Skip to content

GitLab

Commit 60dd93a8 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Mods

parent d6132ea0
Hide whitespace changes
Inline Side-by-side
Showing with 279 additions and 122 deletions
platforms/brook/src/BrookFloatStreamInternal.cpp
View file @ 60dd93a8
......@@ -242,6 +242,12 @@ void BrookFloatStreamInternal::loadFromArray( const void* array, BrookStreamInte
int totalSize = getSize()*getWidth();
//int totalSize = getSize();
/*
fprintf( stderr, "%s %s data=%p stream=%d [%d %d] width=%d type=%d\n",
methodName.c_str(), getName().c_str(), _data, getStreamSize(), _streamHeight, _streamWidth, _width, baseType );
fflush( stderr );
*/
if( baseType == BrookStreamInternal::Float ){
memcpy( _data, array, sizeof( float )*totalSize );
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ 60dd93a8
......@@ -249,7 +249,7 @@ int BrookLangevinDynamics::_updateDerivedParameters( void ){
BrookOpenMMFloat temperature = getTemperature();
BrookOpenMMFloat stepSize = getStepSize();
if( fabsf( float( tau ) ) < epsilon ){
if( fabsf( (float) tau ) < epsilon ){
std::stringstream message;
message << methodName << " tau=" << tau << " too small.";
throw OpenMMException( message.str() );
......@@ -809,18 +809,18 @@ int BrookLangevinDynamics::setup( const std::vector<double>& masses, const Platf
return DefaultReturnValue;
}
/*
* Setup of LangevinDynamics parameters
*
* @param masses masses
* @param platform Brook platform
*
* @return nonzero value if error
/**
* Get T
*
* @param velocities velocities
* @param inverseMassStream inverse masses
* @param numberOfConstraints number of constraints
*
* */
* @return temperature
*/
float BrookLangevinDynamics::getTemperature( BrookStreamInternal* velocities, BrookFloatStreamInternal* inverseMassStream,
BrookShakeAlgorithm& brookShakeAlgorithm ) const {
int numberOfConstraints ) const {
// ---------------------------------------------------------------------------------------
......@@ -838,15 +838,96 @@ float BrookLangevinDynamics::getTemperature( BrookStreamInternal* velocities, Br
int index = 0;
for( int ii = 0; ii < getNumberOfParticles(); ii++ ){
ke += (velocitiesI[index]*velocitiesI[index] + velocitiesI[index+1]*velocitiesI[index+1] + velocitiesI[index+2]*velocitiesI[index+2] )/inverseMassStreamI[ii];
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;
}
int degreesOfFreedom = 3*getNumberOfParticles() - brookShakeAlgorithm.getNumberOfConstraints();
int degreesOfFreedom = 3*getNumberOfParticles() - numberOfConstraints;
(void) fprintf( stderr, "%s ke=%.5e dof=%d\n", methodName.c_str(), ke, degreesOfFreedom );
ke /= ((float) BOLTZ)*((float) ( degreesOfFreedom ));
return ke;
return 0.5f*ke;
}
/**
* Remove velocity com
*
* @param velocities velocities
* @param inverseMassStream inverse masses
*
* @return DefaultReturnValue
*/
int BrookLangevinDynamics::removeCom( BrookStreamInternal* velocities, BrookFloatStreamInternal* inverseMassStream ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookLangevinDynamics::removeCom";
// ---------------------------------------------------------------------------------------
// (void) fprintf( stderr, "%s\n", methodName.c_str() ); fflush( stderr );
void* dataArrayV = velocities->getData( 1 );
float* velocitiesI = (float*) dataArrayV;
void* inverseMassStreamV = inverseMassStream->getData( 1 );
float* inverseMassStreamI = (float*) inverseMassStreamV;
float totalMass = 0.0f;
float com[3] = { 0.0f, 0.0f, 0.0f };
int index = 0;
//(void) fprintf( stderr, "%s strm %d %d\n", methodName.c_str(), velocities->getStreamSize(),velocities->getWidth() ); fflush( stderr );
for( int ii = 0; ii < getNumberOfParticles(); ii++ ){
float mass = 1.0f/inverseMassStreamI[ii];
totalMass += mass;
com[0] += mass*velocitiesI[index];
com[1] += mass*velocitiesI[index+1];
com[2] += mass*velocitiesI[index+2];
index += 3;
}
totalMass = 1.0f/totalMass;
com[0] *= totalMass;
com[1] *= totalMass;
com[2] *= totalMass;
index = 0;
double* newVelocities = new double[velocities->getStreamSize()*velocities->getWidth()];
memset( newVelocities, 0, sizeof( double )*velocities->getStreamSize()*velocities->getWidth() );
for( int ii = 0; ii < getNumberOfParticles(); ii++ ){
newVelocities[index] = (double) velocitiesI[index] - com[0];
newVelocities[index+1] = (double) velocitiesI[index+1] - com[1];
newVelocities[index+2] = (double) velocitiesI[index+2] - com[2];
index += 3;
}
/*
(void) fprintf( stderr, "%s com[%14.5e %14.5e %14.5e]\n", methodName.c_str(), com[0], com[1], com[2] );
for( int ii = 0; ii < velocities->getStreamSize()*3; ii += 3 ){
(void) fprintf( stderr, "%s %d newVelocities[%14.5e %14.5e %14.5e]\n", methodName.c_str(), ii/3, newVelocities[ii], newVelocities[ii+1], newVelocities[ii+2] );
}
*/
velocities->loadFromArray( newVelocities );
dataArrayV = velocities->getData( 1 );
velocitiesI = (float*) dataArrayV;
/*
(void) fprintf( stderr, "%s readback\n", methodName.c_str() );
for( int ii = 0; ii < velocities->getStreamSize()*3; ii += 3 ){
(void) fprintf( stderr, "%s %d velocitiesI[%14.5e %14.5e %14.5e]\n", methodName.c_str(), ii/3, velocitiesI[ii], velocitiesI[ii+1], velocitiesI[ii+2] );
}
*/
velocities->loadFromArray( newVelocities );
delete[] newVelocities;
return DefaultReturnValue;
}
/*
......@@ -950,21 +1031,25 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nBrookLangevinDynamics::update";
int printOn = 0;
int printOn = 1;
FILE* log;
// ---------------------------------------------------------------------------------------
_internalStepCount++;
//setLog( stderr );
printOn = (printOn && getLog()) ? printOn : 0;
// setLog( stderr );
if( printOn && getLog() ){
log = getLog();
} else {
printOn = 0;
}
const BrookOpenMMFloat* derivedParameters = getDerivedParameters();
if( printOn ){
log = getLog();
static int showAux = 1;
if( printOn ){
......@@ -977,7 +1062,10 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
if( showAux ){
showAux = 0;
std::string contents = brookRandomNumberGenerator.getContentsString( );
std::string contents = getContentsString( );
(void) fprintf( log, "%s step=%d contents\n%s", methodName.c_str(), _internalStepCount, contents.c_str() );
contents = brookRandomNumberGenerator.getContentsString( );
(void) fprintf( log, "%s step=%d RNG contents\n%s", methodName.c_str(), _internalStepCount, contents.c_str() );
// brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log );
......@@ -987,6 +1075,15 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
}
}
if( 1 || (_internalStepCount % 10) == 0 ){
FILE* log1 = stderr;
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamImpl();
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 );
}
// first integration step
kupdate_sd1_fix1(
......@@ -1011,7 +1108,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// diagnostics
if( 0 && printOn ){
if( printOn ){
(void) fprintf( log, "\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(),
......@@ -1143,7 +1240,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// diagnostics
if( 0 && printOn ){
if( printOn ){
(void) fprintf( log, "\n%s step=%d Post kupdate_sd2_fix1: particleStrW=%3d rngStrW=%3d rngOff=%5d "
"Sd2pc[]=[%12.5e %12.5e]", methodName.c_str(), _internalStepCount,
getLangevinDynamicsParticleStreamWidth(),
......@@ -1167,7 +1264,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
(void) fprintf( log, "\nXPrimeStream %d \n", _internalStepCount );
getXPrimeStream()->printToFile( log );
(void) fprintf( log, "\ngetSD2XStream %d \n", _internalStepCount );
(void) fprintf( log, "\nSD2XStream %d \n", _internalStepCount );
getSD2XStream()->printToFile( log );
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamImpl();
......@@ -1244,7 +1341,7 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
tagV << _internalStepCount << " Vxx ";
stats = brookStreamInternalPos->printStatistics( tagV.str(), velocityStatistics );
(void) fprintf( log, "\nStep %d Velocity stats:\n%s", _internalStepCount, stats.c_str() );
float temperature = getTemperature( brookStreamInternalPos, getInverseMassStream(), brookShakeAlgorithm );
float temperature = getTemperature( brookStreamInternalPos, getInverseMassStream(), brookShakeAlgorithm.getNumberOfConstraints() );
(void) fprintf( log, "\nVelocityStream %d T=%.3f\n", _internalStepCount, temperature );
brookStreamInternalPos->printToFile( log );
......@@ -1287,6 +1384,20 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
}
}
if( (_internalStepCount % 10) == 0 ){
FILE* log1 = stderr;
BrookStreamInternal* brookStreamInternalPos = velocityStream.getBrookStreamImpl();
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 );
}
return DefaultReturnValue;
}
platforms/brook/src/BrookLangevinDynamics.h
View file @ 60dd93a8
......@@ -258,17 +258,31 @@ class BrookLangevinDynamics : public BrookCommon {
BrookFloatStreamInternal* getInverseMassStream( void ) const;
/**
* Get T
* Get Temperature
*
* @return T
* @param velocities velocities
* @param inverseMassStream inverse masses
* @param numberOfConstraints number of constraints
*
* @return temperature
*
*/
float getTemperature( BrookStreamInternal* velocities, BrookFloatStreamInternal* inverseMassStream,
BrookShakeAlgorithm& brookShakeAlgorithm ) const;
int numberOfConstraints ) const;
/**
* Remove velocity com
*
* @param velocities velocities
* @param inverseMassStream inverse masses
*
* @return DefaultReturnValue
*/
int removeCom( BrookStreamInternal* velocities, BrookFloatStreamInternal* inverseMassStream ) const;
private:
enum DerivedParameters { GDT, EPH, EMH, EP, EM, B, C, D, V, X, Yv, Yx,
......
platforms/brook/src/BrookRandomNumberGenerator.cpp
View file @ 60dd93a8
......@@ -426,6 +426,7 @@ state[3] = 27587;
}
if( printOn ){
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s: stats\n%s\n", methodName.c_str(), getStatisticsString().c_str() );
(void) fflush( log );
}
......@@ -447,7 +448,6 @@ int BrookRandomNumberGenerator::_loadRandomNumberStreamsMersenne( void ){
static const std::string methodName = "\nBrookRandomNumberGenerator::_loadRandomNumberStreamsMersenne";
int printOn = 0;
FILE* log;
// ---------------------------------------------------------------------------------------
......@@ -465,6 +465,7 @@ int BrookRandomNumberGenerator::_loadRandomNumberStreamsMersenne( void ){
}
if( printOn ){
FILE* log = getLog() ? getLog() : stderr;
(void) fprintf( log, "%s: stats\n%s\n", methodName.c_str(), getStatisticsString().c_str() );
(void) fflush( log );
}
......@@ -689,8 +690,9 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
// ---------------------------------------------------------------------------------------
//setLog( stderr );
if( printOn && getLog() ){
log = getLog();
log = getLog();
} else {
printOn = 0;
}
......@@ -703,10 +705,9 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
//Check if we've used up this texture
char* action = "none";
if ( _rvStreamOffset > rvStreamSize - numberOfRandomValuesConsumedPerIteration ){
char* action;
// next one if available
_rvStreamOffset = 0;
......@@ -742,9 +743,27 @@ int BrookRandomNumberGenerator::advanceGVCursor( int numberOfRandomValuesConsume
}
if( printOn ){
(void) fprintf( log, "%s StrmIdx=%d action=%s\n", methodName, _rvStreamIndex, action );
(void) fprintf( log, "%s StrmIdx=%d action=%s\n", methodName.c_str(), _rvStreamIndex, action );
(void) fflush( log );
}
/*
// check rng distribution
static int count = 0;
if( count++ < 2 ){
// accumulate rng -- stats will be in cumulative fields in stat string
int testIterations = 1000;
for( int ii = 0; ii < testIterations; ii++ ){
//_loadRandomNumberStreamsKiss( );
_loadRandomNumberStreamsMersenne( );
getStatisticsString();
}
(void) fprintf( log, "%s: stats\n%s\n", methodName.c_str(), getStatisticsString().c_str() );
}
*/
}
return DefaultReturnValue;
......
platforms/brook/src/BrookShakeAlgorithm.cpp
View file @ 60dd93a8
......@@ -463,6 +463,7 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
particleIterator = constraintIndices.begin();
std::vector<double>::const_iterator distanceIterator = constraintLengths.begin();
_numberOfConstraints = static_cast<int>(constraintIndices.size());
while( particleIterator != constraintIndices.end() ){
float distance = static_cast<float>( *distanceIterator );
......@@ -475,7 +476,7 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
bool firstIsCentral;
if( constraintCount[atomI] > 1 ){
firstIsCentral = true;
} else if (constraintCount[atomJ] > 1 ){
} else if( constraintCount[atomJ] > 1 ){
firstIsCentral = false;
} else if( atomI < atomJ ){
firstIsCentral = true;
......@@ -531,7 +532,6 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, co
// load indices & parameters
int constraintIndex = 0;
_numberOfConstraints = static_cast<int>(_clusters.size());
for( map<int, ShakeCluster>::const_iterator iter = _clusters.begin(); iter != _clusters.end(); ++iter ){
const ShakeCluster& cluster = iter->second;
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp
View file @ 60dd93a8
......@@ -134,87 +134,6 @@ BrookFloatStreamInternal* BrookVelocityCenterOfMassRemoval::getLinearMomentumStr
return _streams[LinearMomentumStream];
}
/**
* Remove velocity-COM
*
* @param velocities velocities
*
* @return DefaultReturnValue
*
*/
int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( BrookStreamImpl& velocityStream ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass";
static const int debug = 0;
// ---------------------------------------------------------------------------------------
if( debug && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocityStream, com );
(void) fprintf( getLog(), "\n%s Pre removal com: [%12.5e %12.5e %12.5e]\n", methodName, com[0], com[1], com[2] );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
int index = 0;
if( debug > 1 ){
for( int ii = 0; ii < getNumberOfParticles(); ii++, index += 3 ){
(void) fprintf( getLog(), "V %d [%12.5e %12.5e %12.5e]\n", ii, vArray[index], vArray[index+1], vArray[index+2] );
}
}
(void) fflush( getLog() );
}
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
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,
getComParticleStreamWidth(), getNumberOfParticles(), getTotalInverseMass(), com[0], com[1], com[2] );
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] );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
void* w1 = getWorkStream()->getData( 1 );
const float* w2 = (float*) w1;
if( debug > 1 ){
int index = 0;
for( int ii = 0; ii < getNumberOfParticles(); 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
*
......@@ -255,6 +174,9 @@ 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] );
}
}
return DefaultReturnValue;
......@@ -394,6 +316,7 @@ 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 );
}
}
......@@ -443,10 +366,12 @@ int BrookVelocityCenterOfMassRemoval::setup( const std::vector<double>& masses,
_setMasses( masses );
if( 1 && getLog() ){
//if( 1 && getLog() ){
if( 1 ){
FILE* log = stderr;
std::string contents = getContentsString( 0 );
(void) fprintf( getLog(), "%s contents:\n%s\n", methodName.c_str(), contents.c_str() );
(void) fflush( getLog() );
(void) fprintf( log, "%s contents:\n%s\n", methodName.c_str(), contents.c_str() );
(void) fflush( log );
}
return DefaultReturnValue;
......@@ -495,7 +420,7 @@ std::string BrookVelocityCenterOfMassRemoval::getContentsString( int level ) con
(void) LOCAL_SPRINTF( value, "%d", getComParticleStreamSize() );
message << _getLine( tab, "Particle stream size:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getTotalInverseMass() );
(void) LOCAL_SPRINTF( value, "%.5e", getTotalInverseMass() );
message << _getLine( tab, "TotalInverseMass:", value );
message << _getLine( tab, "Log:", (getLog() ? Set : NotSet) );
......@@ -515,3 +440,84 @@ std::string BrookVelocityCenterOfMassRemoval::getContentsString( int level ) con
return message.str();
}
/**
* Remove velocity-COM
*
* @param velocities velocities
*
* @return DefaultReturnValue
*
*/
int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( BrookStreamImpl& velocityStream ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass";
static const int debug = 1;
// ---------------------------------------------------------------------------------------
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());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
int index = 0;
if( debug > 1 ){
for( int ii = 0; ii < getNumberOfParticles(); ii++, index += 3 ){
(void) fprintf( getLog(), "V %d [%12.5e %12.5e %12.5e]\n", ii, vArray[index], vArray[index+1], vArray[index+2] );
}
}
(void) fflush( getLog() );
}
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
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] );
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] );
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
void* w1 = getWorkStream()->getData( 1 );
const float* w2 = (float*) w1;
if( debug > 1 ){
int index = 0;
for( int ii = 0; ii < getNumberOfParticles(); 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;
}
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ 60dd93a8
......@@ -546,7 +546,8 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// info
if( printOn > 1 ){
//if( printOn > 1 ){
if( 1 ){
printForcesToFile( context );
}
......
platforms/brook/src/gpu/kshakeh.h
View file @ 60dd93a8
......@@ -52,8 +52,8 @@ void kshakeh_update1_fix1 (
::brook::stream cposq3,
::brook::stream oposq);
void kshakeh_update2_fix1 (const float strwidth,
void kshakeh_update2_fix1 (
const float strwidth,
::brook::stream invmap,
::brook::stream posq,
::brook::stream posqp,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment