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Commit b7c8afa9 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods

parent 980003cc
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Showing with 327 additions and 420 deletions
platforms/brook/src/BrookBonded.cpp
View file @ b7c8afa9
......@@ -62,10 +62,6 @@ BrookBonded::BrookBonded( ){
_setupCompleted = 0;
_numberOfParticles = 0;
//_ljScale = (BrookOpenMMFloat) 0.83333333;
_ljScale = 1.0;
//_coulombFactor = 332.0;
_coulombFactor = (BrookOpenMMFloat) 138.935485;
_particleIndicesStream = NULL;
......@@ -195,17 +191,6 @@ int BrookBonded::getInverseMapStreamWidth( void ) const {
return _inverseMapStreamWidth;
}
/**
* Get LJ 14 scaling parameter
*
* @return LJ 14 scaling parameter
*
*/
BrookOpenMMFloat BrookBonded::getLJ_14Scale( void ) const {
return _ljScale;
}
/**
* Get Coulomb factor
*
......@@ -981,7 +966,6 @@ int saveIbond = ibonded;
* @param bonded14Indices each element contains the indices of two particles whose nonbonded interactions should be reduced since
* they form a bonded 1-4 pair
* @param nonbondedParameters the nonbonded force parameters (charge, sigma, epsilon) for each particle
* @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
* @param log log reference
*
* @return nonzero value if error
......@@ -991,8 +975,7 @@ int saveIbond = ibonded;
int BrookBonded::addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* params[],
BrookOpenMMFloat* charges,
const std::vector<std::vector<int> >& bonded14Indices,
const std::vector<std::vector<double> >& nonbondedParameters,
double lj14Scale, double coulombScale ){
const std::vector<std::vector<double> >& nonbondedParameters ){
// ---------------------------------------------------------------------------------------
......@@ -1192,8 +1175,6 @@ int BrookBonded::loadInvMaps( int nbondeds, int nparticles, int *particles, int
* @param rbTorsionParameters vector of vector of rb torsion bond parameters -- one entry each bond (5 parameters)
* @param bonded14Indices vector of vector of Lennard-Jones 14 particle indices -- one entry each bond (2 particles )
* @param nonbondedParameters vector of vector of Lennard-Jones 14 parameters -- one entry each bond (3 parameters)
* @param lj14Scale scaling factor for 1-4 ixns
* @param coulombScale Coulomb scaling factor for 1-4 ixns
* @param platform Brook platform reference
*
* @return always 1
......@@ -1214,7 +1195,7 @@ int BrookBonded::setup( int numberOfParticles,
BrookBondParameters* periodicTorsionBrookBondParameters,
BrookBondParameters* rbTorsionBrookBondParameters,
BrookBondParameters* nonBonded14ForceParameters,
double lj14Scale, double coulombScale, int particleStreamWidth, int particleStreamSize ){
int particleStreamWidth, int particleStreamSize ){
// ---------------------------------------------------------------------------------------
......@@ -1226,8 +1207,9 @@ int BrookBonded::setup( int numberOfParticles,
if( PrintOn && getLog() ){
(void) fprintf( getLog(), "%s particles=%d\n [%p %p %p %p %p] (bond, angle, pd, rb, 14)\n"
"14Scale=%f %f StreamW=%d StreamSz=%d\n", methodName.c_str(), numberOfParticles, harmonicBondBrookBondParameters, harmonicAngleBrookBondParameters,
periodicTorsionBrookBondParameters, rbTorsionBrookBondParameters, nonBonded14ForceParameters, lj14Scale,coulombScale,
"StreamW=%d StreamSz=%d\n", methodName.c_str(), numberOfParticles, harmonicBondBrookBondParameters,
harmonicAngleBrookBondParameters,
periodicTorsionBrookBondParameters, rbTorsionBrookBondParameters, nonBonded14ForceParameters,
particleStreamWidth, particleStreamSize ); fflush( getLog() );
}
......@@ -1293,7 +1275,7 @@ int BrookBonded::setup( int numberOfParticles,
addBonds( &nbondeds, particles, params, harmonicBondBrookBondParameters->getParticleIndices(), harmonicBondBrookBondParameters->getBondParameters() );
}
if( nonBonded14ForceParameters ){
addPairs( &nbondeds, particles, params, charges, nonBonded14ForceParameters->getParticleIndices(), nonBonded14ForceParameters->getBondParameters(), lj14Scale, coulombScale );
addPairs( &nbondeds, particles, params, charges, nonBonded14ForceParameters->getParticleIndices(), nonBonded14ForceParameters->getBondParameters() );
}
// ---------------------------------------------------------------------------------------
......@@ -1419,11 +1401,6 @@ int BrookBonded::setup( int numberOfParticles,
delete[] particles;
delete[] charges;
// set the fudge factors
//_ljScale = (BrookOpenMMFloat) lj14Scale;
//_coulombFactor = (BrookOpenMMFloat) coulombScale;
// initialize output streams
for( int ii = 0; ii < getNumberOfForceStreams(); ii++ ){
......@@ -1473,12 +1450,6 @@ std::string BrookBonded::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%d", getNumberOfParticles() );
message << _getLine( tab, "Number of particles:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getLJ_14Scale() );
message << _getLine( tab, "LJ 14 scaling:", value );
(void) LOCAL_SPRINTF( value, "%.5f", getCoulombFactor() );
message << _getLine( tab, "Coulomb factor:", value );
(void) LOCAL_SPRINTF( value, "%d", getInverseMapStreamWidth() );
message << _getLine( tab, "Inverse map stream width:", value );
......@@ -1835,7 +1806,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
// bonded
float epsfac = (float) (getLJ_14Scale()*getCoulombFactor());
float epsfac = (float) (getCoulombFactor());
float width = (float) (getInverseMapStreamWidth());
// bonded forces
......@@ -1872,7 +1843,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
int countPrintInvMap[4] = { 3, 5, 2, 4 };
(void) fprintf( getLog(), "\nPost kbonded_CDLJ: epsFac=%.6f %.6f %.6f", epsfac, getLJ_14Scale(), getCoulombFactor());
(void) fprintf( getLog(), "\nPost kbonded_CDLJ: epsFac=%.6f %.6f", epsfac, getCoulombFactor());
(void) fprintf( getLog(), "\nParticle indices stream\n" );
getParticleIndicesStream()->printToFile( getLog() );
......@@ -1922,6 +1893,20 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
forceStream.getBrookStream(), forceStream.getBrookStream() );
} else if( getInverseMapStreamCount( I_Stream ) == 2 && getInverseMapStreamCount( K_Stream ) == 2 ){
kinvmap_gather2_2( width,
inverseStreamMaps[I_Stream][0]->getBrookStream(),
inverseStreamMaps[I_Stream][1]->getBrookStream(),
bondedForceStreams[I_Stream]->getBrookStream(),
inverseStreamMaps[K_Stream][0]->getBrookStream(),
inverseStreamMaps[K_Stream][1]->getBrookStream(),
bondedForceStreams[K_Stream]->getBrookStream(),
forceStream.getBrookStream(), forceStream.getBrookStream() );
} else if( getInverseMapStreamCount( I_Stream ) == 3 && getInverseMapStreamCount( K_Stream ) == 4 ){
kinvmap_gather3_4( width,
......
platforms/brook/src/BrookBonded.h
View file @ b7c8afa9
......@@ -79,8 +79,6 @@ class BrookBonded : public BrookCommon {
* @param bonded14Indices each element contains the indices of two particles whose nonbonded interactions should be reduced since
* they form a bonded 1-4 pair
* @param nonbondedParameters the nonbonded force parameters (charge, sigma, epsilon) for each particle
* @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
* @param coulomb14Scale the factor by which Coulomb interactions should be reduced for bonded 1-4 pairs
* @param log log reference
*
* @return nonzero value if error
......@@ -94,7 +92,7 @@ class BrookBonded : public BrookCommon {
const std::vector<std::vector<int> >& periodicTorsionIndices, const std::vector<std::vector<double> >& periodicTorsionParameters,
const std::vector<std::vector<int> >& rbTorsionIndices, const std::vector<std::vector<double> >& rbTorsionParameters,
const std::vector<std::vector<int> >& bonded14Indices, const std::vector<std::vector<double> >& nonbondedParameters,
double lj14Scale, double coulomb14Scale, const Platform& platform );
const Platform& platform );
*/
int setup( int numberOfParticles,
......@@ -102,7 +100,7 @@ class BrookBonded : public BrookCommon {
BrookBondParameters* harmonicAngleBrookBondParameters,
BrookBondParameters* periodicTorsionBrookBondParameters,
BrookBondParameters* rbTorsionBrookBondParameters,
BrookBondParameters* nonBonded14ForceParameters, double lj14Scale, double coulombScale, int particleStreamWidth, int particleStreamSize );
BrookBondParameters* nonBonded14ForceParameters, int particleStreamWidth, int particleStreamSize );
/**
* Get inverse map stream width
......@@ -168,15 +166,6 @@ class BrookBonded : public BrookCommon {
BrookFloatStreamInternal* getBrookParticleIndices( void ) const;
/**
* Get LJ 14 scale factor
*
* @return LJ 14 scaling (fudge) factor
*
*/
BrookOpenMMFloat getLJ_14Scale( void ) const;
/**
* Get Coulomb factor
*
......@@ -312,7 +301,6 @@ class BrookBonded : public BrookCommon {
// scale factors for 1-4 ixn
BrookOpenMMFloat _ljScale;
BrookOpenMMFloat _coulombFactor;
// streams
......@@ -408,15 +396,13 @@ class BrookBonded : public BrookCommon {
* @param bonded14Indices each element contains the indices of two particles whose nonbonded interactions should be reduced since
* they form a bonded 1-4 pair
* @param nonbondedParameters the nonbonded force parameters (charge, sigma, epsilon) for each particle
* @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
*
* @return nonzero value if error
*
*/
int addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* params[], BrookOpenMMFloat* charges,
const std::vector<std::vector<int> >& bonded14Indices, const std::vector<std::vector<double> >& nonbondedParameters,
double lj14Scale, double coulombScale );
const std::vector<std::vector<int> >& bonded14Indices, const std::vector<std::vector<double> >& nonbondedParameters );
/**
* Create and load inverse maps for bonded ixns
......
platforms/brook/src/BrookBrownianDynamics.cpp
View file @ b7c8afa9
......@@ -524,10 +524,9 @@ int BrookBrownianDynamics::update( Stream& positions, Stream& velocities,
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
10.0f,
25.0f,
(float) getBrownianDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
omega,
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.h
View file @ b7c8afa9
......@@ -152,7 +152,6 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
FILE* _log;
// Brook bond parameters
BrookBondParameters* _brookBondParameters;
......
platforms/brook/src/BrookCalcNonbondedForceKernel.cpp
View file @ b7c8afa9
......@@ -240,7 +240,7 @@ void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& syst
_brookBondParameters->setBond( ii, particles, parameters );
}
_openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters, 1.0, 1.0 );
_openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters );
if( log ){
std::string contents = _brookBondParameters->getContentsString( );
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp
View file @ b7c8afa9
......@@ -58,6 +58,12 @@ BrookIntegrateLangevinStepKernel::BrookIntegrateLangevinStepKernel( std::string
_brookLangevinDynamics = NULL;
_brookShakeAlgorithm = NULL;
_brookRandomNumberGenerator = NULL;
_log = NULL;
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
if( brookPlatform.getLog() != NULL ){
setLog( brookPlatform.getLog() );
}
}
......@@ -80,6 +86,31 @@ BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel( ){
}
/**
* Get log file reference
*
* @return log file reference
*
*/
FILE* BrookIntegrateLangevinStepKernel::getLog( void ) const {
return _log;
}
/**
* Set log file reference
*
* @param log file reference
*
* @return DefaultReturnValue
*
*/
int BrookIntegrateLangevinStepKernel::setLog( FILE* log ){
_log = log;
return DefaultReturnValue;
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
......@@ -92,10 +123,17 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "BrookIntegrateLangevinStepKernel::initialize";
static const int printOn = 1;
static const std::string methodName = "BrookIntegrateLangevinStepKernel::initialize";
// ---------------------------------------------------------------------------------------
FILE* log = getLog();
if( printOn && log ){
(void) fprintf( log, "%s\n", methodName.c_str() );
(void) fflush( log );
}
int numberOfParticles = system.getNumParticles();
// masses
......@@ -103,14 +141,24 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
std::vector<double> masses;
masses.resize( numberOfParticles );
if( printOn && log ){
(void) fprintf( log, "%s %d\n", methodName.c_str(), numberOfParticles );
(void) fflush( log );
}
for( int ii = 0; ii < numberOfParticles; ii++ ){
masses[ii] = static_cast<RealOpenMM>(system.getParticleMass(ii));
masses[ii] = static_cast<double>(system.getParticleMass(ii));
}
// constraints
int numberOfConstraints = system.getNumConstraints();
if( printOn && log ){
(void) fprintf( log, "%s const=%d\n", methodName.c_str(), numberOfConstraints );
(void) fflush( log );
}
std::vector<std::vector<int> > constraintIndicesVector;
constraintIndicesVector.resize( numberOfConstraints );
......@@ -122,13 +170,15 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
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 );
std::vector<int> constraintIndices;
constraintIndicesVector[ii] = constraintIndices;
constraintIndices[0] = particle1;
constraintIndices[1] = particle2;
constraintLengths[ii] = static_cast<RealOpenMM>(distance);
(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 );
constraintLengths.push_back( distance );
}
_brookLangevinDynamics = new BrookLangevinDynamics( );
......@@ -139,9 +189,13 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
// assert( (_brookShakeAlgorithm->getNumberOfConstraints() > 0) );
if( printOn && log ){
(void) fprintf( log, "%s done shake setup const=%d\n", methodName.c_str(), numberOfConstraints );
(void) fflush( log );
}
_brookRandomNumberGenerator = new BrookRandomNumberGenerator( );
_brookRandomNumberGenerator->setup( (int) masses.size(), getPlatform() );
// _brookRandomNumberGenerator->setVerbosity( 1 );
}
......@@ -174,10 +228,10 @@ 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()),
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.h
View file @ b7c8afa9
......@@ -89,8 +89,41 @@ class BrookIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
void execute( OpenMMContextImpl& context, const LangevinIntegrator& integrator );
/**
* Set log file reference
*
* @param log file reference
*
* @return DefaultReturnValue
*
*/
int setLog( FILE* log );
/*
* Get contents of object
*
* @param level of dump
*
* @return string containing contents
*
* */
std::string getContents( int level ) const;
/**
* Get log file reference
*
* @return log file reference
*
*/
FILE* getLog( void ) const;
protected:
FILE* _log;
BrookLangevinDynamics* _brookLangevinDynamics;
BrookShakeAlgorithm* _brookShakeAlgorithm;
BrookRandomNumberGenerator* _brookRandomNumberGenerator;
......
platforms/brook/src/BrookKernelFactory.cpp
View file @ b7c8afa9
......@@ -126,7 +126,7 @@ KernelImpl* BrookKernelFactory::createKernelImpl( std::string name, const Platfo
} else if( name == RemoveCMMotionKernel::Name() ){
// return new BrookRemoveCMMotionKernel( name, platform, openMMBrookInterface );
return new BrookRemoveCMMotionKernel( name, platform, openMMBrookInterface, context.getSystem() );
// KE calculator
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ b7c8afa9
......@@ -371,11 +371,11 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
// unused Shake parameter
float omega = 1.0f;
float numberOfIterations = 25.0f;
static const char* methodName = "\nBrookLangevinDynamics::update";
static const int PrintOn = 0;
static const int PrintOn = 1;
// ---------------------------------------------------------------------------------------
......@@ -482,10 +482,9 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
10.0f,
numberOfIterations,
(float) getLangevinDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
omega,
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......@@ -575,10 +574,9 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
10.0f,
numberOfIterations,
(float) getLangevinDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
omega,
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......
platforms/brook/src/BrookRemoveCMMotionKernel.cpp
View file @ b7c8afa9
......@@ -29,6 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "internal/OpenMMContextImpl.h"
#include "System.h"
#include "BrookRemoveCMMotionKernel.h"
#include "BrookStreamInternal.h"
......@@ -40,11 +42,13 @@ using namespace std;
*
* @param name name of the stream to create
* @param platform platform
* @param openMMBrookInterface OpenMM-Brook interface
* @param System System reference
*
*/
BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel( std::string name, const Platform& platform ) :
RemoveCMMotionKernel( name, platform ){
BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel( std::string name, const Platform& platform, OpenMMBrookInterface& openMMBrookInterface, System& system ) :
RemoveCMMotionKernel( name, platform ), _openMMBrookInterface( openMMBrookInterface ), _system( system ){
// ---------------------------------------------------------------------------------------
......@@ -52,8 +56,16 @@ BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel( std::string name, const Pl
// ---------------------------------------------------------------------------------------
_frequency = 0;
_log = NULL;
_brookVelocityCenterOfMassRemoval = NULL;
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
if( brookPlatform.getLog() != NULL ){
setLog( brookPlatform.getLog() );
}
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
}
/**
......@@ -75,11 +87,12 @@ BrookRemoveCMMotionKernel::~BrookRemoveCMMotionKernel( ){
/**
* Initialize the kernel
*
* @param masses array of particle masses
* @param system System reference
* @param force CMMotionRemover reference
*
*/
void BrookRemoveCMMotionKernel::initialize( const vector<double>& masses ){
void BrookRemoveCMMotionKernel::initialize( const System& system, const CMMotionRemover& force ){
// ---------------------------------------------------------------------------------------
......@@ -87,6 +100,13 @@ void BrookRemoveCMMotionKernel::initialize( const vector<double>& masses ){
// ---------------------------------------------------------------------------------------
_frequency = force.getFrequency();
std::vector<double> masses;
masses.resize( system.getNumParticles() );
for( size_t ii = 0; ii < masses.size(); ii++ ){
masses[ii] = system.getParticleMass(ii);
}
_brookVelocityCenterOfMassRemoval = new BrookVelocityCenterOfMassRemoval();
_brookVelocityCenterOfMassRemoval->setup( masses, getPlatform() );
......@@ -94,14 +114,51 @@ void BrookRemoveCMMotionKernel::initialize( const vector<double>& masses ){
}
/**
* Get log file reference
*
* @return log file reference
*
*/
FILE* BrookRemoveCMMotionKernel::getLog( void ) const {
return _log;
}
/**
* Set log file reference
*
* @param log file reference
*
* @return DefaultReturnValue
*
*/
int BrookRemoveCMMotionKernel::setLog( FILE* log ){
_log = log;
return BrookCommon::DefaultReturnValue;
}
/**
* Get COM removal frequency
*
* @return frequency
*
*/
int BrookRemoveCMMotionKernel::getFrequency( void ) const {
return _frequency;
}
/**
* Execute kernel
*
* @param velocities array of particle velocities
* @param context OpenMMContextImpl reference
*
*/
void BrookRemoveCMMotionKernel::execute( Stream& velocities ){
void BrookRemoveCMMotionKernel::execute( OpenMMContextImpl& context ){
// ---------------------------------------------------------------------------------------
......@@ -109,7 +166,14 @@ void BrookRemoveCMMotionKernel::execute( Stream& velocities ){
// ---------------------------------------------------------------------------------------
_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities );
int step = (int) floor( context.getTime()/context.getIntegrator().getStepSize() );
int frequency = getFrequency();
if( frequency <= 0 || (step % frequency) != 0 ){
return;
}
BrookStreamImpl* velocities = _openMMBrookInterface.getParticleVelocities();
_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( *velocities );
return;
}
platforms/brook/src/BrookRemoveCMMotionKernel.h
View file @ b7c8afa9
......@@ -33,6 +33,7 @@
* -------------------------------------------------------------------------- */
#include "kernels.h"
#include "OpenMMBrookInterface.h"
#include "BrookVelocityCenterOfMassRemoval.h"
namespace OpenMM {
......@@ -50,10 +51,12 @@ class BrookRemoveCMMotionKernel : public RemoveCMMotionKernel {
*
* @param name name of the stream to create
* @param platform platform
* @param openMMBrookInterface OpenMM-Brook interface
* @param System System reference
*
*/
BrookRemoveCMMotionKernel( std::string name, const Platform& platform );
BrookRemoveCMMotionKernel( std::string name, const Platform& platform, OpenMMBrookInterface& openMMBrookInterface, System& system );
/**
* BrookRemoveCMMotionKernel destructor
......@@ -62,26 +65,82 @@ class BrookRemoveCMMotionKernel : public RemoveCMMotionKernel {
~BrookRemoveCMMotionKernel();
/**
* Get COM removal frequency
*
* @return frequency
*
*/
int getFrequency( void ) const;
/**
* Set log file reference
*
* @param log file reference
*
* @return DefaultReturnValue
*
*/
int setLog( FILE* log );
/*
* Get contents of object
*
* @param level of dump
*
* @return string containing contents
*
* */
std::string getContents( int level ) const;
/**
* Get log file reference
*
* @return log file reference
*
*/
FILE* getLog( void ) const;
/**
* Initialize the kernel
*
* @param masses mass of each particle
* @param system System reference
* @param force CMMotionRemover reference
*
*/
void initialize( const std::vector<double>& masses );
void initialize( const System& system, const CMMotionRemover& force );
/**
* Execute the kernel.
*
* @param velocities stream of particle velocities
* @param context OpenMMContextImpl reference
*
*/
void execute( Stream& velocities );
void execute( OpenMMContextImpl& context );
private:
int _frequency;
// log file reference
FILE* _log;
BrookVelocityCenterOfMassRemoval* _brookVelocityCenterOfMassRemoval;
// interface
OpenMMBrookInterface& _openMMBrookInterface;
// System reference
System& _system;
};
} // namespace OpenMM
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp
View file @ b7c8afa9
......@@ -143,7 +143,7 @@ BrookFloatStreamInternal* BrookVelocityCenterOfMassRemoval::getLinearMomentumStr
*
*/
int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& velocities ){
int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( BrookStreamImpl& velocityStream ){
// ---------------------------------------------------------------------------------------
......@@ -154,12 +154,11 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
if( debug && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocities, com );
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] );
BrookStreamImpl& v1 = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (v1.getBrookStreamImpl());
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
void* velV = velocityStream->getData( 1 );
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
int index = 0;
......@@ -174,8 +173,6 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
BrookStreamImpl& velocityStream = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
kCalculateLinearMomentum( getMassStream()->getBrookStream(), velocityStream.getBrookStream(), getWorkStream()->getBrookStream() );
kSumLinearMomentum( (float) getComParticleStreamWidth(), (float) getNumberOfParticles(), getWorkStream()->getBrookStream(), getLinearMomentumStream()->getBrookStream() );
kScale( (float) getTotalInverseMass(), getLinearMomentumStream()->getBrookStream(), getLinearMomentumStream()->getBrookStream() );
......@@ -183,7 +180,7 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
if( (0 || debug) && getLog() ){
BrookOpenMMFloat com[3];
getVelocityCenterOfMass( velocities, com );
getVelocityCenterOfMass( velocityStream, com );
(void) fprintf( getLog(), "%s strW=%d iatm=%d Post removal com: [%12.5e %12.5e %12.5e]", methodName,
getComParticleStreamWidth(), getNumberOfParticles(), com[0], com[1], com[2] );
......@@ -191,10 +188,9 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
float* linMo = (float*) linMoV;
(void) fprintf( getLog(), "LM [%12.5e %12.5e %12.5e]\n", linMo[0], linMo[1], linMo[2] );
BrookStreamImpl& v1 = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (v1.getBrookStreamImpl());
BrookStreamInternal* outputVelocityStream = dynamic_cast<BrookStreamInternal*> (velocityStream.getBrookStreamImpl());
void* velV = velocityStream->getData( 1 );
void* velV = outputVelocityStream->getData( 1 );
const float* vArray = (float*) velV;
void* w1 = getWorkStream()->getData( 1 );
......@@ -225,7 +221,7 @@ int BrookVelocityCenterOfMassRemoval::removeVelocityCenterOfMass( Stream& veloci
*
*/
int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( Stream& velocities, BrookOpenMMFloat velocityCom[3] ){
int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3] ){
// ---------------------------------------------------------------------------------------
......@@ -239,8 +235,7 @@ int BrookVelocityCenterOfMassRemoval::getVelocityCenterOfMass( Stream& velocitie
// calculate linear momentum via reduction
// subtract it (/totalMass) from velocities
BrookStreamImpl& v1 = dynamic_cast<BrookStreamImpl&> (velocities.getImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (v1.getBrookStreamImpl());
BrookStreamInternal* velocityStream = dynamic_cast<BrookStreamInternal*> (vStream.getBrookStreamImpl());
void* velV = velocityStream->getData( 1 );
const float* vArray = (float*) velV;
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.h
View file @ b7c8afa9
......@@ -35,7 +35,8 @@
#include <vector>
#include <set>
#include "BrookFloatStreamInternal.h"
#include "BrookStreamImpl.h"
//#include "BrookFloatStreamInternal.h"
#include "BrookPlatform.h"
#include "BrookCommon.h"
......@@ -98,7 +99,7 @@ class BrookVelocityCenterOfMassRemoval : public BrookCommon {
*
*/
int removeVelocityCenterOfMass( Stream& velocities );
int removeVelocityCenterOfMass( BrookStreamImpl& velocityStream );
/**
* Get velocity center-of-mass
......@@ -110,7 +111,7 @@ class BrookVelocityCenterOfMassRemoval : public BrookCommon {
*
*/
int getVelocityCenterOfMass( Stream& velocities, BrookOpenMMFloat velocityCom[3] );
int getVelocityCenterOfMass( BrookStreamImpl& vStream, BrookOpenMMFloat velocityCom[3] );
/*
* Setup of parameters
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ b7c8afa9
......@@ -185,7 +185,7 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
// unused Shake parameter
float omega = 1.0f;
float numberOfIterations = 25.0f;
static const char* methodName = "\nBrookVerletDynamics::update";
......@@ -261,10 +261,9 @@ int BrookVerletDynamics::update( Stream& positions, Stream& velocities,
if( brookShakeAlgorithm.getNumberOfConstraints() > 0 ){
kshakeh_fix1(
10.0f,
25.0f,
(float) getVerletDynamicsParticleStreamWidth(),
brookShakeAlgorithm.getInverseHydrogenMass(),
omega,
brookShakeAlgorithm.getShakeParticleIndicesStream()->getBrookStream(),
positionStream.getBrookStream(),
getXPrimeStream()->getBrookStream(),
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ b7c8afa9
......@@ -78,9 +78,6 @@ OpenMMBrookInterface::OpenMMBrookInterface( int streamWidth ) : _particleStreamW
_referencePlatform = NULL;
_refVerletIntegrator = NULL;
_lj14Scale = 1.0;
_coulomb14Scale = 1.0;
_particleStreamSize = -1;
for( int ii = 0; ii < LastBondForce; ii++ ){
......@@ -165,28 +162,6 @@ int OpenMMBrookInterface::getParticleStreamSize( void ) const {
return _particleStreamSize;
}
/**
* Get LJ-14 scale factor
*
* @return LJ-14 scale factor
*
*/
double OpenMMBrookInterface::getLj14Scale( void ) const {
return _lj14Scale;
}
/**
* Get Coulomb scale factor
*
* @return Coulomb scale factor
*
*/
double OpenMMBrookInterface::getCoulomb14Scale( void ) const {
return _coulomb14Scale;
}
/**
* Get log file reference
*
......@@ -367,17 +342,12 @@ BrookBondParameters* OpenMMBrookInterface::getNonBonded14ForceParameters( void )
* Set BrookBondParameters for LJ 14 force
*
* @param brookBondParameters brookBondParameters for LJ 14 force
* @param lj14Scale LJ 14 scale factor
* @param coulomb14Scale Coulomb 14 scale factor
*
* @return DefaultReturnValue
*
*/
int OpenMMBrookInterface::setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters,
double lj14Scale, double coulomb14Scale ){
_lj14Scale = lj14Scale;
_coulomb14Scale = coulomb14Scale;
int OpenMMBrookInterface::setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters ){
return _setBondParameters( LJ14Index, brookBondParameters );
}
......@@ -584,19 +554,17 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
(void) fprintf( stderr, "%s done nonbonded: bonded=%d completed=%d\n", methodName.c_str(), _brookBonded.isActive(), _brookBonded.isSetupCompleted() ); (void) fflush( stderr );
if( _brookBonded.isActive() ){
//(void) fprintf( stderr, "%s Bonded\n", methodName.c_str() ); (void) fflush( stderr );
// perform setup first time through
//if( _brookBonded.isSetupCompleted() == 0 ){
if( _brookBonded.isSetupCompleted() >= -1 ){
_brookBonded.setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
getPeriodicTorsionForceParameters(), getRBTorsionForceParameters(),
getNonBonded14ForceParameters(),
getLj14Scale(), getCoulomb14Scale(), getParticleStreamWidth(), getParticleStreamSize() );
getParticleStreamWidth(), getParticleStreamSize() );
}
(void) fprintf( stderr, "%s done setup bonded=%d completed=%d\n", methodName.c_str(), _brookBonded.isActive(), _brookBonded.isSetupCompleted() ); (void) fflush( stderr );
_brookBonded.computeForces( *positions, *forces );
(void) fprintf( stderr, "%s done forces bonded=%d completed=%d\n", methodName.c_str(), _brookBonded.isActive(), _brookBonded.isSetupCompleted() ); (void) fflush( stderr );
// diagnostics
......
platforms/brook/src/OpenMMBrookInterface.h
View file @ b7c8afa9
......@@ -128,24 +128,6 @@ class OpenMMBrookInterface {
int getParticleStreamSize( void ) const;
/**
* Get LJ-14 scale factor
*
* @return LJ-14 scale factor
*
*/
double getLj14Scale( void ) const;
/**
* Get Coulomb scale factor
*
* @return Coulomb scale factor
*
*/
double getCoulomb14Scale( void ) const;
/**
* Get log file reference
*
......@@ -332,14 +314,12 @@ class OpenMMBrookInterface {
* Set BrookBondParameters for LJ 14 force
*
* @param brookBondParameters brookBondParameters for LJ 14 force
* @param lj14Scale LJ 14 scale factor
* @param coulomb14Scale Coulomb 14 scale factor
*
* @return DefaultReturnValue
*
*/
int setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters, double lj14Scale, double coulomb14Scale );
int setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters );
/**
* Get positions stream
......@@ -419,9 +399,6 @@ class OpenMMBrookInterface {
int _numberOfParticles;
double _lj14Scale;
double _coulomb14Scale;
// Brook bonded, nonbonded, Gbsa
BrookBonded _brookBonded;
......
platforms/brook/src/gpu/kinvmap_gather.br
View file @ b7c8afa9
......@@ -249,6 +249,29 @@ kernel void kinvmap_gather6(
}
//Takes three + four inverse maps
kernel void kinvmap_gather2_2(
float strwidth, //stream width of the dihedral forces
float4 invmap3_1<>, //indices into the dihedral forces
float4 invmap3_2<>, //indices into the dihedral forces
float3 forces3[][], //dihedral forces
float4 invmap4_1<>, //indices into the dihedral forces
float4 invmap4_2<>, //indices into the dihedral forces
float3 forces4[][], //dihedral forces
float3 inforce<>, //particle forces before
out float3 outforce<> //particle forces after
)
{
outforce = inforce;
outforce += do_gather_nobranch( strwidth, invmap3_1, forces3 );
outforce += do_gather_nobranch( strwidth, invmap3_2, forces3 );
outforce += do_gather_nobranch( strwidth, invmap4_1, forces4 );
outforce += do_gather_nobranch( strwidth, invmap4_2, forces4 );
}
//Takes three + four inverse maps
kernel void kinvmap_gather3_3(
float strwidth, //stream width of the dihedral forces
......
platforms/brook/src/gpu/kinvmap_gather.h
View file @ b7c8afa9
......@@ -81,6 +81,16 @@ void kinvmap_gather6 (const float strwidth,
::brook::stream outforce);
void kinvmap_gather2_2 (const float strwidth,
::brook::stream invmap3_1,
::brook::stream invmap3_2,
::brook::stream forces3,
::brook::stream invmap4_1,
::brook::stream invmap4_2,
::brook::stream forces4,
::brook::stream inforce,
::brook::stream outforce);
void kinvmap_gather3_3 (const float strwidth,
::brook::stream invmap3_1,
::brook::stream invmap3_2,
......
platforms/brook/src/gpu/kshakeh.br
View file @ b7c8afa9
......@@ -43,169 +43,6 @@
* to avoid stalling
* *************************************************************/
/*
kernel void
kshakeh(
float nit, //number of iterations
float strwidth, //stream width of posq
float invmH, //inverse mass of hydrogen
float omega, //parameter from gromacs, possibly unused
float4 atoms<>, //heavy0, h1, h2, h3
float4 posq[][], //positions before update
float4 posqp[][], //positions after update
float4 params<>, // (1/m0, mu/2, blensq, 0.0f )
out float4 cposq0<>, //constrained position for heavy atom
out float4 cposq1<>, //ditto for h1
out float4 cposq2<>, //ditto for h2
out float4 cposq3<> //ditto for h3
) {
float2 ai, aj1, aj2, aj3; //2d indices, can be precalc.
float i; //iteration count
float3 xi, xj1, xj2, xj3; //coordinates
float3 xpi, xpj1, xpj2, xpj3; //coordinates
float3 rij1, rij2, rij3, rpij, dr;
float rpsqij, rrpr, acor;
float mask2, mask3;
float diff;
ai.y = floor( atoms.x / strwidth );
ai.x = atoms.x - ai.y * strwidth;
aj1.y = floor( atoms.y / strwidth );
aj1.x = atoms.y - aj1.y * strwidth;
//If further hydrogens are absent,
//just set to the coordinates of the first
//so we don't have any junk memory accesses
//or nans/infs in the calcs.
if ( atoms.z > -0.5f ) {
aj2.y = floor( atoms.z / strwidth );
aj2.x = atoms.z - aj2.y * strwidth;
mask2 = 1.0f;
}
else {
aj2 = aj1;
mask2 = 0.0f;
}
if ( atoms.w > -0.5f ) {
aj3.y = floor( atoms.w / strwidth );
aj3.x = atoms.w - aj3.y * strwidth;
mask3 = 1.0f;
}
else {
aj3 = aj1;
mask3 = 0.0f;
}
cposq0 = posq[ai];
cposq1 = posq[aj1];
cposq2 = posq[aj2];
cposq3 = posq[aj3];
xi = cposq0.xyz;
xj1 = cposq1.xyz;
xj2 = cposq2.xyz;
xj3 = cposq3.xyz;
rij1 = xi - xj1;
rij2 = xi - xj2;
rij3 = xi - xj3;
xpi = posqp[ai].xyz;
xpj1 = posqp[aj1].xyz;
xpj2 = posqp[aj2].xyz;
xpj3 = posqp[aj3].xyz;
i = 0.0f;
while ( i < 15.0f ) {
//First hydrogen
rpij = xpi - xpj1;
rpsqij = dot( rpij, rpij );
rrpr = dot( rij1, rpij );
//for debugging only
diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
if ( diff < 1.0f )
acor = 0.0f;
else
//params.y = mu/2, params.z = blen*blen
acor = omega * ( params.z - rpsqij ) * params.y / rrpr ;
dr = rij1 * acor;
xpi += dr * params.x;
xpj1 -= dr * invmH;
//Second hydrogen
rpij = xpi - xpj2;
rpsqij = dot( rpij, rpij );
rrpr = dot( rij2, rpij );
//for debugging only
diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
if ( diff < 1.0f )
acor = 0.0f;
else
//params.y = mu/2, params.z = blen*blen
acor = mask2 * omega * ( params.z - rpsqij ) * params.y / rrpr ;
dr = rij2 * acor;
xpi += dr * params.x;
xpj2 -= dr * invmH;
//Third hydrogen
rpij = xpi - xpj3;
rpsqij = dot( rpij, rpij );
rrpr = dot( rij3, rpij );
//for debugging only
diff = abs( params.z - rpsqij ) / (params.z * 2 * 1e-4 );
if ( diff < 1.0f )
acor = 0.0f;
else
//params.y = mu/2, params.z = blen*blen
acor = mask3 * omega * ( params.z - rpsqij ) * params.y / rrpr ;
dr = rij3 * acor;
xpi += dr * params.x;
xpj3 -= dr * invmH;
i += 1.0f;
}
cposq0.xyz = xpi;
cposq1.xyz = xpj1;
cposq2.xyz = xpj2;
cposq3.xyz = xpj3;
} */
/*Applies the updated positions
*Each atom occurs at one and only one position
* */
/*
kernel void kshakeh_update(
float strwidth, //width of cposq streams
float2 invmap<>, //shakeh inverse map
float4 posq<>, //untouched positions
float4 cposq0[][], //constrained position for heavy atom
float4 cposq1[][], //ditto for h1
float4 cposq2[][], //ditto for h2
float4 cposq3[][], //ditto for h3
out float4 oposq<> //updated positions
){
float2 atom;
atom.y = floor( invmap.x / strwidth );
atom.x = invmap.x - atom.y * strwidth;
if ( invmap.y < 0 )
oposq = posq;
else if ( invmap.y < 0.5f )
oposq = cposq0[ atom ];
else if ( invmap.y < 1.5f )
oposq = cposq1[ atom ];
else if ( invmap.y < 2.5f )
oposq = cposq2[ atom ];
else if ( invmap.y < 3.5f )
oposq = cposq3[ atom ];
} */
/* Fix for precision of terms first order in dt
* To be used with corresponding update kernels
* The input posqp is now changes to posq rather than
......@@ -216,7 +53,6 @@ kshakeh_fix1(
float nit, //number of iterations
float strwidth, //stream width of posq
float invmH, //inverse mass of hydrogen
float omega, //parameter from gromacs, possibly unused
float4 atoms<>, //heavy0, h1, h2, h3
float3 posq[][], //positions before update
float3 posqp[][], //changes to positions
......@@ -329,7 +165,7 @@ kshakeh_fix1(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = omega * ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
acor = ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
dr = rij1 * acor;
xpi += dr * params.x;
xpj1 -= dr * invmH;
......@@ -343,7 +179,7 @@ kshakeh_fix1(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = mask2 * omega * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
acor = mask2 * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
dr = rij2 * acor;
xpi += dr * params.x;
xpj2 -= dr * invmH;
......@@ -357,7 +193,7 @@ kshakeh_fix1(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = mask3 * omega * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
acor = mask3 * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
dr = rij3 * acor;
xpi += dr * params.x;
xpj3 -= dr * invmH;
......@@ -378,7 +214,6 @@ kshakeh_fix2(
float nit, //number of iterations
float strwidth, //stream width of posq
float invmH, //inverse mass of hydrogen
float omega, //parameter from gromacs, possibly unused
float4 atoms<>, //heavy0, h1, h2, h3
float3 posq[][], //positions before update
float3 posqp[][], //changes to positions
......@@ -492,7 +327,7 @@ kshakeh_fix2(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = omega * ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
acor = ( ld1 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij1sq ) ;
dr = rij1 * acor;
xpi += dr * params.x;
xpj1 -= dr * invmH;
......@@ -506,7 +341,7 @@ kshakeh_fix2(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = mask2 * omega * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
acor = mask2 * ( ld2 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij2sq ) ;
dr = rij2 * acor;
xpi += dr * params.x;
xpj2 -= dr * invmH;
......@@ -520,7 +355,7 @@ kshakeh_fix2(
if ( diff < 1.0f )
acor = 0.0f;
else
acor = mask3 * omega * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
acor = mask3 * ( ld3 - 2 * rrpr - rpsqij ) * params.y / ( rrpr + rij3sq ) ;
dr = rij3 * acor;
xpi += dr * params.x;
xpj3 -= dr * invmH;
......@@ -536,36 +371,6 @@ kshakeh_fix2(
}
/*Applies the updated delta's
*Each atom occurs at one and only one position
* */
kernel void kshakeh_update1_fix1Old(
float strwidth, //width of cposq streams
float2 invmap<>, //shakeh inverse map
float3 posq<>, //constrained deltas
float3 cposq0[][], //constrained delta for heavy atom
float3 cposq1[][], //ditto for h1
float3 cposq2[][], //ditto for h2
float3 cposq3[][], //ditto for h3
out float3 oposq<> //updated deltas
){
float2 atom;
//atom.y = floor( invmap.x / strwidth );
atom.y = round( (invmap.x - fmod( invmap.x, strwidth ))/strwidth );
atom.x = invmap.x - atom.y * strwidth;
if ( invmap.y < 0 )
oposq = posq;
else if ( invmap.y < 0.5f )
oposq = cposq0[ atom ];
else if ( invmap.y < 1.5f )
oposq = cposq1[ atom ];
else if ( invmap.y < 2.5f )
oposq = cposq2[ atom ];
else if ( invmap.y < 3.5f )
oposq = cposq3[ atom ];
}
kernel void kshakeh_update2_fix1(
float strwidth, //width of cposq streams
......
platforms/brook/src/gpu/kshakeh.h
View file @ b7c8afa9
......@@ -32,46 +32,6 @@
void kshakeh_fix1 (const float nit,
const float strwidth,
const float invmH,
const float omega,
::brook::stream atoms,
::brook::stream posq,
::brook::stream posqp,
::brook::stream params,
::brook::stream cposq0,
::brook::stream cposq1,
::brook::stream cposq2,
::brook::stream cposq3);
void kshakeh_fix2 (const float nit,
const float strwidth,
const float invmH,
const float omega,
::brook::stream atoms,
::brook::stream posq,
::brook::stream posqp,
::brook::stream params,
::brook::stream cposq0,
::brook::stream cposq1,
::brook::stream cposq2,
::brook::stream cposq3);
void kshakeh_update (const float strwidth,
::brook::stream invmap,
::brook::stream posq,
::brook::stream cposq0,
::brook::stream cposq1,
::brook::stream cposq2,
::brook::stream cposq3,
::brook::stream oposq) ;
void kshakeh (const float nit,
const float strwidth,
const float invmH,
const float omega,
::brook::stream atoms,
::brook::stream posq,
::brook::stream posqp,
......@@ -94,14 +54,6 @@ void kshakeh_update1_fix1 (
::brook::stream cposq3,
::brook::stream oposq);
void kshakeh_update1_fix1Old (const float strwidth,
::brook::stream invmap,
::brook::stream posq,
::brook::stream cposq0,
::brook::stream cposq1,
::brook::stream cposq2,
::brook::stream cposq3,
::brook::stream oposq);
void kshakeh_update2_fix1 (const float strwidth,
::brook::stream invmap,
......
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