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Commit 956f3183 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods

parent ef5f9282
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Showing with 143 additions and 26 deletions
platforms/brook/src/BrookBrownianDynamics.cpp
View file @ 956f3183
......@@ -523,10 +523,12 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
// Shake
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
/*
kshakeh_fix1(
25.0f,
(float) brookShakeAlgorithm.getMaxIterations(),
(float) getBrownianDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
brookShakeAlgorithm.getShakeTolerance(),
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......@@ -549,7 +551,8 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream(),
positionStream.getBrookStream() );
*/
fprintf( stderr, "\nBrownian shake off!!\n" );
// diagnostics
if( PrintOn ){
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp
View file @ 956f3183
......@@ -161,24 +161,21 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
std::vector<std::vector<int> > constraintIndicesVector;
constraintIndicesVector.resize( numberOfConstraints );
std::vector<double> constraintLengths;
constraintLengths.resize( numberOfConstraints );
for( int ii = 0; ii < numberOfConstraints; ii++ ){
int particle1, particle2;
double distance;
(void) fprintf( log, "%s shake setup const=%d ", methodName.c_str(), ii ); fflush( log );
system.getConstraintParameters( ii, particle1, particle2, distance );
constraintIndicesVector[ii] = constraintIndices;
(void) fprintf( log, "[ %d %d %f]\n", methodName.c_str(), particle1, particle2, distance ); fflush( log );
constraintIndicesVector[ii].push_back( particle1 );
constraintIndicesVector[ii].push_back([particle2 );
constraintIndicesVector[ii].push_back([particle2 );
constraintIndicesVector[ii].push_back( particle2 );
constraintLengths.push_back( distance );
//(void) fprintf( log, "%s shake setup const=%d ", methodName.c_str(), ii ); fflush( log );
//(void) fprintf( log, "[ %d %d %f]\n", particle1, particle2, distance ); fflush( log );
}
_brookLangevinDynamics = new BrookLangevinDynamics( );
......@@ -187,6 +184,13 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
_brookShakeAlgorithm = new BrookShakeAlgorithm( );
_brookShakeAlgorithm->setup( masses, constraintIndicesVector, constraintLengths, getPlatform() );
// tolerance
BrookOpenMMFloat tolerance = static_cast<BrookOpenMMFloat>( integrator.getConstraintTolerance() );
_brookShakeAlgorithm->setShakeTolerance( tolerance );
_brookShakeAlgorithm->setMaxIterations( 30 );
_brookShakeAlgorithm->setLog( log );
// assert( (_brookShakeAlgorithm->getNumberOfConstraints() > 0) );
if( printOn && log ){
......@@ -211,7 +215,7 @@ void BrookIntegrateLangevinStepKernel::execute( OpenMMContextImpl& context, cons
// ---------------------------------------------------------------------------------------
double epsilon = 1.0e-04;
double epsilon = 1.0e-06;
static const std::string methodName = "BrookIntegrateLangevinStepKernel::execute";
// ---------------------------------------------------------------------------------------
......@@ -228,11 +232,11 @@ void BrookIntegrateLangevinStepKernel::execute( OpenMMContextImpl& context, cons
differences[1] = integrator.getFriction() - (double) _brookLangevinDynamics->getFriction();
differences[2] = integrator.getStepSize() - (double) _brookLangevinDynamics->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() );
_brookLangevinDynamics->updateParameters( integrator.getTemperature(), integrator.getFriction(), integrator.getStepSize() );
} else {
printf( "%s NOT calling updateParameters\n", methodName.c_str() );
}
//printf( "%s NOT calling updateParameters\n", methodName.c_str() );
}
_brookLangevinDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()),
*(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm, *_brookRandomNumberGenerator );
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ 956f3183
......@@ -369,13 +369,9 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// ---------------------------------------------------------------------------------------
// unused Shake parameter
float numberOfIterations = 25.0f;
static const char* methodName = "\nBrookLangevinDynamics::update";
static const int PrintOn = 1;
static const int PrintOn = 0;
// ---------------------------------------------------------------------------------------
......@@ -482,9 +478,10 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
numberOfIterations,
(float) brookShakeAlgorithm.getMaxIterations(),
(float) getLangevinDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
brookShakeAlgorithm.getShakeTolerance(),
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......@@ -498,11 +495,9 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
kshakeh_update1_fix1(
(float) getLangevinDynamicsParticleStreamWidth(),
derivedParameters[Sd2pc1],
brookShakeAlgorithm.getShakeInverseMapStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
getVPrimeStream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons0Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons1Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons2Stream()->getBrookStream(),
......@@ -574,9 +569,10 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
numberOfIterations,
(float) brookShakeAlgorithm.getMaxIterations(),
(float) getLangevinDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
brookShakeAlgorithm.getShakeTolerance(),
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......
platforms/brook/src/BrookShakeAlgorithm.cpp
View file @ 956f3183
......@@ -57,6 +57,8 @@ BrookShakeAlgorithm::BrookShakeAlgorithm( ){
_numberOfParticles = -1;
_numberOfConstraints = -1;
_maxIterations = 25;
_shakeTolerance = static_cast<BrookOpenMMFloat>(1.0e-04);
// mark stream dimension variables as unset
......@@ -112,6 +114,56 @@ int BrookShakeAlgorithm::getNumberOfConstraints( void ) const {
return _numberOfConstraints;
}
/**
* Get max iterations
*
* @return max iterations
*
*/
int BrookShakeAlgorithm::getMaxIterations( void ) const {
return _maxIterations;
}
/**
* Set max iterations
*
* @param max iterations
*
* @return DefaultReturnValue
*
*/
int BrookShakeAlgorithm::setMaxIterations( int maxIterations ){
_maxIterations = maxIterations;
return DefaultReturnValue;
}
/**
* Get SHAKE tolerance
*
* @return SHAKE tolerance
*
*/
BrookOpenMMFloat BrookShakeAlgorithm::getShakeTolerance( void ) const {
return _shakeTolerance;
}
/**
* Set SHAKE tolerance
*
* @param SHAKE tolerance
*
* @return DefaultReturnValue
*
*/
int BrookShakeAlgorithm::setShakeTolerance( BrookOpenMMFloat tolerance ){
_shakeTolerance = tolerance;
return DefaultReturnValue;
}
/**
* Get inverse of hydrogen mass
*
......@@ -585,6 +637,12 @@ std::string BrookShakeAlgorithm::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%d", getNumberOfParticles() );
message << _getLine( tab, "Number of particles:", value );
(void) LOCAL_SPRINTF( value, "%d", getMaxIterations() );
message << _getLine( tab, "Max iterations:", value );
(void) LOCAL_SPRINTF( value, "%2e", getShakeTolerance() );
message << _getLine( tab, "Tolerance:", value );
(void) LOCAL_SPRINTF( value, "%d", getParticleStreamWidth() );
message << _getLine( tab, "Particle stream width:", value );
......
platforms/brook/src/BrookShakeAlgorithm.h
View file @ 956f3183
......@@ -74,6 +74,46 @@ class BrookShakeAlgorithm : public BrookCommon {
int getNumberOfConstraints( void ) const;
/**
* Get max iterations
*
* @return max iterations
*
*/
int getMaxIterations( void ) const;
/**
* Set max iterations
*
* @param max iterations
*
* @return DefaultReturnValue
*
*/
int setMaxIterations( int maxIterations );
/**
* Get SHAKE tolerance
*
* @return SHAKE tolerance
*
*/
BrookOpenMMFloat getShakeTolerance( void ) const;
/**
* Set SHAKE tolerance
*
* @param SHAKE tolerance
*
* @return DefaultReturnValue
*
*/
int setShakeTolerance( BrookOpenMMFloat tolerance );
/**
* Get inverse of hydrogen mass
*
......@@ -247,6 +287,10 @@ class BrookShakeAlgorithm : public BrookCommon {
int _numberOfConstraints;
// max iterations
int _maxIterations;
// inverse of H mass
BrookOpenMMFloat _inverseHydrogenMass;
......@@ -263,6 +307,10 @@ class BrookShakeAlgorithm : public BrookCommon {
int _shakeConstraintStreamWidth;
int _shakeConstraintStreamHeight;
// SHAKE tolerance
BrookOpenMMFloat _shakeTolerance;
// inverse sqrt masses
BrookOpenMMFloat* _inverseSqrtMasses;
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ 956f3183
......@@ -260,10 +260,12 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
/*
kshakeh_fix1(
25.0f,
(float) brookShakeAlgorithm.getMaxIterations(),
(float) getVerletDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
brookShakeAlgorithm.getShakeTolerance(),
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......@@ -272,6 +274,8 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
brookShakeAlgorithm.getShakeXCons1Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons2Stream()->getBrookStream(),
brookShakeAlgorithm.getShakeXCons3Stream()->getBrookStream() );
*/
fprintf( stderr, "\nVerlet shake off!!\n" );
if( (1|| PrintOn) && getLog() ){
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ 956f3183
......@@ -551,13 +551,17 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// bonded forces
(void) fprintf( stderr, "%s done nonbonded: bonded=%d completed=%d\n", methodName.c_str(), _brookBonded.isActive(), _brookBonded.isSetupCompleted() ); (void) fflush( stderr );
if( PrintOn && getLog() ){
(void) fprintf( getLog(), "%s done nonbonded: bonded=%d completed=%d\n", methodName.c_str(),
_brookBonded.isActive(), _brookBonded.isSetupCompleted() );
(void) fflush( getLog() );
}
if( _brookBonded.isActive() ){
// perform setup first time through
//if( _brookBonded.isSetupCompleted() == 0 ){
if( _brookBonded.isSetupCompleted() >= -1 ){
if( _brookBonded.isSetupCompleted() == 0 ){
_brookBonded.setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
getPeriodicTorsionForceParameters(), getRBTorsionForceParameters(),
getNonBonded14ForceParameters(),
......
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