
* @return nonzero value if error
*
*/
int _initializeStreams( const Platform& platform );
/*
* Set Shake streams
*
* @param masses masses
* @param constraintIndices constraint atom indices
* @param constraintLengths constraint lengths
*
* @return ErrorReturnValue if error
*
* @throw OpenMMException if constraintIndices.size() != constraintLengths.size()
*
*/
int _setShakeStreams( const std::vector<double>& masses, const std::vector< std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths );
};
} // namespace OpenMM
#endif /* OPENMM_BROOK_SHAKE_H_ */
platforms/brook/src/BrookStochasticDynamics.cpp
View file @ 4ed00931
......@@ -52,7 +52,7 @@ BrookStochasticDynamics::BrookStochasticDynamics( ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookStochasticDynamics::BrookStochasticDynamics";
//static const std::string methodName = "BrookStochasticDynamics::BrookStochasticDynamics";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
......@@ -76,7 +76,9 @@ BrookStochasticDynamics::BrookStochasticDynamics( ){
_derivedParameters[ii] = oneMinus;
}
_temperature = _stepSize = _tau = oneMinus;
_temperature = oneMinus;
_stepSize = oneMinus;
_tau = oneMinus;
// setup inverse sqrt masses
......@@ -84,6 +86,8 @@ BrookStochasticDynamics::BrookStochasticDynamics( ){
// set randomNumber seed
_randomNumberSeed = 1393;
//_randomNumberSeed = randomNumberSeed ? randomNumberSeed : 1393;
//SimTKOpenMMUtilities::setRandomNumberSeed( randomNumberSeed );
}
......@@ -120,6 +124,19 @@ BrookOpenMMFloat BrookStochasticDynamics::getTau( void ) const {
return _tau;
}
/**
* Get friction
*
* @return friction
*
*/
BrookOpenMMFloat BrookStochasticDynamics::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
*
......@@ -147,13 +164,13 @@ BrookOpenMMFloat BrookStochasticDynamics::getStepSize( void ) const {
*
* @param tau new tau value
*
* @return DefaultReturn
* @return DefaultReturnValue
*
*/
int BrookStochasticDynamics::_setTau( BrookOpenMMFloat tau ){
_tau = tau;
return DefaultReturn;
return DefaultReturnValue;
}
/**
......@@ -161,13 +178,13 @@ int BrookStochasticDynamics::_setTau( BrookOpenMMFloat tau ){
*
* @param friction new friction value
*
* @return DefaultReturn
* @return DefaultReturnValue
*
*/
int BrookStochasticDynamics::_setFriction( BrookOpenMMFloat friction ){
_tau = (BrookOpenMMFloat) ( (friction != 0.0) ? 1.0/friction : 0.0);
return DefaultReturn;
return DefaultReturnValue;
}
/**
......@@ -175,13 +192,13 @@ int BrookStochasticDynamics::_setFriction( BrookOpenMMFloat friction ){
*
* @parameter temperature
*
* @return DefaultReturn
* @return DefaultReturnValue
*
*/
int BrookStochasticDynamics::_setTemperature( BrookOpenMMFloat temperature ){
_temperature = temperature;
return DefaultReturn;
return DefaultReturnValue;
}
/**
......@@ -189,19 +206,19 @@ int BrookStochasticDynamics::_setTemperature( BrookOpenMMFloat temperature ){
*
* @param stepSize
*
* @return DefaultReturn
* @return DefaultReturnValue
*
*/
int BrookStochasticDynamics::_setStepSize( BrookOpenMMFloat stepSize ){
_stepSize = stepSize;
return DefaultReturn;
return DefaultReturnValue;
}
/**
* Update derived parameters
*
* @return DefaultReturn
* @return DefaultReturnValue
*
*/
......@@ -272,7 +289,7 @@ int BrookStochasticDynamics::_updateDerivedParameters( void ){
_derivedParameters[Sd2pc1] = one/_derivedParameters[Sd1pc2];
_derivedParameters[Sd2pc2] = tau*_derivedParameters[D]/( _derivedParameters[EM] - one );
return DefaultReturn;
return DefaultReturnValue;
};
......@@ -295,24 +312,51 @@ int BrookStochasticDynamics::updateParameters( double temperature, double fricti
// ---------------------------------------------------------------------------------------
_setStepSize( stepSize );
_setFriction( friction );
_setTemperature( temperature );
_setStepSize( (BrookOpenMMFloat) stepSize );
_setFriction( (BrookOpenMMFloat) friction );
_setTemperature( (BrookOpenMMFloat) temperature );
_updateDerivedParameters( );
_updateSdStreams( );
return DefaultReturn;
return DefaultReturnValue;
};
/**---------------------------------------------------------------------------------------
/**
* Update
*
* @param positions atom positions
* @param velocities atom velocities
* @param forces atom forces
* @param brookShakeAlgorithm BrookShakeAlgorithm reference
*
* @return DefaultReturnValue
*
*/
int BrookStochasticDynamics::update( Stream& positions, Stream& velocities,
const Stream& forces,
BrookShakeAlgorithm& brookShakeAlgorithm ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nBrookStochasticDynamics::update";
// ---------------------------------------------------------------------------------------
Get array of derived parameters indexed by 'DerivedParameters' enums
@return array
return DefaultReturnValue;
};
--------------------------------------------------------------------------------------- */
/**
*
* Get array of derived parameters indexed by 'DerivedParameters' enums
*
* @return array
*
*/
const BrookOpenMMFloat* BrookStochasticDynamics::getDerivedParameters( void ) const {
......@@ -364,7 +408,7 @@ int BrookStochasticDynamics::getStochasticDynamicsAtomStreamHeight( void ) const
*
*/
BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC1( void ) const {
BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC1Stream( void ) const {
return _sdStreams[SDPC1Stream];
}
......@@ -375,7 +419,7 @@ BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC1( void ) const {
*
*/
BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC2( void ) const {
BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC2Stream( void ) const {
return _sdStreams[SDPC2Stream];
}
......@@ -386,7 +430,7 @@ BrookFloatStreamInternal* BrookStochasticDynamics::getSDPC2( void ) const {
*
*/
BrookFloatStreamInternal* BrookStochasticDynamics::getSD2X( void ) const {
BrookFloatStreamInternal* BrookStochasticDynamics::getSD2XStream( void ) const {
return _sdStreams[SD2XStream];
}
......@@ -397,7 +441,7 @@ BrookFloatStreamInternal* BrookStochasticDynamics::getSD2X( void ) const {
*
*/
BrookFloatStreamInternal* BrookStochasticDynamics::getSD1V( void ) const {
BrookFloatStreamInternal* BrookStochasticDynamics::getSD1VStream( void ) const {
return _sdStreams[SD1VStream];
}
......@@ -436,7 +480,8 @@ int BrookStochasticDynamics::_initializeStreamSizes( int numberOfAtoms, const Pl
*
*/
std::string BrookStochasticDynamics::_getDerivedParametersString( BrookStochasticDynamics::DerivedParameters derivedParametersIndex ) const {
//std::string BrookStochasticDynamics::_getDerivedParametersString( BrookStochasticDynamics::DerivedParameters derivedParametersIndex ) const {
std::string BrookStochasticDynamics::_getDerivedParametersString( int derivedParametersIndex ) const {
// ---------------------------------------------------------------------------------------
......@@ -539,6 +584,8 @@ int BrookStochasticDynamics::_initializeStreams( const Platform& platform ){
//static const std::string methodName = "BrookStochasticDynamics::_initializeStreams";
BrookOpenMMFloat dangleValue = (BrookOpenMMFloat) 0.0;
// ---------------------------------------------------------------------------------------
int sdAtomStreamSize = getStochasticDynamicsAtomStreamSize();
......@@ -580,7 +627,7 @@ int BrookStochasticDynamics::_updateSdStreams( void ){
int sdAtomStreamSize = getStochasticDynamicsAtomStreamSize();
BrookOpenMMFloat sdpc[2];
BrookOpenMMFloat* sdpc[2];
for( int ii = 0; ii < 2; ii++ ){
sdpc[ii] = new BrookOpenMMFloat[2*sdAtomStreamSize];
memset( sdpc[ii], 0, 2*sdAtomStreamSize*sizeof( BrookOpenMMFloat ) );
......@@ -589,7 +636,7 @@ int BrookStochasticDynamics::_updateSdStreams( void ){
const BrookOpenMMFloat* derivedParameters = getDerivedParameters( );
int numberOfAtoms = getNumberOfAtoms();
int index = 0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfAtoms; ii++, index += 2 ){
sdpc[0][index] = _inverseSqrtMasses[ii]*( static_cast<BrookOpenMMFloat> (derivedParameters[Yv]) );
sdpc[0][index+1] = _inverseSqrtMasses[ii]*( static_cast<BrookOpenMMFloat> (derivedParameters[V]) );
......@@ -597,7 +644,6 @@ int BrookStochasticDynamics::_updateSdStreams( void ){
sdpc[1][index] = _inverseSqrtMasses[ii]*( static_cast<BrookOpenMMFloat> (derivedParameters[Yx]) );
sdpc[1][index+1] = _inverseSqrtMasses[ii]*( static_cast<BrookOpenMMFloat> (derivedParameters[X]) );
index += 2;
}
_sdStreams[SDPC1Stream]->loadFromArray( sdpc[0] );
......@@ -609,12 +655,13 @@ int BrookStochasticDynamics::_updateSdStreams( void ){
// initialize SD2X
sd2x = new BrookOpenMMFloat[3*sdAtomStreamSize];
SimTKOpenMMUtilities::setRandomNumberSeed( (uint32_t) getRandomNumberSeed() );
BrookOpenMMFloat* sd2x = new BrookOpenMMFloat[3*sdAtomStreamSize];
//SimTKOpenMMUtilities::setRandomNumberSeed( (uint32_t) getRandomNumberSeed() );
memset( sd2x, 0, 3*sdAtomStreamSize*sizeof( BrookOpenMMFloat ) );
for( int ii = 0; ii < numberOfAtoms; ii++ ){
index = 0;
for( int ii = 0; ii < numberOfAtoms; ii++, index += 3 ){
sd2x[index] = _inverseSqrtMasses[ii]*derivedParameters[X]*( static_cast<BrookOpenMMFloat> (SimTKOpenMMUtilities::getNormallyDistributedRandomNumber()) );
sd2x[index+1] = _inverseSqrtMasses[ii]*derivedParameters[X]*( static_cast<BrookOpenMMFloat> (SimTKOpenMMUtilities::getNormallyDistributedRandomNumber()) );
sd2x[index+2] = _inverseSqrtMasses[ii]*derivedParameters[X]*( static_cast<BrookOpenMMFloat> (SimTKOpenMMUtilities::getNormallyDistributedRandomNumber()) );
......@@ -639,7 +686,10 @@ int BrookStochasticDynamics::_setInverseSqrtMasses( const std::vector<double>& m
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookStochasticDynamics::_setInverseSqrtMasses";
//static const std::string methodName = "BrookStochasticDynamics::_setInverseSqrtMasses";
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
BrookOpenMMFloat one = (BrookOpenMMFloat) 1.0;
// ---------------------------------------------------------------------------------------
......@@ -647,9 +697,10 @@ int BrookStochasticDynamics::_setInverseSqrtMasses( const std::vector<double>& m
_inverseSqrtMasses = new BrookOpenMMFloat[masses.size()];
int index = 0;
for( std::vector<double>::const_interator ii = masses.begin(); ii != masses.end(); ii++, index++ ){
for( std::vector<double>::const_iterator ii = masses.begin(); ii != masses.end(); ii++, index++ ){
if( *ii != 0.0 ){
_inverseSqrtMasses[index] = ( SQRT( one/(*ii) ) );
BrookOpenMMFloat value = static_cast<BrookOpenMMFloat>(*ii);
_inverseSqrtMasses[index] = ( SQRT( one/value ) );
} else {
_inverseSqrtMasses[index] = zero;
}
......@@ -668,7 +719,7 @@ int BrookStochasticDynamics::_setInverseSqrtMasses( const std::vector<double>& m
*
* */
int BrookStochasticDynamics::setup( const std::vector<<double> >& masses, const Platform& platform ){
int BrookStochasticDynamics::setup( const std::vector<double>& masses, const Platform& platform ){
// ---------------------------------------------------------------------------------------
......@@ -679,58 +730,19 @@ int BrookStochasticDynamics::setup( const std::vector<<double> >& masses, const
int numberOfAtoms = (int) masses.size();
setNumberOfAtoms( numberOfAtoms );
_setInverseSqrtMasses( masses );
return DefaultReturnValue;
}
/*
* Setup of stream dimensions for partial force streams
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* */
int BrookStochasticDynamics::initializePartialForceStreamSize( int atomStreamSize, int atomStreamWidth ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookStochasticDynamics::initializePartialForceStreamSize";
//static const int debug = 1;
// ---------------------------------------------------------------------------------------
int innerUnroll = getInnerLoopUnroll();
if( innerUnroll < 1 ){
std::stringstream message;
message << methodName << " innerUnrolls=" << innerUnroll << " is less than 1.";
throw OpenMMException( message.str() );
return ErrorReturnValue;
}
// set stream sizes and then create streams
if( _partialForceStreamWidth < 1 ){
std::stringstream message;
message << methodName << " partial force stream width=" << _partialForceStreamWidth << " is less than 1.";
throw OpenMMException( message.str() );
return ErrorReturnValue;
}
_initializeStreamSizes( numberOfAtoms, platform );
_initializeStreams( platform );
_partialForceStreamSize = atomStreamSize*getDuplicationFactor()/innerUnroll;
_partialForceStreamHeight = _partialForceStreamSize/_partialForceStreamWidth;
_partialForceStreamHeight += ( (_partialForceStreamSize % _partialForceStreamWidth) ? 1 : 0);
_setInverseSqrtMasses( masses );
return DefaultReturnValue;
}
/*
* Setup of j-stream dimensions
*
* Get contents of object
*
*
* @param level level of dump
*
* @return string containing contents
......@@ -762,21 +774,6 @@ std::string BrookStochasticDynamics::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%d", getNumberOfAtoms() );
message << _getLine( tab, "Number of atoms:", value );
(void) LOCAL_SPRINTF( value, "%d", getNumberOfForceStreams() );
message << _getLine( tab, "Number of force streams:", value );
(void) LOCAL_SPRINTF( value, "%d", getDuplicationFactor() );
message << _getLine( tab, "Duplication factor:", value );
(void) LOCAL_SPRINTF( value, "%d", getInnerLoopUnroll () )
message << _getLine( tab, "Inner loop unroll:", value );
(void) LOCAL_SPRINTF( value, "%d", getOuterLoopUnroll() )
message << _getLine( tab, "Outer loop unroll:", value );
(void) LOCAL_SPRINTF( value, "%d", getAtomSizeCeiling() );
message << _getLine( tab, "Atom ceiling:", value );
(void) LOCAL_SPRINTF( value, "%d", getAtomStreamWidth() );
message << _getLine( tab, "Atom stream width:", value );
......@@ -786,23 +783,30 @@ std::string BrookStochasticDynamics::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%d", getAtomStreamSize() );
message << _getLine( tab, "Atom stream size:", value );
(void) LOCAL_SPRINTF( value, "%d", getPartialForceStreamWidth() );
message << _getLine( tab, "Partial force stream width:", 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, "%d", getPartialForceStreamHeight() );
message << _getLine( tab, "Partial force stream height:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getStepSize() );
message << _getLine( tab, "Step size:", value );
const BrookOpenMMFloat* derivedParameters = getDerivedParameters();
for( int ii = 0; ii < MaxDerivedParameters; ii++ ){
(void) LOCAL_SPRINTF( value, "%.5e", derivedParameters[ii] );
message << _getLine( tab, _getDerivedParametersString( ii ), value );
}
(void) LOCAL_SPRINTF( value, "%d", getPartialForceStreamSize() );
message << _getLine( tab, "Partial force stream size:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getTemperature() );
message << _getLine( tab, "Temperature:", value );
message << _getLine( tab, "Log:", (getLog() ? Set : NotSet) );
/*
message << _getLine( tab, "ExclusionStream:", (getExclusionStream() ? Set : NotSet) );
message << _getLine( tab, "VdwStream:", (getOuterVdwStream() ? Set : NotSet) );
message << _getLine( tab, "ChargeStream:", (getChargeStream() ? Set : NotSet) );
message << _getLine( tab, "SigmaStream:", (getInnerSigmaStream() ? Set : NotSet) );
message << _getLine( tab, "EpsilonStream:", (getInnerEpsilonStream() ? Set : NotSet) );
*/
message << _getLine( tab, "SDPC1:", (getSDPC1Stream() ? Set : NotSet) );
message << _getLine( tab, "SDPC2:", (getSDPC2Stream() ? Set : NotSet) );
message << _getLine( tab, "SD2X:", (getSD2XStream() ? Set : NotSet) );
message << _getLine( tab, "SD1V:", (getSD1VStream() ? Set : NotSet) );
for( int ii = 0; ii < LastStreamIndex; ii++ ){
message << std::endl;
......@@ -811,21 +815,6 @@ std::string BrookStochasticDynamics::getContentsString( int level ) const {
}
}
// force streams
for( int ii = 0; ii < getNumberOfForceStreams(); ii++ ){
char description[256];
(void) LOCAL_SPRINTF( description, "PartialForceStream %d", ii );
message << _getLine( tab, description, (isForceStreamSet(ii) ? Set : NotSet) );
}
for( int ii = 0; ii < getNumberOfForceStreams(); ii++ ){
message << std::endl;
if( _sdForceStreams[ii] ){
message << _sdForceStreams[ii]->getContentsString( );
}
}
#undef LOCAL_SPRINTF
return message.str();
......
platforms/brook/src/BrookStochasticDynamics.h
View file @ 4ed00931
......@@ -36,6 +36,7 @@
#include <set>
#include "BrookFloatStreamInternal.h"
#include "BrookShakeAlgorithm.h"
#include "BrookPlatform.h"
#include "BrookCommon.h"
......@@ -54,12 +55,9 @@ class BrookStochasticDynamics : public BrookCommon {
/**
* Constructor
*
* @param masses atomic masses
* @param randomNumberSeed random number seed
*
*/
BrookStochasticDynamics( const std::vector<double>& masses, uint32_t randomNumberSeed = 1364 );
BrookStochasticDynamics( );
/**
* Destructor
......@@ -76,6 +74,14 @@ class BrookStochasticDynamics : public BrookCommon {
BrookOpenMMFloat getTau( void ) const;
/**
* Get friction
*
* @return friction
*/
BrookOpenMMFloat getFriction( void ) const;
/**
* Get temperature
*
......@@ -92,6 +98,16 @@ class BrookStochasticDynamics : public BrookCommon {
BrookOpenMMFloat getStepSize( void ) const;
/**
*
* Get array of derived parameters indexed by 'DerivedParameters' enums
*
* @return array
*
*/
const BrookOpenMMFloat* getDerivedParameters( void ) const;
/**
* Get StochasticDynamics atom stream width
*
......@@ -121,13 +137,28 @@ class BrookStochasticDynamics : public BrookCommon {
*
* @param temperature temperature
* @param friction friction
* @param step size step size
*
* @return solute dielectric
* @return DefaultReturnValue
*
*/
int updateParameters( double temperature, double friction );
int updateParameters( double temperature, double friction, double stepSize );
/**
* Update
*
* @param positions atom positions
* @param velocities atom velocities
* @param forces atom forces
* @param brookShakeAlgorithm BrookShakeAlgorithm reference
*
* @return DefaultReturnValue
*
*/
int update( Stream& positions, Stream& velocities,
const Stream& forces, BrookShakeAlgorithm& brookShakeAlgorithm );
/**
* Get array of StochasticDynamics streams
*
......@@ -140,19 +171,14 @@ class BrookStochasticDynamics : public BrookCommon {
/*
* Setup of StochasticDynamics parameters
*
* @param atomParameters vector of OBC parameters [atomI][0=charge]
* [atomI][1=radius]
* [atomI][2=scaling factor]
* @param solventDielectric solvent dielectric
* @param soluteDielectric solute dielectric
* @param masses atom masses
* @param platform Brook platform
*
* @return nonzero value if error
* @return ErrorReturnValue value if error, else DefaultReturnValue
*
* */
int setup( const std::vector<std::vector<double> >& atomParameters,
double solventDielectric, double soluteDielectric, const Platform& platform );
int setup( const std::vector<double>& masses, const Platform& platform );
/*
* Get contents of object
......@@ -172,7 +198,7 @@ class BrookStochasticDynamics : public BrookCommon {
*
*/
BrookFloatStreamInternal* getSDPC1( void ) const;
BrookFloatStreamInternal* getSDPC1Stream( void ) const;
/**
* Get SDPC2 stream
......@@ -181,7 +207,7 @@ class BrookStochasticDynamics : public BrookCommon {
*
*/
BrookFloatStreamInternal* getSDPC2( void ) const;
BrookFloatStreamInternal* getSDPC2Stream( void ) const;
/**
* Get SD2X stream
......@@ -190,7 +216,7 @@ class BrookStochasticDynamics : public BrookCommon {
*
*/
BrookFloatStreamInternal* getSD2X( void ) const;
BrookFloatStreamInternal* getSD2XStream( void ) const;
/**
* Get SD1V stream
......@@ -199,7 +225,7 @@ class BrookStochasticDynamics : public BrookCommon {
*
*/
BrookFloatStreamInternal* getSD1V( void ) const;
BrookFloatStreamInternal* getSD1VStream( void ) const;
private:
......@@ -210,7 +236,7 @@ class BrookStochasticDynamics : public BrookCommon {
// streams indices
enum {
enum BrookStochasticDynamicsStreams {
SDPC1Stream,
SDPC2Stream,
SD2XStream,
......@@ -220,7 +246,7 @@ class BrookStochasticDynamics : public BrookCommon {
// randomNumberSeed
uint32_t _randomNumberSeed;
unsigned int _randomNumberSeed;
BrookOpenMMFloat _tau;
BrookOpenMMFloat _temperature;
......@@ -239,7 +265,8 @@ class BrookStochasticDynamics : public BrookCommon {
*
*/
std::string _getDerivedParametersString( BrookStochasticDynamics::DerivedParameters ) const;
//std::string _getDerivedParametersString( BrookStochasticDynamics::DerivedParameters ) const;
std::string _getDerivedParametersString( int id ) const;
/**
* Update derived parameters
......
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