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Commit e3a1a218 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Mods

parent 60dd93a8
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Showing with 605 additions and 266 deletions
platforms/brook/src/BrookBonded.cpp
View file @ e3a1a218
......@@ -1911,7 +1911,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
/*
(void) fprintf( log, "\nNB1 forces" );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
*/
......@@ -2036,7 +2036,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
if( printOn ){
(void) fprintf( log, "%s Post 3_4/3_5 forces\n", methodName.c_str() );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
}
......@@ -2103,7 +2103,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
if( printOn ){
(void) fprintf( log, "%s Final forces", methodName.c_str() );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
}
......
platforms/brook/src/BrookBrownianDynamics.cpp
View file @ e3a1a218
......@@ -448,13 +448,13 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
//StreamImpl& positionStreamImpl = positionStream.getImpl();
//const BrookStreamImpl brookPositions = dynamic_cast<BrookStreamImpl&> (positionStreamImpl);
/*
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
*/
double forceSum[3];
BrookStreamInternal* brookStreamInternalFF = forceStream.getBrookStreamImpl();
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] );
......@@ -468,7 +468,7 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
*/
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
}
......@@ -499,12 +499,12 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
//StreamImpl& positionStreamImpl = positionStream.getImpl();
//const BrookStreamImpl brookPositions = dynamic_cast<BrookStreamImpl&> (positionStreamImpl);
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nForceStream\n" );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
......@@ -557,14 +557,14 @@ fprintf( stderr, "\nBrownian shake off!!\n" );
(void) fprintf( getLog(), "\nPost kupdate_bd:\n" );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
......@@ -587,11 +587,11 @@ fprintf( stderr, "\nBrownian shake off!!\n" );
(void) fprintf( getLog(), "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nPositionStream\n" );
brookStreamInternalPos->printToFile( getLog() );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( getLog(), "\nVelocityStream\n" );
brookStreamInternalVel->printToFile( getLog() );
......
platforms/brook/src/BrookCommon.cpp
View file @ e3a1a218
......@@ -92,6 +92,7 @@ const std::string BrookCommon::ShakeInverseMapStream
// Random number streams
const std::string BrookCommon::ShuffleStream = "ShuffleStream";
const std::string BrookCommon::RandomValuesStream = "RandomValuesStream";
// Random number streams
......
platforms/brook/src/BrookCommon.h
View file @ e3a1a218
......@@ -107,6 +107,7 @@ class BrookCommon {
// Random number generator streams
static const std::string ShuffleStream;
static const std::string RandomValuesStream;
// BrookVelocityCenterOfMassRemoval streams
......
platforms/brook/src/BrookGbsa.cpp
View file @ e3a1a218
......@@ -965,7 +965,7 @@ void BrookGbsa::computeForces( BrookStreamImpl& positionStream, BrookStreamImpl&
getParticleStreamWidth( ),
getPartialForceStreamWidth( ) );
BrookStreamInternal* brookStreamInternalF = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream\n" );
brookStreamInternalF->printToFile( log );
......@@ -1006,7 +1006,7 @@ void BrookGbsa::computeForces( BrookStreamImpl& positionStream, BrookStreamImpl&
getParticleStreamWidth( ),
getPartialForceStreamWidth( ) );
BrookStreamInternal* brookStreamInternalF = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream\n" );
brookStreamInternalF->printToFile( log );
......@@ -1060,7 +1060,7 @@ void BrookGbsa::computeForces( BrookStreamImpl& positionStream, BrookStreamImpl&
getSoluteDielectric(),
getSolventDielectric(), includeAceTerm );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPost kObcLoop1 PositionStream\n" );
brookStreamInternalPos->printToFile( log );
......@@ -1167,7 +1167,7 @@ void BrookGbsa::computeForces( BrookStreamImpl& positionStream, BrookStreamImpl&
getParticleStreamWidth( ),
getPartialForceStreamWidth( ) );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPost kObcLoop2: PositionStream\n" );
brookStreamInternalPos->printToFile( log );
......@@ -1230,7 +1230,7 @@ void BrookGbsa::computeForces( BrookStreamImpl& positionStream, BrookStreamImpl&
gbsaForceStreams[ii]->printToFile( log );
}
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
(void) fprintf( log, "\nPost kPostObcLoop2_nobranch: ForceStream\n" );
brookStreamInternalF->printToFile( log );
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ e3a1a218
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* -i------------------------------------------------------------------------- *
* 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 *
......@@ -727,11 +727,32 @@ int BrookLangevinDynamics::_updateSdStreams( void ){
memset( sd2x, 0, 3*sdParticleStreamSize*sizeof( BrookOpenMMFloat ) );
index = 0;
int useFixedRandomValue = 0;
if( useFixedRandomValue ){
// diagnostics only!
BrookOpenMMFloat fixedRandomValue = static_cast<BrookOpenMMFloat>( 0.1 );
for( int ii = 0; ii < numberOfParticles; ii++, index += 3 ){
BrookOpenMMFloat value = _inverseSqrtMasses[ii]*derivedParameters[X]*fixedRandomValue;
sd2x[index] = value;
sd2x[index+1] = value;
sd2x[index+2] = value;
}
// print message letting user know non-random value being used
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s using fixed 'random value'=%.3f to initialize sd2x\n", methodName.c_str(), fixedRandomValue );
} else {
for( int ii = 0; ii < numberOfParticles; 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()) );
}
}
_sdStreams[SD2XStream]->loadFromArray( sd2x );
......@@ -837,18 +858,24 @@ float BrookLangevinDynamics::getTemperature( BrookStreamInternal* velocities, Br
float ke = 0.0f;
int index = 0;
for( int ii = 0; ii < getNumberOfParticles(); ii++ ){
int numberOfParticles = getNumberOfParticles();
for( int ii = 0; ii < numberOfParticles; ii++, index += 3 ){
ke += (velocitiesI[index]*velocitiesI[index] + velocitiesI[index+1]*velocitiesI[index+1] + velocitiesI[index+2]*velocitiesI[index+2] )/inverseMassStreamI[ii];
//(void) fprintf( stderr, "%s %d Velocities[%14.5e %14.5e %14.5e]\n", methodName.c_str(), index/3, velocitiesI[index], velocitiesI[index+1], velocitiesI[index+2] );
index += 3;
/*
if( ii < 3 || ii >= (numberOfParticles - 3) ){
(void) fprintf( stderr, "%s %6d m=%14.5e v[%14.5e %14.5e %14.5e]\n", methodName.c_str(), ii, 1.0/inverseMassStreamI[ii],
velocitiesI[index], velocitiesI[index+1], velocitiesI[index+2] );
} */
}
int degreesOfFreedom = 3*getNumberOfParticles() - numberOfConstraints;
float denominator = 1.0f/( ((float) BOLTZ)*((float) ( degreesOfFreedom )) );
//(void) fprintf( stderr, "%s ke=%.5e T=%.3f dof=%d\n", methodName.c_str(), ke, (ke*denominator), degreesOfFreedom );
ke *= denominator;
(void) fprintf( stderr, "%s ke=%.5e dof=%d\n", methodName.c_str(), ke, degreesOfFreedom );
ke /= ((float) BOLTZ)*((float) ( degreesOfFreedom ));
return 0.5f*ke;
return ke;
}
/**
......@@ -930,6 +957,41 @@ int BrookLangevinDynamics::removeCom( BrookStreamInternal* velocities, BrookFloa
return DefaultReturnValue;
}
/**
* Reset velocities (diagnostics)
*
* @param velocities velocities
*
* @return DefaultReturnValue
*/
int BrookLangevinDynamics::resetVelocities( BrookStreamInternal* velocities ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookLangevinDynamics::resetVelocities";
// ---------------------------------------------------------------------------------------
(void) fprintf( stderr, "%s\n", methodName.c_str() ); fflush( stderr );
// resset v to determinisitic values
double* newVelocities = new double[velocities->getStreamSize()*velocities->getWidth()];
memset( newVelocities, 0, sizeof( double )*velocities->getStreamSize()*velocities->getWidth() );
for( int ii = 1; ii <= 3*getNumberOfParticles(); ii++ ){
int jj = ii % 10;
double sign = jj % 2 ? 0.1 : -0.1;
newVelocities[ii-1] = sign*( (double) jj);
}
velocities->loadFromArray( newVelocities );
delete[] newVelocities;
return DefaultReturnValue;
}
/*
* Get contents of object
*
......@@ -1031,14 +1093,14 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nBrookLangevinDynamics::update";
int printOn = 1;
int printOn = 0;
FILE* log;
// ---------------------------------------------------------------------------------------
_internalStepCount++;
// setLog( stderr );
//setLog( stderr );
if( printOn && getLog() ){
log = getLog();
......@@ -1075,13 +1137,34 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
}
}
if( 1 || (_internalStepCount % 10) == 0 ){
if( 0 && _internalStepCount == 1 ){
//resetVelocities( velocityStream.getBrookStreamInternal() );
std::string velocityFileName = "kupdate_sd1_strV.in";
std::string rvName0 = "kupdate_sd1_0.fgauss.in";
std::string rvName1 = "kupdate_sd1_1.fgauss.in";
std::string sd2xName = "kupdate_sd1_strSD2X.in";
velocityStream.getBrookStreamInternal()->loadStreamGivenFileName( velocityFileName );
brookRandomNumberGenerator.getRandomNumberStream( 0 )->loadStreamGivenFileName( rvName0 );
brookRandomNumberGenerator.getRandomNumberStream( 1 )->loadStreamGivenFileName( rvName1 );
getSD2XStream()->loadStreamGivenFileName( sd2xName );
}
if( 0 && (_internalStepCount % 10) == 0 ){
FILE* log1 = stderr;
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamImpl();
(void) fprintf( log1, "\nVelocityStream %d XX\n", _internalStepCount ); fflush( log1 );
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamInternal();
float temperature = getTemperature( brookStreamInternalPos, getInverseMassStream(), brookShakeAlgorithm.getNumberOfConstraints() );
// removeCom( brookStreamInternalPos, getInverseMassStream() );
float temperaturePost = getTemperature( brookStreamInternalPos, getInverseMassStream(), brookShakeAlgorithm.getNumberOfConstraints() );
(void) fprintf( log1, "\nVelocityStream %d Tp=%.3f %.3f\n", _internalStepCount, temperature, temperaturePost );
(void) fprintf( log1, "\n%s step=%d Post kupdate_sd1_fix1: particleStrW=%3d rngStrW=%3d rngOff=%5d "
"EM=%12.5e Sd1pc[]=[%12.5e %12.5e %12.5e]", methodName.c_str(), _internalStepCount,
getLangevinDynamicsParticleStreamWidth(),
brookRandomNumberGenerator.getRandomNumberStreamWidth(),
brookRandomNumberGenerator.getRvStreamOffset(),
derivedParameters[EM], derivedParameters[Sd1pc1], derivedParameters[Sd1pc2], derivedParameters[Sd1pc3] );
(void) fprintf( log1, "\nRvStreamIndex=%d step=%d\n", brookRandomNumberGenerator.getRvStreamIndex(), _internalStepCount );
fflush( log1 );
}
// first integration step
......@@ -1103,8 +1186,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
getInverseMassStream()->getBrookStream(),
getSD1VStream()->getBrookStream(),
getVPrimeStream()->getBrookStream(),
getXPrimeStream()->getBrookStream()
);
getXPrimeStream()->getBrookStream() );
// diagnostics
......@@ -1117,38 +1199,46 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
derivedParameters[EM], derivedParameters[Sd1pc1], derivedParameters[Sd1pc2], derivedParameters[Sd1pc3] );
if( _internalStepCount == 1 ){
(void) fprintf( log, "\nSDPC1Stream %d\n", _internalStepCount );
(void) fprintf( log, "\nSDPC1Stream fixed input sd1 step=%d\n", _internalStepCount );
getSDPC1Stream()->printToFile( log );
(void) fprintf( log, "\nSD2XStream %d\n", _internalStepCount );
(void) fprintf( log, "\nSD2XStream fixed input sd1 step=%d\n", _internalStepCount );
getSD2XStream()->printToFile( log );
(void) fprintf( log, "\nInverseMassStream %d\n", _internalStepCount );
(void) fprintf( log, "\nInverseMassStream fixed input sd1 step=%d\n", _internalStepCount );
getInverseMassStream()->printToFile( log );
}
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream input sd1 step=%d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
(void) fprintf( log, "\nForceStream %d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
(void) fprintf( log, "\nForceStream input sd1 step=%d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
BrookStreamInternal* brookStreamInternalV = velocityStream.getBrookStreamImpl();
(void) fprintf( log, "\nVelocityStream %d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalV = velocityStream.getBrookStreamInternal();
(void) fprintf( log, "\nVelocityStream input sd1 step=%d\n", _internalStepCount );
brookStreamInternalV->printToFile( log );
(void) fprintf( log, "\nSD1VStream %d\n", _internalStepCount );
(void) fprintf( log, "\nSD1VStream output sd1 step=%d\n", _internalStepCount );
getSD1VStream()->printToFile( log );
(void) fprintf( log, "\nVPrimeStream %d\n", _internalStepCount );
(void) fprintf( log, "\nVPrimeStream output sd1 step=%d\n", _internalStepCount );
getVPrimeStream()->printToFile( log );
(void) fprintf( log, "\nXPrimeStream %d\n", _internalStepCount );
(void) fprintf( log, "\nXPrimeStream output sd1 step=%d\n", _internalStepCount );
getXPrimeStream()->printToFile( log );
if( _internalStepCount == 1 ){
std::vector<BrookStreamInternal*> streams;
streams.push_back( brookStreamInternalPos );
streams.push_back( getXPrimeStream() );
std::stringstream fileNameBaseS;
fileNameBaseS << "Brook_Sd1PreShk_" << _internalStepCount << ".txt";
BrookStreamInternal::printStreamsToFile( fileNameBaseS.str(), streams );
}
(void) fprintf( log, "\nRvStreamIndex=%d step=%d\n", brookRandomNumberGenerator.getRvStreamIndex(), _internalStepCount );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log );
}
......@@ -1186,35 +1276,45 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream(),
getXPrimeStream()->getBrookStream() );
if( 0 && printOn ){
if( printOn ){
(void) fprintf( log, "\n%s Post kshakeh_update2_fix1: ShakeConstraintStreamWidth=%3d",
methodName.c_str(), brookShakeAlgorithm.getShakeConstraintStreamWidth() );
(void) fprintf( log, "\n%s Post kshakeh_update1: sw=%d ShkCnstStrW=%3d tol=%.3f maxIt=%d",
methodName.c_str(), getLangevinDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getShakeConstraintStreamWidth(),
brookShakeAlgorithm.getShakeTolerance(), brookShakeAlgorithm.getMaxIterations() );
if( _internalStepCount == 1 ){
(void) fprintf( log, "\nShakeInverseMapStream %d\n" );
(void) fprintf( log, "\nShakeInverseMapStream fixed input sd shake1 at step=%d\n" );
brookShakeAlgorithm.getShakeInverseMapStream()->printToFile( log );
}
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream input sd shake1 at step=%d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
(void) fprintf( log, "\nXPrimeStream %d\n", _internalStepCount );
(void) fprintf( log, "\nXPrimeStream output sd shake1 at step=%d\n", _internalStepCount );
getXPrimeStream()->printToFile( log );
(void) fprintf( log, "\nShakeXCons0 %d\n", _internalStepCount );
(void) fprintf( log, "\nShakeXCons0 output sd shake1 at step=%d\n", _internalStepCount );
brookShakeAlgorithm.getShakeXCons0Stream()->printToFile( log );
(void) fprintf( log, "\nShakeXCons1 %d\n", _internalStepCount );
(void) fprintf( log, "\nShakeXCons1 output sd shake1 at step=%d\n", _internalStepCount );
brookShakeAlgorithm.getShakeXCons1Stream()->printToFile( log );
(void) fprintf( log, "\nShakeXCons2 %d\n", _internalStepCount );
(void) fprintf( log, "\nShakeXCons2 output sd shake1 at step=%d\n", _internalStepCount );
brookShakeAlgorithm.getShakeXCons2Stream()->printToFile( log );
(void) fprintf( log, "\nShakeXCons3 %d\n", _internalStepCount );
(void) fprintf( log, "\nShakeXCons3 output sd shake1 at step=%d\n", _internalStepCount );
brookShakeAlgorithm.getShakeXCons3Stream()->printToFile( log );
if( _internalStepCount < 2 ){
std::vector<BrookStreamInternal*> streams;
streams.push_back( brookStreamInternalPos );
streams.push_back( getXPrimeStream() );
std::stringstream fileNameBaseS;
fileNameBaseS << "Brook_Sd1PostShk_" << _internalStepCount << ".txt";
BrookStreamInternal::printStreamsToFile( fileNameBaseS.str(), streams );
}
}
}
......@@ -1248,31 +1348,40 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
brookRandomNumberGenerator.getRvStreamOffset(),
derivedParameters[Sd2pc1], derivedParameters[Sd2pc2] );
(void) fprintf( log, "\nSDPC2Stream %d \n", _internalStepCount );
(void) fprintf( log, "\nSDPC2Stream input sd2 step=%d\n", _internalStepCount );
getSDPC2Stream()->printToFile( log );
(void) fprintf( log, "\nSD2XStream %d \n", _internalStepCount );
(void) fprintf( log, "\ngetSD1VStream input sd2 step=%d\n", _internalStepCount );
getSD1VStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
(void) fprintf( log, "\nPositionStream %d \n", _internalStepCount );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream input sd2 step=%d \n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
(void) fprintf( log, "\nVPrimeStream %d \n", _internalStepCount );
(void) fprintf( log, "\nVPrimeStream input sd2 step=%d\n", _internalStepCount );
getVPrimeStream()->printToFile( log );
(void) fprintf( log, "\nXPrimeStream %d \n", _internalStepCount );
(void) fprintf( log, "\nXPrimeStream output sd2 step=%d\n", _internalStepCount );
getXPrimeStream()->printToFile( log );
(void) fprintf( log, "\nSD2XStream %d \n", _internalStepCount );
(void) fprintf( log, "\nSD2XStream output sd2 step=%d\n", _internalStepCount );
getSD2XStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamImpl();
(void) fprintf( log, "\nVelocityStream %d \n", _internalStepCount );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
(void) fprintf( log, "\nVelocityStream output sd2 step=%d\n", _internalStepCount );
brookStreamInternalVel->printToFile( log );
(void) fprintf( log, "\nRvStreamIndex=%d step=%d\n", brookRandomNumberGenerator.getRvStreamIndex(), _internalStepCount );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log );
if( _internalStepCount < 3 ){
std::vector<BrookStreamInternal*> streams;
streams.push_back( brookStreamInternalVel );
streams.push_back( getXPrimeStream() );
std::stringstream fileNameBaseS;
fileNameBaseS << "Brook_Sd2Out_" << _internalStepCount << ".txt";
BrookStreamInternal::printStreamsToFile( fileNameBaseS.str(), streams );
}
}
// advance random number cursor
......@@ -1319,12 +1428,12 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
brookRandomNumberGenerator.getRvStreamOffset(),
derivedParameters[Sd2pc1], derivedParameters[Sd2pc2] );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
brookShakeAlgorithm.checkConstraints( brookStreamInternalPos, log, 0.0001f );
(void) fprintf( log, "\nPositionStream\n" );
(void) fprintf( log, "\nPositionStream output sd shake2 step=%d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
std::vector<std::vector<double> > forceStatistics;
brookStreamInternalF->getStatistics( forceStatistics, getNumberOfParticles() );
......@@ -1334,7 +1443,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
(void) fprintf( log, "\nStep %d Force stats:\n%s", _internalStepCount, stats.c_str() );
brookStreamInternalF->printToFile( log );
brookStreamInternalPos = velocityStream.getBrookStreamImpl();
brookStreamInternalPos = velocityStream.getBrookStreamInternal();
std::vector<std::vector<double> > velocityStatistics;
brookStreamInternalPos->getStatistics( velocityStatistics, getNumberOfParticles() );
std::stringstream tagV;
......@@ -1345,7 +1454,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
(void) fprintf( log, "\nVelocityStream %d T=%.3f\n", _internalStepCount, temperature );
brookStreamInternalPos->printToFile( log );
(void) fprintf( log, "\nXPrimeStream\n" );
(void) fprintf( log, "\nXPrimeStream input sd shake2 step=%d\n", _internalStepCount );
getXPrimeStream()->printToFile( log );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log );
......@@ -1360,7 +1469,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// (void) fprintf( log, "\nXPrimeStream\n" );
// getXPrimeStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream\n" );
brookStreamInternalPos->printToFile( log );
}
......@@ -1376,7 +1485,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
(void) fprintf( log, "\nXPrimeStream\n" );
getXPrimeStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream\n" );
brookStreamInternalPos->printToFile( log );
......@@ -1384,15 +1493,17 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
}
}
if( (_internalStepCount % 10) == 0 ){
if( (_internalStepCount % 400) == 0 ){
FILE* log1 = stderr;
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamInternal();
/*
std::vector<std::vector<double> > velocityStatistics;
brookStreamInternalPos->getStatistics( velocityStatistics, getNumberOfParticles() );
std::stringstream tagV;
tagV << _internalStepCount << " Vxx ";
std::string stats = brookStreamInternalPos->printStatistics( tagV.str(), velocityStatistics );
(void) fprintf( log1, "\nStep %d Velocity stats:\n%s", _internalStepCount, stats.c_str() );
*/
float temperature = getTemperature( brookStreamInternalPos, getInverseMassStream(), brookShakeAlgorithm.getNumberOfConstraints() );
//removeCom( brookStreamInternalPos, getInverseMassStream() );
(void) fprintf( log1, "\nVelocityStream %d T=%.3f\n", _internalStepCount, temperature );
......
platforms/brook/src/BrookLangevinDynamics.h
View file @ e3a1a218
......@@ -283,6 +283,16 @@ class BrookLangevinDynamics : public BrookCommon {
int removeCom( BrookStreamInternal* velocities, BrookFloatStreamInternal* inverseMassStream ) const;
/**
* Reset velocities (diagnostics)
*
* @param velocities velocities
*
* @return DefaultReturnValue
*/
int resetVelocities( BrookStreamInternal* velocities ) const;
private:
enum DerivedParameters { GDT, EPH, EMH, EP, EM, B, C, D, V, X, Yv, Yx,
......
platforms/brook/src/BrookNonBonded.cpp
View file @ e3a1a218
......@@ -1341,7 +1341,7 @@ nonbondedForceStreams[3]->fillWithValue( &zerof );
(void) fprintf( log, "\n pFrc=%6d eps=%12.5e\n", getPartialForceStreamWidth( ), epsfac );
(void) fprintf( log, "\nFinal NB & bonded forces" );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
(void) fprintf( log, "\nOuterVdwStreamd\n" );
......@@ -1387,7 +1387,7 @@ nonbondedForceStreams[3]->fillWithValue( &zerof );
if( printOn ){
(void) fprintf( log, "\n%s NB forces\n", methodName.c_str() );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( log );
(void) fprintf( log, "\n%s Done\n", methodName.c_str() ); (void) fflush( log );
......
platforms/brook/src/BrookPlatform.cpp
View file @ e3a1a218
......@@ -44,7 +44,6 @@
using namespace OpenMM;
/**
* BrookPlatformData constructor
*
......@@ -314,9 +313,12 @@ void BrookPlatform::_setBrookRuntime( const std::string& runtime ){
throw OpenMMException( message.str() );
}
if( getLog() ){
(void) fprintf( getLog(), "%s Brook initializing to runtime=<%s>\n", methodName.c_str(), _runtime.c_str() );
(void) fflush( getLog() );
// let user know runtime setting
if( 1 ){
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s Brook initializing to runtime=<%s>\n", methodName.c_str(), _runtime.c_str() );
(void) fflush( log );
}
brook::initialize( _runtime.c_str(), NULL );
......
platforms/brook/src/BrookRandomNumberGenerator.cpp
View file @ e3a1a218
......@@ -81,6 +81,7 @@ BrookRandomNumberGenerator::BrookRandomNumberGenerator( ){
_randomNumberSeed = 1393;
//_randomNumberGenerator = Mersenne;
_randomNumberGenerator = Kiss;
//_randomNumberGenerator = FixedValue;
//SimTKOpenMMUtilities::setRandomNumberSeed( randomNumberSeed );
}
......@@ -473,6 +474,38 @@ int BrookRandomNumberGenerator::_loadRandomNumberStreamsMersenne( void ){
return DefaultReturnValue;
}
/**
* Load random number streams w/ fixed value
*
*
* @return DefaultReturnValue;
*/
int BrookRandomNumberGenerator::_loadRandomNumberStreamsFixedValue( void ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nBrookRandomNumberGenerator::_loadRandomNumberStreamsFixedValue";
int printOn = 1;
// ---------------------------------------------------------------------------------------
// load fixed value
float fixedValue = 0.1f;
for( int jj = 0; jj < getNumberOfRandomNumberStreams(); jj++ ){
getRandomNumberStream( jj )->fillWithValue( &fixedValue );
}
if( printOn ){
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s: stats\n%s\n", methodName.c_str(), getStatisticsString().c_str() );
(void) fflush( log );
}
return DefaultReturnValue;
}
/**
* Load random number streams using original gpu algorithm
*
......@@ -595,7 +628,8 @@ int BrookRandomNumberGenerator::_loadGVShuffle( void ){
const int np = sizeof(p) / sizeof(p[0]);
const int pmax = p[np-1];
// static const std::string methodName = "\nBrookRandomNumberGenerator::loadGVShuffle";
static const std::string methodName = "\nBrookRandomNumberGenerator::loadGVShuffle";
int printOn = 0;
// ---------------------------------------------------------------------------------------
......@@ -636,6 +670,25 @@ int BrookRandomNumberGenerator::_loadGVShuffle( void ){
}
_getShuffleStream()->loadFromArray( loadBuffer );
if( printOn ){
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s: sz=%d pmax=%d np=%d sample indices:\n", methodName.c_str(), rvSize, pmax, np );
float maxIdx = -1.0f;
float minIdx = (float) (rvSize)*2.0f;
for( int ii = 0; ii < rvSize; ii++ ){
if( ii < 30 || ii > (rvSize-30) ){
(void) fprintf( log, " %d %.8f\n", ii, loadBuffer[ii] );
}
if( loadBuffer[ii] < minIdx ){
minIdx = loadBuffer[ii];
}
if( loadBuffer[ii] > maxIdx ){
maxIdx = loadBuffer[ii];
}
}
(void) fprintf( log, "%s: min-max indices: %.8f %.8f\n", methodName.c_str(), minIdx, maxIdx );
}
return DefaultReturnValue;
}
......@@ -685,12 +738,12 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookRandomNumberGenerator::advanceGVCursor";
int printOn = 0;
int printOn = 1;
FILE* log;
// ---------------------------------------------------------------------------------------
//setLog( stderr );
setLog( stderr );
if( printOn && getLog() ){
log = getLog();
} else {
......@@ -728,14 +781,17 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
} else { //Need to refresh random numbers from cpu
if( _randomNumberGenerator == Mersenne ){
action = "loaded new values from GPU using Mersenne rng";
action = "loaded new values to GPU using Mersenne rng";
_loadRandomNumberStreamsMersenne( );
} else if( _randomNumberGenerator == Kiss ){
action = "loaded new values from GPU using KISS rng";
action = "loaded new values to GPU using KISS rng";
_loadRandomNumberStreamsKiss( );
} else if( _randomNumberGenerator == Original ){
action = "loaded new values from GPU using original Gromac's rng";
action = "loaded new values to GPU using original Gromac's rng";
_loadGVStreamsOriginal( );
} else if( _randomNumberGenerator == FixedValue ){
action = "loaded new fixed values to GPU";
_loadRandomNumberStreamsFixedValue( );
}
_numberOfShuffles = 0;
}
......@@ -743,7 +799,9 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
}
if( printOn ){
(void) fprintf( log, "%s StrmIdx=%d action=%s\n", methodName.c_str(), _rvStreamIndex, action );
(void) fprintf( log, "%s offset=%d consume/itr=%d StrmSz=%d idx=%d shffle=%d action=%s\n",
methodName.c_str(), _rvStreamOffset, numberOfRandomValuesConsumedPerIteration,
rvStreamSize, _rvStreamIndex, _numberOfShuffles, action );
(void) fflush( log );
}
......@@ -802,7 +860,7 @@ BrookFloatStreamInternal* BrookRandomNumberGenerator::_getShuffleStream( void )
*
*/
BrookFloatStreamInternal* BrookRandomNumberGenerator::getRandomNumberStream( int index ) const {
BrookFloatStreamInternal* BrookRandomNumberGenerator::getRandomNumberStream( int index ){
// ---------------------------------------------------------------------------------------
......@@ -944,16 +1002,20 @@ int BrookRandomNumberGenerator::_initializeStreams( const Platform& platform ){
_randomNumberGeneratorStreams = new BrookFloatStreamInternal*[_numberOfRandomNumberStreams];
for( int ii = 0; ii < _numberOfRandomNumberStreams; ii++ ){
_randomNumberGeneratorStreams[ii] = new BrookFloatStreamInternal( BrookCommon::ShuffleStream,
_randomNumberGeneratorStreams[ii] = new BrookFloatStreamInternal( BrookCommon::RandomValuesStream,
randomNumberStreamSize, randomNumberStreamWidth,
BrookStreamInternal::Float3, dangleValue );
}
// create shuffle stream
_loadGVShuffle();
return DefaultReturnValue;
}
/*
* Setup of StochasticDynamics parameters
* Setup of streams, ... associated w/ random number generator
*
* @param numberOfParticles number of particles
* @param platform Brook platform
......@@ -984,6 +1046,8 @@ int BrookRandomNumberGenerator::setup( int numberOfParticles, const Platform& p
_loadRandomNumberStreamsKiss( );
} else if( _randomNumberGenerator == Original ){
_loadGVStreamsOriginal( );
} else if( _randomNumberGenerator == FixedValue ){
_loadRandomNumberStreamsFixedValue( );
}
return DefaultReturnValue;
......@@ -1027,6 +1091,8 @@ std::string BrookRandomNumberGenerator::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%s", "Kiss Rng");
} else if( _randomNumberGenerator == Original ){
(void) LOCAL_SPRINTF( value, "%s", "Original Gromacs Rng");
} else if( _randomNumberGenerator == FixedValue ){
(void) LOCAL_SPRINTF( value, "%s", "Fixed value Rng");
}
message << _getLine( tab, "Random number generator:", value );
......@@ -1061,6 +1127,8 @@ std::string BrookRandomNumberGenerator::getContentsString( int level ) const {
message << _getLine( tab, "Shuffle:", (_getShuffleStream() ? Set : NotSet) );
// show stats
message << getStatisticsString( );
for( int ii = 0; ii < LastStreamIndex; ii++ ){
......@@ -1070,6 +1138,12 @@ std::string BrookRandomNumberGenerator::getContentsString( int level ) const {
}
}
for( int ii = 0; ii < _numberOfRandomNumberStreams; ii++ ){
message << std::endl;
if( _randomNumberGeneratorStreams[ii] ){
message << _randomNumberGeneratorStreams[ii]->getContentsString();
}
}
#undef LOCAL_SPRINTF
return message.str();
......@@ -1201,29 +1275,30 @@ int BrookRandomNumberGenerator::getStatistics( double statistics[7], int streamI
for( int ii = 0; ii < _numberOfRandomNumberStreams; ii++ ){
if( streamIndex < 0 || ii == streamIndex ){
void* dataArrayV = _randomNumberGeneratorStreams[ii]->getData( 1 );
int streamSize = _randomNumberGeneratorStreams[ii]->getStreamSize();
int index = 0;
int numberOfValues = _randomNumberGeneratorStreams[ii]->getStreamSize()*_randomNumberGeneratorStreams[ii]->getWidth();
const float* dataArray = (float*) dataArrayV;
for( int ii = 0; ii < streamSize; ii++, index++ ){
for( int ii = 0; ii < numberOfValues; ii++ ){
statistics[0] += dataArray[index];
statistics[0] += dataArray[ii];
double rv2 = dataArray[index]*dataArray[index];
double rv2 = dataArray[ii]*dataArray[ii];
statistics[1] += rv2;
statistics[2] += rv2*dataArray[index];
statistics[2] += rv2*dataArray[ii];
statistics[3] += rv2*rv2;
if( statistics[5] > dataArray[index] ){
statistics[5] = dataArray[index];
if( statistics[5] > dataArray[ii] ){
statistics[5] = dataArray[ii];
}
if( statistics[6] < dataArray[index] ){
statistics[6] = dataArray[index];
if( statistics[6] < dataArray[ii] ){
statistics[6] = dataArray[ii];
}
}
statistics[4] += (double) index;
statistics[4] += (double) numberOfValues;
}
}
// accumulate moments, ... in cumulativeStatistics array
for( int ii = 0; ii < 5; ii++ ){
cumulativeStatistics[ii] += statistics[ii];
}
......
platforms/brook/src/BrookRandomNumberGenerator.h
View file @ e3a1a218
......@@ -46,9 +46,9 @@ class BrookRandomNumberGenerator : public BrookCommon {
public:
// toggle between original, Mersenne, & Kiss (Nvidia) random generators
// toggle between original, Mersenne, & Kiss (Nvidia), fixed value random generators
enum Rngs { Original, Kiss, Mersenne };
enum Rngs { Original, Kiss, Mersenne, FixedValue };
/**
* Constructor
......@@ -147,7 +147,7 @@ class BrookRandomNumberGenerator : public BrookCommon {
*
*/
BrookFloatStreamInternal* getRandomNumberStream( int index ) const;
BrookFloatStreamInternal* getRandomNumberStream( int index );
/**
* Get random number seed
......@@ -381,6 +381,16 @@ class BrookRandomNumberGenerator : public BrookCommon {
int _loadGVStreamsOriginal( void );
/**
* Load fixed value 'random number' streams using original gpu algorithm
* used for diagnostics
*
*
* @return DefaultReturnValue;
*/
int _loadRandomNumberStreamsFixedValue( void );
/**
* Loads a permutation of indices from 0 to gvSize-1 in
* sdp->strShuffle. To make sure that the order of the
......
platforms/brook/src/BrookStreamImpl.cpp
View file @ e3a1a218
......@@ -298,6 +298,6 @@ brook::stream& BrookStreamImpl::getBrookStream( void ){
* @return Brook stream impl
*/
BrookStreamInternal* BrookStreamImpl::getBrookStreamImpl( void ) const {
BrookStreamInternal* BrookStreamImpl::getBrookStreamInternal( void ) const {
return _brookStreamInternal;
}
platforms/brook/src/BrookStreamImpl.h
View file @ e3a1a218
......@@ -173,7 +173,7 @@ class BrookStreamImpl : public StreamImpl {
* @return Brook stream impl
*/
BrookStreamInternal* getBrookStreamImpl( void ) const;
BrookStreamInternal* getBrookStreamInternal( void ) const;
protected:
......
platforms/brook/src/BrookStreamInternal.cpp
View file @ e3a1a218
......@@ -448,3 +448,222 @@ std::string BrookStreamInternal::printStatistics( std::string tag, std::vector<s
return message.str();
}
/*
* Print streams to file
*
* @param fileName file name
* @param streams streams to print
*
* @return DefaultReturnValue
*
* */
int BrookStreamInternal::printStreamsToFile( std::string fileName, std::vector<BrookStreamInternal*>& streams ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookStreamInternal::printStreamsToFile";
// ---------------------------------------------------------------------------------------
FILE* filePtr = fopen( fileName.c_str(), "w" );
if( !filePtr ){
(void) fprintf( stderr, "%s could not open file=<%s>\n", methodName.c_str(), fileName.c_str() );
(void) fflush( stderr );
return ErrorReturnValue;
}
// gather arrays, widths for eah stream, and set index for each stream
// also set minimum of stream sizes
int minIndex = 10000000;
float** arrays = new float*[streams.size()];
float** sums = new float*[streams.size()];
int* widths = new int[streams.size()];
int* indices = new int[streams.size()];
for( unsigned int ii = 0; ii < streams.size(); ii++ ){
BrookStreamInternal* stream = streams[ii];
void* dataArrayV = stream->getData( 1 );
arrays[ii] = (float*) dataArrayV;
widths[ii] = stream->getWidth();
indices[ii] = 0;
sums[ii] = new float[4];
sums[ii][0] = sums[ii][1] = sums[ii][2] = sums[ii][3] = 0.0f;
if( minIndex > stream->getSize() ){
minIndex = stream->getSize();
}
}
// sum columns
for( int ii = 0; ii < minIndex; ii++ ){
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
for( int jj = 0; jj < widths[kk]; jj++ ){
sums[kk][jj] += arrays[kk][indices[kk]++];
}
}
}
// reinitialize indices
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
indices[kk] = 0;
}
// show column sums
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
(void) fprintf( filePtr, "Sms " );
for( int jj = 0; jj < widths[kk]; jj++ ){
(void) fprintf( filePtr, "%15.5e ", sums[kk][jj] );
}
}
(void) fprintf( filePtr, "\n" );
for( int ii = 0; ii < minIndex; ii++ ){
(void) fprintf( filePtr, "%6d ", ii );
// streams
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
// (void) fprintf( filePtr, "[ " );
// ii elements of stream kk
for( int jj = 0; jj < widths[kk]; jj++ ){
(void) fprintf( filePtr, "%15.5e ", arrays[kk][indices[kk]++] );
}
// (void) fprintf( filePtr, " ]", ii );
}
(void) fprintf( filePtr, "\n", ii );
}
// cleanup
(void) fclose( filePtr );
delete[] arrays;
delete[] widths;
delete[] indices;
for( int ii = 0; ii < 4; ii++ ){
delete[] sums[ii];
}
delete[] sums;
return DefaultReturnValue;
}
typedef struct {
unsigned int type;
unsigned int dimensions;
unsigned int dims[4];
} STREAM_HEADER;
#include <winsock.h>
#include <stdarg.h>
#include <limits>
#include <set>
int BrookStreamInternal::loadStreamGivenFileName( std::string& filename ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookStreamInternal::loadStreamGivenFileName";
// ---------------------------------------------------------------------------------------
FILE* log = stderr;
/* open file, read header */
FILE * filePtr = fopen( filename.c_str(), "rb" );
if( filePtr == NULL ){
(void) fprintf( log, "%s Unable to open/read %s for stream creation\n", methodName.c_str(), filename.c_str() );
return ErrorReturnValue;
}
STREAM_HEADER header;
if( 1 != fread( &header, sizeof( header ), 1, filePtr ) ){
(void) fprintf( log, "%s Unable to read %s header for stream %s\n", methodName.c_str(), filename.c_str() );
(void) fclose( filePtr );
return ErrorReturnValue;
}
/* fix endian */
// header.type = ntohl( header.type );
// header.dimensions = ntohl( header.dimensions );
/*
for( int ii = 0; ii < 4; ii++ ){
// header.dims[ii] = ntohl( header.dims[ii] );
(void) fprintf( log, "%s header %d %d for stream %s from %s\n", methodName.c_str(), ii, header.dims[ii], getName().c_str(), filename.c_str() );
}
(void) fflush( log );
*/
/*
if( header.dimensions[0]
(unsigned int) header.dimensions, (const ::brook::StreamType *) &type,
(bool) false );
*/
/* ok, load in the data */
/*
if( getStreamSize()*getWidth() != header.dims[0]*header.dims[1] ){
(void) fprintf( log, "%s dimension inconsistency for stream %s from %s dim:[%d %d %d %d] sz=%d != sz=%d containerW=%d\n",
methodName.c_str(), getName().c_str(), filename.c_str(),
header.dims[0], header.dims[1], header.dims[2], header.dims[3], header.dims[0]*header.dims[1],
getStreamSize(), getWidth() );
(void) fclose( filePtr );
return ErrorReturnValue;
}
*/
// always float
int bytesToRead = getStreamSize()*getWidth()*sizeof( float );
void* dataBuffer = (void*) malloc( bytesToRead );
if( dataBuffer == NULL ){
(void) fprintf( log, "%s Memory Error for file=%s\n", methodName.c_str(), filename.c_str() );
(void) fclose( filePtr );
return ErrorReturnValue;
}
size_t bytesRead = fread( dataBuffer, bytesToRead, 1, filePtr );
if( bytesRead != 1 ){
(void) fprintf( log, "%s Unable to read %d bytes=%d stream from %s\n", methodName.c_str(), bytesRead, bytesToRead, filename.c_str() );
free( dataBuffer );
(void) fclose( filePtr );
return ErrorReturnValue;
}
// float/integer case -- nothing more to do but load; if double, then convert float to double
if( getBaseDataType() == Float || getBaseDataType() == Integer ){
loadFromArray( dataBuffer );
} else {
double* loadBuffer = (double*) malloc( bytesToRead*2 );
float* readBuffer = (float*) dataBuffer;
for( int ii = 0; ii < getStreamSize()*getWidth(); ii++ ){
loadBuffer[ii] = (double) readBuffer[ii];
}
loadFromArray( loadBuffer );
free( loadBuffer );
}
(void) fclose( filePtr );
free( dataBuffer );
(void) fprintf( log, "%s read %d bytes for stream %s from %s dim:[%d %d %d %d] container=%d %d\n", methodName.c_str(), bytesToRead, getName().c_str(), filename.c_str(),
header.dims[0], header.dims[0], header.dims[0], header.dims[0], getStreamSize(), getWidth() );
(void) fflush( log );
return DefaultReturnValue;
}
platforms/brook/src/BrookStreamInternal.h
View file @ e3a1a218
......@@ -263,10 +263,33 @@ class BrookStreamInternal {
*
* @return stat string
*
* */
**/
std::string printStatistics( std::string tag, std::vector<std::vector<double> >& statistics ) const;
/*
* Read stream from file
*
* @param fileName file name
*
* @return DefaultReturnValue or ErrorReturnValue if problems
*
**/
int loadStreamGivenFileName( std::string& filename );
/*
* Print streams to file
*
* @param fileName file name
* @param streams streams to print
*
* @return DefaultReturnValue
*
**/
static int printStreamsToFile( std::string fileName, std::vector<BrookStreamInternal*>& streams );
protected:
std::string _name;
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp
View file @ e3a1a218
......@@ -144,7 +144,7 @@ BrookFloatStreamInternal* BrookVelocityCenterOfMassRemoval::getLinearMomentumStr
*
*/
int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3] ){
int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3], BrookOpenMMFloat* ke ){
// ---------------------------------------------------------------------------------------
......@@ -157,7 +157,8 @@ int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( BrookStreamImpl&
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (vStream.getBrookStreamImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (vStream.getBrookStreamInternal());
*ke = static_cast<BrookOpenMMFloat>(0.0);
void* velV = velocityStream->getData( 1 );
const float* vArray = (float*) velV;
......@@ -174,11 +175,14 @@ int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( BrookStreamImpl&
velocityCom[0] += mArray[ii]*vArray[index];
velocityCom[1] += mArray[ii]*vArray[index+1];
velocityCom[2] += mArray[ii]*vArray[index+2];
if( ii < 10 ){
fprintf( stderr, "getVelocityCenterOfMass %d %d m=%15.6e v[%15.6e %15.6e %15.6e ]\n", ii, index, mArray[ii], vArray[index], vArray[index+1], vArray[index+2] );
*ke += mArray[ii]*( vArray[index]*vArray[index] + vArray[index+1]*vArray[index+1] + vArray[index+2]*vArray[index+2] );
if( ii < 3 ){
fprintf( stderr, "getVelocityCenterOfMass %5d %5d m=%15.6e v[%15.6e %15.6e %15.6e ] %d\n", ii, index, mArray[ii], vArray[index], vArray[index+1], vArray[index+2], numberOfParticles );
}
}
*ke *= static_cast<BrookOpenMMFloat>(0.5);
return DefaultReturnValue;
}
......@@ -316,7 +320,6 @@ int BrookVelocityCenterOfMassRemoval::_setMasses( const std::vector<double>& mas
BrookOpenMMFloat value = static_cast<BrookOpenMMFloat>(*ii);
localMasses[index] = value;
_totalInverseMass += value;
fprintf( stderr, "%s %d mass=%.3f\n", methodName.c_str(), index, value );
}
}
......@@ -455,15 +458,19 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( BrookStreamImp
static const std::string methodName = "BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass";
static const int debug = 1;
static const double boltz = 8.3145112119486e-03;
BrookOpenMMFloat ke;
// ---------------------------------------------------------------------------------------
setLog( stderr );
if( debug && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocityStream, com );
(void) fprintf( getLog(), "%s Pre removal com: [%12.5e %12.5e %12.5e]\n", methodName.c_str(), com[0], com[1], com[2] );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
getVelocityCenterOfMass( velocityStream, com, &ke );
BrookOpenMMFloat denomiator = (( (float) 3*getNumberOfParticles()))*boltz;
(void) fprintf( getLog(), "%s Pre removal com: [%12.5e %12.5e %12.5e] ke=%.3f ~T=%.3f\n",
methodName.c_str(), com[0], com[1], com[2], ke, ke/denomiator );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamInternal());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
......@@ -483,20 +490,22 @@ setLog( stderr );
kCalculateLinearMomentum( getMassStream()->getBrookStream(), velocityStream.getBrookStream(), getWorkStream()->getBrookStream() );
kSumLinearMomentum( (float) getComParticleStreamWidth(), (float) getNumberOfParticles(), (float) getTotalInverseMass(),
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( velocityStream, com );
(void) fprintf( getLog(), "%s strW=%d iatm=%d invMass=%.4e Post removal com: [%12.5e %12.5e %12.5e]", methodName.c_str(),
getComParticleStreamWidth(), getNumberOfParticles(), getTotalInverseMass(), com[0], com[1], com[2] );
getVelocityCenterOfMass( velocityStream, com, &ke );
BrookOpenMMFloat denomiator = (( (float) 3*getNumberOfParticles()))*boltz;
(void) fprintf( getLog(), "%s strW=%d iatm=%d invMass=%.4e\n Post removal com: [%12.5e %12.5e %12.5e] ke=%.3f ~T=%.3f\n",
methodName.c_str(),
getComParticleStreamWidth(), getNumberOfParticles(), getTotalInverseMass(), com[0], com[1], com[2],
ke, ke/denomiator );
void* linMoV = getLinearMomentumStream()->getData( 1 );
float* linMo = (float*) linMoV;
(void) fprintf( getLog(), "LM [%12.5e %12.5e %12.5e]\n", linMo[0], linMo[1], linMo[2] );
(void) fprintf( getLog(), " LM [%12.5e %12.5e %12.5e]\n", linMo[0], linMo[1], linMo[2] );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamInternal());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.h
View file @ e3a1a218
......@@ -102,16 +102,17 @@ class BrookVelocityCenterOfMassRemoval : public BrookCommon {
int removeVelocityCenterOfMass( BrookStreamImpl& velocityStream );
/**
* Get velocity center-of-mass
* Get velocity center-of-mass and kinetic energy (used for diagnostics)
*
* @param velocities particle velocities
* @param velocityCom output velocity com
* @param ke output kinetic energy
*
* @return DefaultReturnValue
*
*/
int getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3] );
int getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3], BrookOpenMMFloat* ke );
/*
* Setup of parameters
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ e3a1a218
......@@ -519,12 +519,12 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
(void) fprintf( log, "\nInverseMassStream %d\n", _internalStepCount );
getInverseMassStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
(void) fprintf( log, "\nForceStream %d\n", _internalStepCount );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
std::vector<std::vector<double> > forceStatistics;
brookStreamInternalF->getStatistics( forceStatistics, getNumberOfParticles() );
......@@ -535,7 +535,7 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
brookStreamInternalF->printToFile( log );
BrookStreamInternal* brookStreamInternalV = velocityStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalV = velocityStream.getBrookStreamInternal();
std::vector<std::vector<double> > velocityStatistics;
brookStreamInternalV->getStatistics( velocityStatistics, getNumberOfParticles() );
std::stringstream tagV;
......@@ -571,7 +571,7 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
(void) fprintf( log, "\nShakeParticleIndicesStream %d\n", _internalStepCount );
brookShakeAlgorithm.getShakeParticleIndicesStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
......@@ -616,7 +616,7 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
(void) fprintf( log, "\nShakeInverseMapStream %d\n", _internalStepCount );
brookShakeAlgorithm.getShakeInverseMapStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
......@@ -651,7 +651,7 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
(void) fprintf( log, "\n%s step=%d Post kupdate_md2: inverseStepSize=%3e",
methodName.c_str(), _internalStepCount, inverseStepSize );
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
brookShakeAlgorithm.checkConstraints( brookStreamInternalPos, log, 0.0001f );
(void) fprintf( log, "\nPositionStream %d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
......@@ -659,7 +659,7 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
(void) fprintf( log, "\nXPrimeStream %d\n", _internalStepCount );
getXPrimeStream()->printToFile( log );
brookStreamInternalPos = velocityStream.getBrookStreamImpl();
brookStreamInternalPos = velocityStream.getBrookStreamInternal();
(void) fprintf( log, "\nVelocityStream %d\n", _internalStepCount );
brookStreamInternalPos->printToFile( log );
}
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ e3a1a218
......@@ -591,7 +591,7 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
/*
(void) fprintf( getLog(), "\nFinal NB & bonded forces" );
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamImpl();
BrookStreamInternal* brookStreamInternalF = forceStream.getBrookStreamInternal();
brookStreamInternalF->printToFile( getLog() );
void* dataV = brookStreamInternalF->getData(1);
float* data = (float*) dataV;
......@@ -636,7 +636,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
// first step only?
if( step > 20 ){
if( step > 0 ){
return;
}
......@@ -650,9 +650,9 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
BrookStreamImpl* positions = getParticlePositions();
BrookStreamImpl* forces = getParticleForces();
std::vector<BrookStreamImpl*> streams;
streams.push_back( positions );
streams.push_back( forces );
std::vector<BrookStreamInternal*> streams;
streams.push_back( positions->getBrookStreamInternal() );
streams.push_back( forces->getBrookStreamInternal() );
// ---------------------------------------------------------------------------------------
......@@ -662,7 +662,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
forces->fillWithValue( &zero );
_brookNonBonded.computeForces( *positions, *forces );
std::string fileName = fileNameBase + "NonBonded.txt";
printStreamsToFile( fileName, streams );
BrookStreamInternal::printStreamsToFile( fileName, streams );
}
// ---------------------------------------------------------------------------------------
......@@ -684,7 +684,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
forces->fillWithValue( &zero );
_brookBonded.computeForces( *positions, *forces );
std::string fileName = fileNameBase + "Bonded.txt";
printStreamsToFile( fileName, streams );
BrookStreamInternal::printStreamsToFile( fileName, streams );
}
......@@ -699,7 +699,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
_brookGbsa.computeForces( *positions, *forces );
std::string fileName = fileNameBase + "Obc.txt";
printStreamsToFile( fileName, streams );
BrookStreamInternal::printStreamsToFile( fileName, streams );
}
forces->fillWithValue( &zero );
......@@ -723,7 +723,7 @@ void OpenMMBrookInterface::printForcesToFile( OpenMMContextImpl& context ){
}
std::string fileName = fileNameBase + "AllF.txt";
printStreamsToFile( fileName, streams );
BrookStreamInternal::printStreamsToFile( fileName, streams );
}
(void) fprintf( stderr, "%s done computeForces\n", methodName.c_str() );
......@@ -770,114 +770,3 @@ double OpenMMBrookInterface::computeEnergy( OpenMMContextImpl& context, System&
return refContext.getState(State::Energy).getPotentialEnergy();
}
/*
* Print contents of object to file
*
* @param fileName file name
* @param streams streams to print
*
* @return DefaultReturnValue
*
* */
int OpenMMBrookInterface::printStreamsToFile( std::string fileName, std::vector<BrookStreamImpl*>& streams ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "OpenMMBrookInterface::printStreamsToFile";
// ---------------------------------------------------------------------------------------
FILE* filePtr = fopen( fileName.c_str(), "w" );
if( !filePtr ){
(void) fprintf( stderr, "%s coud not open file=<%s>\n", methodName.c_str(), fileName.c_str() );
(void) fflush( stderr );
return ErrorReturnValue;
}
// gather arrays, widths for eah stream, and set index for each stream
// also set minimum of stream sizes
int minIndex = 10000000;
float** arrays = new float*[streams.size()];
float** sums = new float*[streams.size()];
int* widths = new int[streams.size()];
int* indices = new int[streams.size()];
for( unsigned int ii = 0; ii < streams.size(); ii++ ){
BrookStreamImpl* stream = streams[ii];
void* dataArrayV = stream->getData( 1 );
arrays[ii] = (float*) dataArrayV;
widths[ii] = stream->getWidth();
indices[ii] = 0;
sums[ii] = new float[4];
sums[ii][0] = sums[ii][1] = sums[ii][2] = sums[ii][3] = 0.0f;
if( minIndex > stream->getStreamSize() ){
minIndex = stream->getStreamSize();
}
}
minIndex = minIndex > getNumberOfParticles() ? getNumberOfParticles() : minIndex;
// sum columns
for( int ii = 0; ii < minIndex; ii++ ){
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
for( int jj = 0; jj < widths[kk]; jj++ ){
sums[kk][jj] += arrays[kk][indices[kk]++];
}
}
}
// reinitialize indices
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
indices[kk] = 0;
}
// show column sums
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
(void) fprintf( filePtr, "Sms " );
for( int jj = 0; jj < widths[kk]; jj++ ){
(void) fprintf( filePtr, "%12.5e ", sums[kk][jj] );
}
}
(void) fprintf( filePtr, "\n" );
for( int ii = 0; ii < minIndex; ii++ ){
(void) fprintf( filePtr, "%d ", ii );
// streams
for( unsigned int kk = 0; kk < streams.size(); kk++ ){
// (void) fprintf( filePtr, "[ " );
// ii elements of stream kk
for( int jj = 0; jj < widths[kk]; jj++ ){
(void) fprintf( filePtr, "%12.5e ", arrays[kk][indices[kk]++] );
}
// (void) fprintf( filePtr, " ]", ii );
}
(void) fprintf( filePtr, "\n", ii );
}
// cleanup
(void) fclose( filePtr );
delete[] arrays;
delete[] widths;
delete[] indices;
for( int ii = 0; ii < 4; ii++ ){
delete[] sums[ii];
}
delete[] sums;
return DefaultReturnValue;
}
platforms/brook/src/OpenMMBrookInterface.h
View file @ e3a1a218
......@@ -390,18 +390,6 @@ class OpenMMBrookInterface {
void printForcesToFile( OpenMMContextImpl& context );
/*
* Print contents of object to file
*
* @param fileName file name
* @param streams streams to print
*
* @return DefaultReturnValue
*
* */
int printStreamsToFile( std::string fileName, std::vector<BrookStreamImpl*>& streams );
private:
static const int DefaultReturnValue = 0;
......
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