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Commit d3614c8b authored by Mark Friedrichs's avatar Mark Friedrichs
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Added functionality to BrookRemoveCMMotionKernel' fixed problem w/ BrookVelocityCenterOfMassRemoval

parent e763e1cd
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Showing with 314 additions and 156 deletions
platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp
View file @ d3614c8b
......@@ -144,7 +144,7 @@ void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& veloc
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 ){
printf( "%s calling updateParameters\n", methodName.c_str() );
//printf( "%s calling updateParameters\n", methodName.c_str() );
_brookStochasticDynamics->updateParameters( temperature, friction, stepSize );
} else {
//printf( "%s NOT calling updateParameters\n", methodName.c_str() );
......
platforms/brook/src/BrookKernelFactory.cpp
View file @ d3614c8b
......@@ -35,6 +35,7 @@
#include "BrookIntegrateVerletStepKernel.h"
#include "BrookCalcKineticEnergyKernel.h"
#include "BrookCalcGBSAOBCForceFieldKernel.h"
#include "BrookRemoveCMMotionKernel.h"
using namespace OpenMM;
......@@ -70,7 +71,7 @@ KernelImpl* BrookKernelFactory::createKernelImpl( std::string name, const Platfo
// return new BrookIntegrateBrownianStepKernel( name, platform );
// Andersen thermostat
// Andersen thermostat
} else if( name == ApplyAndersenThermostatKernel::Name() ){
......@@ -82,6 +83,12 @@ KernelImpl* BrookKernelFactory::createKernelImpl( std::string name, const Platfo
return new BrookIntegrateLangevinStepKernel( name, platform );
// Remove com
} else if( name == RemoveCMMotionKernel::Name() ){
return new BrookRemoveCMMotionKernel( name, platform );
// KE calculator
} else if( name == CalcKineticEnergyKernel::Name() ){
......
platforms/brook/src/BrookPlatform.cpp
View file @ d3614c8b
......@@ -160,6 +160,7 @@ void BrookPlatform::_initializeKernelFactory( void ){
//registerKernelFactory( IntegrateBrownianStepKernel::Name(), factory);
//registerKernelFactory( ApplyAndersenThermostatKernel::Name(), factory);
registerKernelFactory( CalcKineticEnergyKernel::Name(), factory);
registerKernelFactory( RemoveCMMotionKernel::Name(), factory);
}
......
platforms/brook/src/BrookRemoveCMMotionKernel.cpp
View file @ d3614c8b
......@@ -52,6 +52,8 @@ BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel( std::string name, const Pl
// ---------------------------------------------------------------------------------------
_brookVelocityCenterOfMassRemoval = NULL;
}
/**
......@@ -67,6 +69,7 @@ BrookRemoveCMMotionKernel::~BrookRemoveCMMotionKernel( ){
// ---------------------------------------------------------------------------------------
delete _brookVelocityCenterOfMassRemoval;
}
/**
......@@ -84,11 +87,8 @@ void BrookRemoveCMMotionKernel::initialize( const vector<double>& masses ){
// ---------------------------------------------------------------------------------------
/*
this->masses.resize(masses.size());
for (size_t i = 0; i < masses.size(); ++i)
this->masses[i] = masses[i];
*/
_brookVelocityCenterOfMassRemoval = new BrookVelocityCenterOfMassRemoval();
_brookVelocityCenterOfMassRemoval->setup( masses, getPlatform() );
return;
......@@ -109,28 +109,7 @@ void BrookRemoveCMMotionKernel::execute( Stream& velocities ){
// ---------------------------------------------------------------------------------------
/*
RealOpenMM** velData = ((BrookFloatStreamImpl&) velocities.getImpl()).getData();
// Calculate the center of mass momentum.
RealOpenMM momentum[] = {0.0, 0.0, 0.0};
for (size_t i = 0; i < masses.size(); ++i) {
momentum[0] += static_cast<RealOpenMM>( masses[i]*velData[i][0] );
momentum[1] += static_cast<RealOpenMM>( masses[i]*velData[i][1] );
momentum[2] += static_cast<RealOpenMM>( masses[i]*velData[i][2] );
}
// Adjust the atom velocities.
momentum[0] /= static_cast<RealOpenMM>( masses.size() );
momentum[1] /= static_cast<RealOpenMM>( masses.size() );
momentum[2] /= static_cast<RealOpenMM>( masses.size() );
for (size_t i = 0; i < masses.size(); ++i) {
velData[i][0] -= static_cast<RealOpenMM>( momentum[0]/masses[i] );
velData[i][1] -= static_cast<RealOpenMM>( momentum[1]/masses[i] );
velData[i][2] -= static_cast<RealOpenMM>( momentum[2]/masses[i] );
}
*/
_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities );
return;
}
platforms/brook/src/BrookRemoveCMMotionKernel.h
View file @ d3614c8b
......@@ -33,6 +33,7 @@
* -------------------------------------------------------------------------- */
#include "kernels.h"
#include "BrookVelocityCenterOfMassRemoval.h"
namespace OpenMM {
......@@ -80,6 +81,7 @@ class BrookRemoveCMMotionKernel : public RemoveCMMotionKernel {
private:
BrookVelocityCenterOfMassRemoval* _brookVelocityCenterOfMassRemoval;
};
} // namespace OpenMM
......
platforms/brook/src/BrookShakeAlgorithm.cpp
View file @ d3614c8b
......@@ -331,19 +331,19 @@ int BrookShakeAlgorithm::_initializeStreams( const Platform& platform ){
_shakeStreams[ShakeXCons0Stream] = new BrookFloatStreamInternal( BrookCommon::ShakeXCons0Stream,
shakeConstraintStreamSize, shakeConstraintStreamWidth,
BrookStreamInternal::Float4, dangleValue );
BrookStreamInternal::Float3, dangleValue );
_shakeStreams[ShakeXCons1Stream] = new BrookFloatStreamInternal( BrookCommon::ShakeXCons1Stream,
shakeConstraintStreamSize, shakeConstraintStreamWidth,
BrookStreamInternal::Float4, dangleValue );
BrookStreamInternal::Float3, dangleValue );
_shakeStreams[ShakeXCons2Stream] = new BrookFloatStreamInternal( BrookCommon::ShakeXCons2Stream,
shakeConstraintStreamSize, shakeConstraintStreamWidth,
BrookStreamInternal::Float4, dangleValue );
BrookStreamInternal::Float3, dangleValue );
_shakeStreams[ShakeXCons3Stream] = new BrookFloatStreamInternal( BrookCommon::ShakeXCons3Stream,
shakeConstraintStreamSize, shakeConstraintStreamWidth,
BrookStreamInternal::Float4, dangleValue );
BrookStreamInternal::Float3, dangleValue );
_shakeStreams[ShakeInverseMapStream] = new BrookFloatStreamInternal( BrookCommon::ShakeInverseMapStream,
shakeAtomStreamSize, shakeAtomStreamWidth,
......@@ -402,6 +402,7 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
std::vector<double>::const_iterator distanceIterator = constraintLengths.begin();
int constraintIndex = 0;
_numberOfConstraints = 0;
while( atomIterator != constraintIndices.end() ){
std::vector<int> atomVector = *atomIterator;
......@@ -434,6 +435,21 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
}
}
// skip negative indices
if( atomIndex1 < 0 || atomIndex2 < 0 ){
atomIterator++;
distanceIterator++;
continue;
}
if( atomIndex1 >= (int) masses.size() || atomIndex2 >= (int) masses.size() ){
std::stringstream message;
message << methodName << " constraint indices=[" << atomIndex1 << ", " << atomIndex2 << "] greater than mass array size=" << masses.size();
throw OpenMMException( message.str() );
return ErrorReturnValue;
}
// insure heavy atom is first
if( masses[atomIndex1] < masses[atomIndex2] ){
......@@ -460,6 +476,7 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
atomIterator++;
distanceIterator++;
constraintIndex += 4;
_numberOfConstraints++;
}
// write entries to board
......
platforms/brook/src/BrookStochasticDynamics.cpp
View file @ d3614c8b
......@@ -91,8 +91,6 @@ BrookStochasticDynamics::BrookStochasticDynamics( ){
_randomNumberSeed = 1393;
_brookVelocityCenterOfMassRemoval = NULL;
//_randomNumberSeed = randomNumberSeed ? randomNumberSeed : 1393;
//SimTKOpenMMUtilities::setRandomNumberSeed( randomNumberSeed );
}
......@@ -116,8 +114,6 @@ BrookStochasticDynamics::~BrookStochasticDynamics( ){
delete[] _inverseSqrtMasses;
delete _brookVelocityCenterOfMassRemoval;
}
/**
......@@ -344,7 +340,7 @@ int BrookStochasticDynamics::updateParameters( double temperature, double fricti
if( showUpdate && getLog() && (showUpdate++ < maxShowUpdate) ){
std::string contents = getContentsString( );
(void) fprintf( getLog(), "%s contents %s", methodName, contents.c_str() );
(void) fprintf( getLog(), "%s contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
......@@ -403,11 +399,14 @@ int BrookStochasticDynamics::update( Stream& positions, Stream& velocities,
if( showAux ){
showAux = 0;
std::string contents = _brookVelocityCenterOfMassRemoval->getContentsString( );
(void) fprintf( getLog(), "%s VelocityCenterOfMassRemoval contents\n%s", methodName, contents.c_str() );
contents = brookRandomNumberGenerator.getContentsString( );
std::string contents = brookRandomNumberGenerator.getContentsString( );
(void) fprintf( getLog(), "%s RNG contents\n%s", methodName, contents.c_str() );
brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
contents = brookShakeAlgorithm.getContentsString( );
(void) fprintf( getLog(), "%s Shake contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
}
......@@ -612,8 +611,6 @@ int BrookStochasticDynamics::update( Stream& positions, Stream& velocities,
ksetStr3( getXPrimeStream()->getBrookStream(), positionStream.getBrookStream() );
}
_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities );
return DefaultReturnValue;
};
......@@ -1059,9 +1056,6 @@ int BrookStochasticDynamics::setup( const std::vector<double>& masses, const Pla
_setInverseSqrtMasses( masses );
_brookVelocityCenterOfMassRemoval = new BrookVelocityCenterOfMassRemoval();
_brookVelocityCenterOfMassRemoval->setup( masses, platform );
return DefaultReturnValue;
}
......
platforms/brook/src/BrookStochasticDynamics.h
View file @ d3614c8b
......@@ -38,7 +38,6 @@
#include "BrookFloatStreamInternal.h"
#include "BrookShakeAlgorithm.h"
#include "BrookRandomNumberGenerator.h"
#include "BrookVelocityCenterOfMassRemoval.h"
#include "BrookPlatform.h"
#include "BrookCommon.h"
......@@ -324,10 +323,6 @@ class BrookStochasticDynamics : public BrookCommon {
BrookOpenMMFloat* _inverseSqrtMasses;
// remove com
BrookVelocityCenterOfMassRemoval* _brookVelocityCenterOfMassRemoval;
// internal streams
BrookFloatStreamInternal* _sdStreams[LastStreamIndex];
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp
View file @ d3614c8b
......@@ -55,7 +55,7 @@ BrookVelocityCenterOfMassRemoval::BrookVelocityCenterOfMassRemoval( ){
// ---------------------------------------------------------------------------------------
_numberOfAtoms = -1;
_numberOfAtoms = -1;
// mark stream dimension variables as unset
......@@ -147,29 +147,102 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nBrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass";
static const char* methodName = "BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass";
static int debug = 0;
// static char* testName[2] = { "kCalculateLinearMomentum", "kRemoveLinearMomentum" };
// char fileName[128];
float zero = 0.0f;
float one = 1.0f;
static int debug = 0;
float zero = 0.0f;
// ---------------------------------------------------------------------------------------
if( debug && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocities, com );
(void) fprintf( getLog(), "\n%s Pre removal com: [%12.5e %12.5e %12.5e]\n", methodName, com[0], com[1], com[2] );
}
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
BrookStreamImpl& velocityStream = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
kCalculateLinearMomentum( getMassStream()->getBrookStream(), velocityStream.getBrookStream(), getWorkStream()->getBrookStream() );
kScale( zero, getLinearMomentumStream()->getBrookStream(), getLinearMomentumStream()->getBrookStream() );
kSumLinearMomentum( (float) getComAtomStreamWidth(), (float) getNumberOfAtoms(), getWorkStream()->getBrookStream(), getLinearMomentumStream()->getBrookStream() );
kScale( (float) getTotalInverseMass(), getLinearMomentumStream()->getBrookStream(), getLinearMomentumStream()->getBrookStream() );
kRemoveLinearMomentum( getLinearMomentumStream()->getBrookStream(), velocityStream.getBrookStream(), velocityStream.getBrookStream() );
if( (0 || debug) && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocities, com );
(void) fprintf( getLog(), "\n%s strW=%d iatm=%d Post removal com: [%12.5e %12.5e %12.5e]\n", methodName,
getComAtomStreamWidth(), getNumberOfAtoms(), com[0], com[1], com[2] );
/*
(void) fprintf( getLog(), "LM [%12.5e %12.5e %12.5e]\n", com[0], com[1], com[2] );
BrookStreamImpl& v1 = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (v1.getBrookStreamImpl());
void* velV = velocityStream->getData( 1 );
const float* vArray = (float*) velV;
void* w1 = getWorkStream()->getData( 1 );
const float* w2 = (float*) w1;
int index = 0;
for( int ii = 0; ii < getNumberOfAtoms(); ii++, index += 3 ){
(void) fprintf( getLog(), "V %d [%12.5e %12.5e %12.5e] [%12.5e %12.5e %12.5e]\n", ii,
vArray[index], vArray[index+1], vArray[index+2], w2[index], w2[index+1], w2[index+2] );
}
(void) fflush( getLog() );
*/
//exit(0);
}
return DefaultReturnValue;
}
/**
* Get velocity-COM
*
* @param velocities velocities
* @param velocityCom output velocity com
*
* @return DefaultReturnValue
*
*/
int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( Stream& velocities, BrookOpenMMFloat velocityCom[3] ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nBrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass";
static int debug = 0;
BrookOpenMMFloat zero = (BrookOpenMMFloat) 0.0;
// ---------------------------------------------------------------------------------------
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
BrookStreamImpl& v1 = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (v1.getBrookStreamImpl());
void* velV = velocityStream->getData( 1 );
const float* vArray = (float*) velV;
void* massV = getMassStream()->getData( 1);
const float* mArray = (float*) massV;
int numberOfAtoms = getNumberOfAtoms();
int index = 0;
velocityCom[0] = velocityCom[1] = velocityCom[2] = zero;
for( int ii = 0; ii < numberOfAtoms; ii++, index += 3 ){
velocityCom[0] += mArray[ii]*vArray[index];
velocityCom[1] += mArray[ii]*vArray[index+1];
velocityCom[2] += mArray[ii]*vArray[index+2];
}
return DefaultReturnValue;
}
......@@ -254,7 +327,7 @@ int BrookVelocityCenterOfMassRemoval::_initializeStreams( const Platform& platfo
_streams[WorkStream] = new BrookFloatStreamInternal( BrookCommon::BrookVelocityCenterOfMassRemovalWorkStream,
atomStreamSize, atomStreamWidth,
BrookStreamInternal::Float, dangleValue );
BrookStreamInternal::Float3, dangleValue );
_streams[MassStream] = new BrookFloatStreamInternal( BrookCommon::BrookVelocityCenterOfMassRemovalMassStream,
......@@ -263,14 +336,14 @@ int BrookVelocityCenterOfMassRemoval::_initializeStreams( const Platform& platfo
_streams[LinearMomentumStream] = new BrookFloatStreamInternal( "LinearMomentumStream",
1, 3, BrookStreamInternal::Float, dangleValue );
1, 1, BrookStreamInternal::Float3, dangleValue );
return DefaultReturnValue;
}
/**
* Set inverse masses
* Set masses & _totalInverseMass
*
* @param masses atomic masses
*
......@@ -287,36 +360,40 @@ int BrookVelocityCenterOfMassRemoval::_setMasses( const std::vector<double>& mas
// ---------------------------------------------------------------------------------------
// check that masses vector is not larger than expected
if( (int) masses.size() > getComAtomStreamSize() ){
std::stringstream message;
message << methodName << " mass array size=" << masses.size() << " is larger than stream size=" << getComAtomStreamSize();
throw OpenMMException( message.str() );
}
// setup masses
// setup inverse sqrt masses
BrookOpenMMFloat* inverseMasses = new BrookOpenMMFloat[getComAtomStreamSize()];
memset( inverseMasses, 0, sizeof( BrookOpenMMFloat )*getComAtomStreamSize() );
BrookOpenMMFloat* localMasses = new BrookOpenMMFloat[getComAtomStreamSize()];
memset( localMasses, 0, sizeof( BrookOpenMMFloat )*getComAtomStreamSize() );
int index = 0;
_totalInverseMass = (BrookOpenMMFloat) 0.0;
for( std::vector<double>::const_iterator ii = masses.begin(); ii != masses.end(); ii++, index++ ){
if( *ii != 0.0 ){
BrookOpenMMFloat value = static_cast<BrookOpenMMFloat>(*ii);
inverseMasses[index] = value;
localMasses[index] = value;
_totalInverseMass += value;
} else {
inverseMasses[index] = zero;
}
}
// 1/Sum[masses]
if( _totalInverseMass > zero ){
_totalInverseMass = one/_totalInverseMass;
}
_streams[MassStream]->loadFromArray( inverseMasses );
// write masses to board
_streams[MassStream]->loadFromArray( localMasses );
delete[] inverseMasses;
delete[] localMasses;
return DefaultReturnValue;
}
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.h
View file @ d3614c8b
......@@ -90,13 +90,9 @@ class BrookVelocityCenterOfMassRemoval : public BrookCommon {
int getComAtomStreamSize( void ) const;
/**
* Update
* Remove velocity center-of-mass
*
* @param positions atom positions
* @param velocities atom velocities
* @param forces atom forces
* @param brookShakeAlgorithm BrookShakeAlgorithm reference
* @param brookRandomNumberGenerator BrookRandomNumberGenerator reference
*
* @return DefaultReturnValue
*
......@@ -104,6 +100,18 @@ class BrookVelocityCenterOfMassRemoval : public BrookCommon {
int removeVelocityCenterOfMass( Stream& velocities );
/**
* Get velocity center-of-mass
*
* @param velocities atom velocities
* @param velocityCom output velocity com
*
* @return DefaultReturnValue
*
*/
int getVelocityCenterOfMass( Stream& velocities, BrookOpenMMFloat velocityCom[3] );
/*
* Setup of parameters
*
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ d3614c8b
......@@ -148,14 +148,14 @@ int BrookVerletDynamics::updateParameters( double stepSize ){
// ---------------------------------------------------------------------------------------
_setStepSize( (BrookOpenMMFloat) stepSize );
_setStepSize( (BrookOpenMMFloat) stepSize );
_updateVerletStreams( );
// show update
if( showUpdate && getLog() && (showUpdate++ < maxShowUpdate) ){
std::string contents = getContentsString( );
(void) fprintf( getLog(), "%s contents %s", methodName, contents.c_str() );
(void) fprintf( getLog(), "%s contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
......@@ -189,7 +189,7 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
static const char* methodName = "\nBrookVerletDynamics::update";
static const int PrintOn = 1;
static const int PrintOn = 0;
// ---------------------------------------------------------------------------------------
......@@ -198,10 +198,26 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
const BrookStreamImpl& forceStreamC = dynamic_cast<const BrookStreamImpl&> (forces.getImpl());
BrookStreamImpl& forceStream = const_cast<BrookStreamImpl&> (forceStreamC);
if( PrintOn && getLog() ){
if( (1 || PrintOn) && getLog() ){
static int showAux = 1;
(void) fprintf( getLog(), "%s shake=%d\n", methodName, brookShakeAlgorithm.getNumberOfConstraints() );
(void) fflush( getLog() );
if( showAux ){
showAux = 0;
/*
std::string contents = _brookVelocityCenterOfMassRemoval->getContentsString( );
(void) fprintf( getLog(), "%s VelocityCenterOfMassRemoval contents\n%s", methodName, contents.c_str() );
*/
std::string contents = brookShakeAlgorithm.getContentsString( );
(void) fprintf( getLog(), "%s Shake contents\n%s", methodName, contents.c_str() );
(void) fflush( getLog() );
}
}
// integration step
......@@ -243,6 +259,7 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
// second Shake step
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
10.0f,
(float) getVerletDynamicsAtomStreamWidth(),
......@@ -257,6 +274,38 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
brookShakeAlgorithm.getShakeXCons2Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream() );
if( (1|| PrintOn) && getLog() ){
(void) fprintf( getLog(), "\nPost kshakeh_fix1: atomStrW=%3d invMass_H=%.5f",
getVerletDynamicsAtomStreamWidth(), brookShakeAlgorithm.getInverseHydrogenMass() );
(void) fprintf( getLog(), "\nShakeAtomIndicesStream\n" );
brookShakeAlgorithm.getShakeAtomIndicesStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeAtomParameterStream\n" );
brookShakeAlgorithm.getShakeAtomParameterStream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons0\n" );
brookShakeAlgorithm.getShakeXCons0Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons1\n" );
brookShakeAlgorithm.getShakeXCons1Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons2\n" );
brookShakeAlgorithm.getShakeXCons2Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons3\n" );
brookShakeAlgorithm.getShakeXCons3Stream()->printToFile( getLog() );
}
// second Shake gather
kshakeh_update2_fix1(
......@@ -270,11 +319,42 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream(),
positionStream.getBrookStream() );
if( ( 1 || PrintOn) && getLog() ){
(void) fprintf( getLog(), "\nPost kshakeh_update2_fix1: atomStrW=%3d",
getVerletDynamicsAtomStreamWidth() );
(void) fprintf( getLog(), "\nShakeInverseMapStream\n" );
brookShakeAlgorithm.getShakeInverseMapStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons0\n" );
brookShakeAlgorithm.getShakeXCons0Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons1\n" );
brookShakeAlgorithm.getShakeXCons1Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons2\n" );
brookShakeAlgorithm.getShakeXCons2Stream()->printToFile( getLog() );
(void) fprintf( getLog(), "\nShakeXCons3\n" );
brookShakeAlgorithm.getShakeXCons3Stream()->printToFile( getLog() );
}
} else {
//kadd3( getXPrimeStream()->getBrookStream(), positionStream.getBrookStream() );
ksetStr3( getXPrimeStream()->getBrookStream(), positionStream.getBrookStream() );
}
//_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities );
return DefaultReturnValue;
};
......
platforms/brook/src/gpu/kshakeh.br
View file @ d3614c8b
......@@ -193,13 +193,13 @@ kshakeh_fix1(
float invmH, //inverse mass of hydrogen
float omega, //parameter from gromacs, possibly unused
float4 atoms<>, //heavy0, h1, h2, h3
float4 posq[][], //positions before update
float4 posqp[][], //changes to positions
float3 posq[][], //positions before update
float3 posqp[][], //changes to positions
float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
out float4 cposq0<>, //constrained position for heavy atom
out float4 cposq1<>, //ditto for h1
out float4 cposq2<>, //ditto for h2
out float4 cposq3<> //ditto for h3
out float3 cposq0<>, //constrained position for heavy atom
out float3 cposq1<>, //ditto for h1
out float3 cposq2<>, //ditto for h2
out float3 cposq3<> //ditto for h3
) {
float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
float i; //iteration count
......@@ -246,16 +246,15 @@ kshakeh_fix1(
mask3 = 0.0f;
}
cposq0 = posq[ai];
cposq1 = posq[aj1];
cposq2 = posq[aj2];
cposq3 = posq[aj3];
xi = cposq0.xyz;
xj1 = cposq1.xyz;
xj2 = cposq2.xyz;
xj3 = cposq3.xyz;
xi = cposq0;
xj1 = cposq1;
xj2 = cposq2;
xj3 = cposq3;
rij1 = xi - xj1;
rij2 = xi - xj2;
......@@ -270,17 +269,17 @@ kshakeh_fix1(
ld3 = params.z - rij3sq;
/*
xpi = posqp[ai].xyz;
xpj1 = posqp[aj1].xyz;
xpj2 = posqp[aj2].xyz;
xpj3 = posqp[aj3].xyz;
xpi = posqp[ai];
xpj1 = posqp[aj1];
xpj2 = posqp[aj2];
xpj3 = posqp[aj3];
*/
xpi = posqp[ai].xyz - xi;
xpj1 = posqp[aj1].xyz - xj1;
xpj2 = posqp[aj2].xyz - xj2;
xpj3 = posqp[aj3].xyz - xj3;
xpi = posqp[ai] - xi;
xpj1 = posqp[aj1] - xj1;
xpj2 = posqp[aj2] - xj2;
xpj3 = posqp[aj3] - xj3;
// XXX
......@@ -342,10 +341,10 @@ kshakeh_fix1(
}
//Output modified delta's
cposq0.xyz = xpi;
cposq1.xyz = xpj1;
cposq2.xyz = xpj2;
cposq3.xyz = xpj3;
cposq0 = xpi;
cposq1 = xpj1;
cposq2 = xpj2;
cposq3 = xpj3;
}
......@@ -356,13 +355,13 @@ kshakeh_fix2(
float invmH, //inverse mass of hydrogen
float omega, //parameter from gromacs, possibly unused
float4 atoms<>, //heavy0, h1, h2, h3
float4 posq[][], //positions before update
float4 posqp[][], //changes to positions
float3 posq[][], //positions before update
float3 posqp[][], //changes to positions
float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
out float4 cposq0<>, //constrained position for heavy atom
out float4 cposq1<>, //ditto for h1
out float4 cposq2<>, //ditto for h2
out float4 cposq3<> //ditto for h3
out float3 cposq0<>, //constrained position for heavy atom
out float3 cposq1<>, //ditto for h1
out float3 cposq2<>, //ditto for h2
out float3 cposq3<> //ditto for h3
) {
float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
float i; //iteration count
......@@ -415,10 +414,10 @@ kshakeh_fix2(
cposq2 = posq[aj2];
cposq3 = posq[aj3];
xi = cposq0.xyz;
xj1 = cposq1.xyz;
xj2 = cposq2.xyz;
xj3 = cposq3.xyz;
xi = cposq0;
xj1 = cposq1;
xj2 = cposq2;
xj3 = cposq3;
rij1 = xi - xj1;
rij2 = xi - xj2;
......@@ -432,17 +431,17 @@ kshakeh_fix2(
ld2 = params.z - rij2sq;
ld3 = params.z - rij3sq;
xpi = posqp[ai].xyz;
xpj1 = posqp[aj1].xyz;
xpj2 = posqp[aj2].xyz;
xpj3 = posqp[aj3].xyz;
xpi = posqp[ai];
xpj1 = posqp[aj1];
xpj2 = posqp[aj2];
xpj3 = posqp[aj3];
/*
xpi = posqp[ai].xyz - xi;
xpj1 = posqp[aj1].xyz - xj1;
xpj2 = posqp[aj2].xyz - xj2;
xpj3 = posqp[aj3].xyz - xj3;
xpi = posqp[ai] - xi;
xpj1 = posqp[aj1] - xj1;
xpj2 = posqp[aj2] - xj2;
xpj3 = posqp[aj3] - xj3;
*/
......@@ -505,10 +504,10 @@ kshakeh_fix2(
}
//Output modified delta's
cposq0.xyz = xpi;
cposq1.xyz = xpj1;
cposq2.xyz = xpj2;
cposq3.xyz = xpj3;
cposq0 = xpi;
cposq1 = xpj1;
cposq2 = xpj2;
cposq3 = xpj3;
}
......@@ -518,12 +517,12 @@ kshakeh_fix2(
kernel void kshakeh_update1_fix1Old(
float strwidth, //width of cposq streams
float2 invmap<>, //shakeh inverse map
float4 posq<>, //constrained deltas
float4 cposq0[][], //constrained delta for heavy atom
float4 cposq1[][], //ditto for h1
float4 cposq2[][], //ditto for h2
float4 cposq3[][], //ditto for h3
out float4 oposq<> //updated deltas
float3 posq<>, //constrained deltas
float3 cposq0[][], //constrained delta for heavy atom
float3 cposq1[][], //ditto for h1
float3 cposq2[][], //ditto for h2
float3 cposq3[][], //ditto for h3
out float3 oposq<> //updated deltas
){
float2 atom;
......@@ -546,13 +545,13 @@ kernel void kshakeh_update1_fix1Old(
kernel void kshakeh_update2_fix1(
float strwidth, //width of cposq streams
float2 invmap<>, //shakeh inverse map
float4 posq<>, //old positions
float4 posqp<>, //deltas from sd2
float4 cposq0[][], //constrained delta for heavy atom
float4 cposq1[][], //ditto for h1
float4 cposq2[][], //ditto for h2
float4 cposq3[][], //ditto for h3
out float4 oposq<> //updated deltas
float3 posq<>, //old positions
float3 posqp<>, //deltas from sd2
float3 cposq0[][], //constrained delta for heavy atom
float3 cposq1[][], //ditto for h1
float3 cposq2[][], //ditto for h2
float3 cposq3[][], //ditto for h3
out float3 oposq<> //updated deltas
){
float2 atom;
......@@ -561,8 +560,7 @@ kernel void kshakeh_update2_fix1(
atom.x = invmap.x - atom.y * strwidth;
if ( invmap.y < 0 ){
oposq.w = posq.w;
oposq.xyz = posqp.xyz - posq.xyz;
oposq = posqp - posq;
} else if ( invmap.y < 0.5f )
oposq = cposq0[ atom ];
else if ( invmap.y < 1.5f)
......@@ -572,21 +570,21 @@ kernel void kshakeh_update2_fix1(
else if ( invmap.y < 3.5f )
oposq = cposq3[ atom ];
oposq.xyz += posq.xyz;
oposq += posq;
}
kernel void kshakeh_update1_fix1(
float strwidth, //width of cposq streams
float sdFactor,
float2 invmap<>, //shakeh inverse map
float4 posq<>, //old positions
float4 posqp<>, //deltas from sd2
float3 posq<>, //old positions
float3 posqp<>, //deltas from sd2
float3 vp<>, //deltas from sd2
float4 cposq0[][], //constrained delta for heavy atom
float4 cposq1[][], //ditto for h1
float4 cposq2[][], //ditto for h2
float4 cposq3[][], //ditto for h3
out float4 oposq<> //updated deltas
float3 cposq0[][], //constrained delta for heavy atom
float3 cposq1[][], //ditto for h1
float3 cposq2[][], //ditto for h2
float3 cposq3[][], //ditto for h3
out float3 oposq<> //updated deltas
){
float2 atom;
......@@ -598,12 +596,12 @@ kernel void kshakeh_update1_fix1(
if ( invmap.y < 0 ){
oposq = posqp;
} else if ( invmap.y < 0.5f )
oposq.xyz += cposq0[ atom ].xyz;
oposq += cposq0[ atom ];
else if ( invmap.y < 1.5f )
oposq.xyz += cposq1[ atom ].xyz;
oposq += cposq1[ atom ];
else if ( invmap.y < 2.5f )
oposq.xyz += cposq2[ atom ].xyz;
oposq += cposq2[ atom ];
else if ( invmap.y < 3.5f )
oposq.xyz += cposq3[ atom ].xyz;
oposq += cposq3[ atom ];
}
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