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Commit 7ed51ce4 authored by Mark Friedrichs's avatar Mark Friedrichs
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Bonded forces ok

parent 08c2e027
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Showing with 221 additions and 137 deletions
platforms/brook/src/BrookBonded.cpp
View file @ 7ed51ce4
......@@ -521,8 +521,8 @@ int BrookBonded::matchTorsion( int i, int j, int k, int l, int nbondeds, int *pa
* in the fourth component and match the middle two components
*
* The last bit will not be needed as long as gromacs generates
* all dihedrals. But I think there are force fields that don't
* use all dihedrals.
* all torsions. But I think there are force fields that don't
* use all torsions.
*
* @return ErrorReturnValue if error; else particle index
*
......@@ -711,7 +711,7 @@ int BrookBonded::matchPair( int i, int j, int nbondeds, int *particles ){
*
*/
int BrookBonded::addRBDihedrals( int *nbondeds, int *particles, float *params[],
int BrookBonded::addRBTorsions( int *nbondeds, int *particles, float *params[],
const vector<vector<int> >& rbTorsionIndices,
const vector<vector<double> >& rbTorsionParameters ){
......@@ -779,13 +779,13 @@ int BrookBonded::addRBDihedrals( int *nbondeds, int *particles, float *params[],
*
*/
int BrookBonded::addPDihedrals( int *nbondeds, int *particles, BrookOpenMMFloat* params[],
int BrookBonded::addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* params[],
const vector<vector<int> >& periodicTorsionIndices,
const vector<vector<double> >& periodicTorsionParameters ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBonded::addPDihedrals";
static const std::string methodName = "BrookBonded::addPTorsion";
static const int debug = 0;
// ---------------------------------------------------------------------------------------
......@@ -815,9 +815,12 @@ int BrookBonded::addPDihedrals( int *nbondeds, int *particles, BrookOpenMMFloat*
ATOMS( ibonded, 3 ) = l;
(*nbondeds)++;
}
PARAMS( ibonded, 1, 1 ) = (BrookOpenMMFloat) pTParameters[0];
// note: parameters 0 & 2 switched
PARAMS( ibonded, 1, 1 ) = (BrookOpenMMFloat) pTParameters[2];
PARAMS( ibonded, 1, 2 ) = (BrookOpenMMFloat) pTParameters[1];
PARAMS( ibonded, 1, 3 ) = (BrookOpenMMFloat) pTParameters[2];
PARAMS( ibonded, 1, 3 ) = (BrookOpenMMFloat) pTParameters[0];
if( debug && getLog() ){
(void) fprintf( getLog(), " %d [%d %d %d %d] %.3e %.3e %.3e\n", ibonded, i, j, k, l,
......@@ -910,7 +913,7 @@ int BrookBonded::addBonds( int *nbondeds, int *particles, float *params[], const
// ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBonded::addBonds";
static const int debug = 1;
static const int debug = 0;
// ---------------------------------------------------------------------------------------
......@@ -1269,10 +1272,18 @@ int BrookBonded::setup( int numberOfParticles,
int nbondeds = 0;
addRBDihedrals( &nbondeds, particles, params, rbTorsionBrookBondParameters->getParticleIndices(), rbTorsionBrookBondParameters->getBondParameters() );
addPDihedrals ( &nbondeds, particles, params, periodicTorsionBrookBondParameters->getParticleIndices(), periodicTorsionBrookBondParameters->getBondParameters() );
if( rbTorsionBrookBondParameters ){
addRBTorsions( &nbondeds, particles, params, rbTorsionBrookBondParameters->getParticleIndices(), rbTorsionBrookBondParameters->getBondParameters() );
}
if( periodicTorsionBrookBondParameters ){
addPTorsions( &nbondeds, particles, params, periodicTorsionBrookBondParameters->getParticleIndices(), periodicTorsionBrookBondParameters->getBondParameters() );
}
if( harmonicAngleBrookBondParameters ){
addAngles( &nbondeds, particles, params, harmonicAngleBrookBondParameters->getParticleIndices(), harmonicAngleBrookBondParameters->getBondParameters() );
}
if( harmonicBondBrookBondParameters ){
addBonds( &nbondeds, particles, params, harmonicBondBrookBondParameters->getParticleIndices(), harmonicBondBrookBondParameters->getBondParameters() );
}
// ---------------------------------------------------------------------------------------
......@@ -1287,13 +1298,15 @@ int BrookBonded::setup( int numberOfParticles,
//(void) fprintf( getLog(), "%s Post addBonds particles=%d number of bonds=%d maxBonds=%d\n", methodName.c_str(), numberOfParticles, nbondeds, maxBonds );
if( nonBonded14ForceParameters ){
addPairs( &nbondeds, particles, params, charges, nonBonded14ForceParameters->getParticleIndices(), nonBonded14ForceParameters->getBondParameters(), lj14Scale, coulombScale );
}
// check that number of bonds not too large for memory allocated
if( nbondeds >= maxBonds ){
std::stringstream message;
message << methodName << " number of bonds=" << nbondeds << " is greater than maxBonds=" << maxBonds;
message << methodName << " number of bonds=" << nbondeds << " is greater than maxBonds=" << maxBonds << " numberOfParticles=" << numberOfParticles;
throw OpenMMException( message.str() );
} else if( PrintOn && getLog() ){
(void) fprintf( getLog(), "%s particles=%d number of bonds=%d maxBonds=%d\n", methodName.c_str(), numberOfParticles, nbondeds, maxBonds );
......@@ -1515,7 +1528,7 @@ std::string BrookBonded::getContentsString( int level ) const {
* forces are to be picked up from and stores the position
* in the appropriate index.
*
* Input: number of dihedrals, the particle indices, and a flag indicating
* Input: number of torsions, the particle indices, and a flag indicating
* whether we're doing i(0), j(1), k(2) or l(3)
* Output: an array of counts per particle
* arrays of inversemaps
......@@ -1595,12 +1608,12 @@ if( particle > particleRange[1] ){
//Check to make sure we're inside the limits
if ( counts[particle] > nmaps * 4 ){
if( PrintOn && getLog() ){
(void) fprintf( getLog(), "%s Particle %d has too many proper dihedrals(%d, max %d)\n",
(void) fprintf( getLog(), "%s Particle %d has too many proper torsions (%d, max %d)\n",
methodName.c_str(), particle, counts[particle], nmaps*4 );
(void) fflush( getLog() );
}
std::stringstream message;
message << methodName << " Particle " << particle << " has too many proper dihedrals; valid range:(" << counts[particle] << ", " << nmaps*4 << ")";
message << methodName << " Particle " << particle << " has too many proper torsions; valid range:(" << counts[particle] << ", " << nmaps*4 << ")";
throw OpenMMException( message.str() );
}
......@@ -1869,8 +1882,9 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
brookStreamInternalF->printToFile( getLog() );
*/
(void) fprintf( getLog(), "\nInverse map streams -- K_Stream cnt=%d\n", getInverseMapStreamCount( K_Stream ) );
(void) fprintf( getLog(), "\nInverse map streams\n" );
for( int ii = 0; ii < 4; ii++ ){
(void) fprintf( getLog(), "\nInverse map streams -- StreamIndex=%d cnt=%d\n", ii, getInverseMapStreamCount( ii ) );
for( int jj = 0; jj < countPrintInvMap[ii]; jj++ ){
(void) fprintf( getLog(), "\n Inverse map streams index=%d %d\n", ii, jj );
inverseStreamMaps[ii][jj]->printToFile( getLog() );
......@@ -1928,11 +1942,20 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
bondedForceStreams[K_Stream]->getBrookStream(),
forceStream.getBrookStream(), forceStream.getBrookStream() );
} else if( getInverseMapStreamCount( I_Stream ) == 1 && getInverseMapStreamCount( K_Stream ) == 1 ){
kinvmap_gather1_1( width,
inverseStreamMaps[I_Stream][0]->getBrookStream(),
bondedForceStreams[I_Stream]->getBrookStream(),
inverseStreamMaps[K_Stream][0]->getBrookStream(),
bondedForceStreams[K_Stream]->getBrookStream(),
forceStream.getBrookStream(), forceStream.getBrookStream() );
} else {
// case not handled -- throw an exception
if( getLog() && ErrorMessages++ < MaxErrorMessages ){
if( getLog() && ErrorMessages++ < MaxErrorMessages && getInverseMapStreamCount( I_Stream ) > 0 && getInverseMapStreamCount( K_Stream ) > 0 ){
(void) fprintf( getLog(), "%s case: I-map=%d K-map=%d -- not handled.\n",
methodName.c_str(), getInverseMapStreamCount( I_Stream ),
getInverseMapStreamCount( K_Stream ) );
......@@ -1988,13 +2011,16 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
// case not handled -- throw an exception
if( getLog() && ErrorMessages++ < MaxErrorMessages ){
if( getLog() && ErrorMessages++ < MaxErrorMessages && getInverseMapStreamCount( J_Stream ) > 0 && getInverseMapStreamCount( L_Stream ) > 0 ){
(void) fprintf( getLog(), "%s case: J-map=%d L-map=%d -- not handled.\n",
methodName.c_str(), getInverseMapStreamCount( J_Stream ),
getInverseMapStreamCount( L_Stream ) );
(void) fflush( getLog() );
}
// this is for testing purposes a-- may need to be cleaned
// or add new gather functions
kinvmap_gather5_2( width,
inverseStreamMaps[J_Stream][0]->getBrookStream(),
inverseStreamMaps[J_Stream][1]->getBrookStream(),
......@@ -2006,6 +2032,7 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
inverseStreamMaps[L_Stream][1]->getBrookStream(),
bondedForceStreams[L_Stream]->getBrookStream(),
forceStream.getBrookStream(), forceStream.getBrookStream() );
/*
std::stringstream message;
message << methodName << "J-maps=" << getInverseMapStreamCount( J_Stream ) << " and " <<
......
platforms/brook/src/BrookBonded.h
View file @ 7ed51ce4
......@@ -347,7 +347,7 @@ class BrookBonded : public BrookCommon {
*
*/
int addRBDihedrals( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& rbTorsionIndices,
int addRBTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& rbTorsionIndices,
const std::vector<std::vector<double> >& rbTorsionParameters );
/**
......@@ -363,7 +363,7 @@ class BrookBonded : public BrookCommon {
*
*/
int addPDihedrals( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& periodicTorsionIndices,
int addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& periodicTorsionIndices,
const std::vector<std::vector<double> >& periodicTorsionParameters );
/**
......@@ -456,7 +456,7 @@ class BrookBonded : public BrookCommon {
* forces are to be picked up from and stores the position
* in the appropriate index.
*
* Input: number of dihedrals, the particle indices, and a flag indicating
* Input: number of torsions, the particle indices, and a flag indicating
* whether we're doing i(0), j(1), k(2) or l(3)
* Output: an array of counts per particle
* arrays of inversemaps
......
platforms/brook/src/BrookCalcGBSAOBCForceKernel.cpp
View file @ 7ed51ce4
......@@ -64,7 +64,6 @@ BrookCalcGBSAOBCForceKernel::BrookCalcGBSAOBCForceKernel( std::string name, cons
// ---------------------------------------------------------------------------------------
_numberOfParticles = 0;
_brookGbsa = NULL;
_log = NULL;
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
......@@ -72,6 +71,7 @@ BrookCalcGBSAOBCForceKernel::BrookCalcGBSAOBCForceKernel( std::string name, cons
setLog( brookPlatform.getLog() );
}
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
}
/**
......@@ -88,7 +88,6 @@ BrookCalcGBSAOBCForceKernel::~BrookCalcGBSAOBCForceKernel( ){
// ---------------------------------------------------------------------------------------
delete _brookGbsa;
}
/**
......@@ -136,11 +135,7 @@ void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOB
// ---------------------------------------------------------------------------------------
if( _brookGbsa ){
delete _brookGbsa;
}
_brookGbsa = new BrookGbsa();
_brookGbsa->setLog( log );
BrookGbsa& brookGbsa = _openMMBrookInterface.getBrookGbsa();
// get parameters from force object
// and initialize brookGbsa
......@@ -159,13 +154,13 @@ void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOB
parameters[1] = radius;
parameters[2] = scalingFactor;
}
_brookGbsa->setup( particleParameters, force.getSolventDielectric(), force.getSoluteDielectric(), getPlatform() );
brookGbsa.setup( particleParameters, force.getSolventDielectric(), force.getSoluteDielectric(), getPlatform() );
_openMMBrookInterface.setTriggerForceKernel( this );
_openMMBrookInterface.setTriggerEnergyKernel( this );
if( log ){
std::string contents = _brookGbsa->getContentsString( );
std::string contents = brookGbsa.getContentsString( );
(void) fprintf( log, "%s brookGbsa::contents\n%s", methodName.c_str(), contents.c_str() );
(void) fflush( log );
}
......@@ -213,7 +208,7 @@ double BrookCalcGBSAOBCForceKernel::executeEnergy( OpenMMContextImpl& context ){
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcGBSAOBCForceKernel.h
View file @ 7ed51ce4
......@@ -122,6 +122,15 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
FILE* getLog( void ) const;
/**
* Get Brook GBSA reference
*
* @return Brook GBSA reference
*
*/
BrookGbsa& getBrookGbsa( void ) const;
private:
// log file reference
......@@ -132,10 +141,6 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
int _numberOfParticles;
// Brook Gbsa
BrookGbsa* _brookGbsa;
// interface
OpenMMBrookInterface& _openMMBrookInterface;
......
platforms/brook/src/BrookCalcHarmonicAngleForceKernel.cpp
View file @ 7ed51ce4
......@@ -66,6 +66,7 @@ BrookCalcHarmonicAngleForceKernel::BrookCalcHarmonicAngleForceKernel( std::strin
if( brookPlatform.getLog() != NULL ){
setLog( brookPlatform.getLog() );
}
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
}
......@@ -214,7 +215,7 @@ double BrookCalcHarmonicAngleForceKernel::executeEnergy( OpenMMContextImpl& cont
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp
View file @ 7ed51ce4
......@@ -67,6 +67,8 @@ BrookCalcHarmonicBondForceKernel::BrookCalcHarmonicBondForceKernel( std::string
setLog( brookPlatform.getLog() );
}
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
}
/**
......@@ -215,7 +217,7 @@ double BrookCalcHarmonicBondForceKernel::executeEnergy( OpenMMContextImpl& conte
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcKineticEnergyKernel.cpp
View file @ 7ed51ce4
......@@ -56,7 +56,8 @@ BrookCalcKineticEnergyKernel::BrookCalcKineticEnergyKernel( std::string name, co
// ---------------------------------------------------------------------------------------
_numberOfParticles = 0;
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
_numberOfParticles = system.getNumParticles();
_masses = NULL;
}
......
platforms/brook/src/BrookCalcNonbondedForceKernel.cpp
View file @ 7ed51ce4
......@@ -61,8 +61,9 @@ BrookCalcNonbondedForceKernel::BrookCalcNonbondedForceKernel( std::string name,
// ---------------------------------------------------------------------------------------
_numberOfParticles = 0;
_brookNonBonded = NULL;
_numberOfParticles = system.getNumParticles();
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
_brookBondParameters = NULL;
_log = NULL;
......@@ -94,7 +95,6 @@ BrookCalcNonbondedForceKernel::~BrookCalcNonbondedForceKernel( ){
// ---------------------------------------------------------------------------------------
//delete _brookBondParameters;
delete _brookNonBonded;
// deleted w/ kernel delete? If activated, program crashes
......@@ -168,11 +168,7 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
// nonbonded
if( _brookNonBonded ){
delete _brookNonBonded;
}
_brookNonBonded = new BrookNonBonded();
_brookNonBonded->setLog( log );
BrookNonBonded& brookNonBonded = _openMMBrookInterface.getBrookNonBonded();
// charge & LJ parameters
......@@ -187,15 +183,14 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
particleParamArray[2] = charge;
}
_brookNonBonded->setup( _numberOfParticles, nonbondedParameters, exclusions, getPlatform() );
brookNonBonded.setup( _numberOfParticles, nonbondedParameters, exclusions, getPlatform() );
_openMMBrookInterface.setTriggerForceKernel( this );
_openMMBrookInterface.setTriggerEnergyKernel( this );
// echo contents
if( log ){
std::string contents = _brookNonBonded->getContentsString( );
std::string contents = brookNonBonded.getContentsString( );
(void) fprintf( log, "%s brookNonBonded::contents\n%s", methodName.c_str(), contents.c_str() );
(void) fflush( log );
}
......@@ -303,7 +298,7 @@ double BrookCalcNonbondedForceKernel::executeEnergy( OpenMMContextImpl& context
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcNonbondedForceKernel.h
View file @ 7ed51ce4
......@@ -169,10 +169,6 @@ class BrookCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
int _numberOfParticles;
// Brook nonbonded
BrookNonBonded* _brookNonBonded;
OpenMMBrookInterface& _openMMBrookInterface;
System& _system;
......
platforms/brook/src/BrookCalcPeriodicTorsionForceKernel.cpp
View file @ 7ed51ce4
......@@ -36,7 +36,7 @@
using namespace OpenMM;
using namespace std;
const std::string BrookCalcPeriodicTorsionForceKernel::BondName = "ProperDihedral";
const std::string BrookCalcPeriodicTorsionForceKernel::BondName = "ProperTorsion";
/**
* BrookCalcPeriodicTorsionForceKernel constructor
......@@ -61,6 +61,7 @@ BrookCalcPeriodicTorsionForceKernel::BrookCalcPeriodicTorsionForceKernel( std::s
_brookBondParameters = NULL;
_log = NULL;
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
if( brookPlatform.getLog() != NULL ){
......@@ -115,7 +116,7 @@ int BrookCalcPeriodicTorsionForceKernel::setLog( FILE* log ){
* Initialize the kernel, setting up the values of all the force field parameters.
*
* @param system System reference
* @param force ProperDihedralForce reference
* @param force ProperTorsionForce reference
*
*/
......@@ -216,7 +217,7 @@ double BrookCalcPeriodicTorsionForceKernel::executeEnergy( OpenMMContextImpl& co
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcPeriodicTorsionForceKernel.h
View file @ 7ed51ce4
......@@ -63,7 +63,7 @@ class BrookCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKerne
* Initialize the kernel, setting up the values to calculate harmonic bond force & energy
*
* @param system System reference
* @param force ProperDihedralForce reference
* @param force ProperTorsionForce reference
*
*/
......
platforms/brook/src/BrookCalcRBTorsionForceKernel.cpp
View file @ 7ed51ce4
......@@ -36,7 +36,7 @@
using namespace OpenMM;
using namespace std;
const std::string BrookCalcRBTorsionForceKernel::BondName = "RbDihedral";
const std::string BrookCalcRBTorsionForceKernel::BondName = "RbTorsion";
/**
* BrookCalcRBTorsionForceKernel constructor
......@@ -61,6 +61,7 @@ BrookCalcRBTorsionForceKernel::BrookCalcRBTorsionForceKernel( std::string name,
_brookBondParameters = NULL;
_log = NULL;
_openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );
const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
if( brookPlatform.getLog() != NULL ){
......@@ -115,7 +116,7 @@ int BrookCalcRBTorsionForceKernel::setLog( FILE* log ){
* Initialize the kernel, setting up the values of all the force field parameters.
*
* @param system System reference
* @param force RbDihedralForce reference
* @param force RbTorsionForce reference
*
*/
......@@ -219,7 +220,7 @@ double BrookCalcRBTorsionForceKernel::executeEnergy( OpenMMContextImpl& context
// ---------------------------------------------------------------------------------------
if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
return (double) _openMMBrookInterface.computeEnergy( context );
return (double) _openMMBrookInterface.computeEnergy( context, _system );
} else {
return 0.0;
}
......
platforms/brook/src/BrookCalcRBTorsionForceKernel.h
View file @ 7ed51ce4
......@@ -63,7 +63,7 @@ class BrookCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
* Initialize the kernel, setting up the values to calculate harmonic bond force & energy
*
* @param system System reference
* @param force RbDihedralForce reference
* @param force RbTorsionForce reference
*
*/
......
platforms/brook/src/BrookCommon.cpp
View file @ 7ed51ce4
......@@ -120,7 +120,7 @@ BrookCommon::BrookCommon( ){
_particleStreamSize = -1;
_log = NULL;
_verbosity = 0;
_isActive = 0;
}
......@@ -347,27 +347,27 @@ int BrookCommon::setLog( FILE* log ){
}
/**
* Get verbosity
* Get flag signalling whether active
*
* @return verbosity
* @return flag signalling whether active
*
*/
int BrookCommon::getVerbosity( void ) const {
return _verbosity;
int BrookCommon::isActive( void ) const {
return _isActive;
}
/**
* Set verbosity
* Set flag signalling whether active
*
* @param verbosity
* @param flag signalling whether active
*
* @return DefaultReturnValue
*
*/
int BrookCommon::setVerbosity( int verbosity ){
_verbosity = verbosity;
int BrookCommon::setIsActive( int isActive ){
_isActive= isActive;
return BrookCommon::DefaultReturnValue;
}
......
platforms/brook/src/BrookCommon.h
View file @ 7ed51ce4
......@@ -201,6 +201,24 @@ class BrookCommon {
int getParticleStreamSize( void ) const;
/**
* Get flag signalling whether active
*
* @return flag signalling whether active
*/
int isActive( void ) const;
/**
* Set flag signalling whether active
*
* @param isActive flag signalling whether active
*
* @return DefaultReturnValue
*/
int setIsActive( int isActive );
/**
* Set log file reference
*
......@@ -232,24 +250,6 @@ class BrookCommon {
FILE* getLog( void ) const;
/**
* Get verbose flag
*
* @return verbosity flag
*
*/
int getVerbosity( void ) const;
/**
* Set verbosity flag
*
* @param verbosity flag
*
*/
int setVerbosity( int verbosity );
/*
* Given number of stream elements and width, returns the appropriate
* height of the stream
......@@ -332,9 +332,9 @@ class BrookCommon {
FILE* _log;
// verbosity
// active flag
int _verbosity;
int _isActive;
/**
* Set number of particles
......
platforms/brook/src/BrookIntegrateBrownianStepKernel.cpp
View file @ 7ed51ce4
......@@ -106,7 +106,7 @@ void BrookIntegrateBrownianStepKernel::initialize( const vector<double>& masses,
_brookRandomNumberGenerator = new BrookRandomNumberGenerator( );
_brookRandomNumberGenerator->setup( (int) masses.size(), getPlatform() );
_brookRandomNumberGenerator->setVerbosity( 1 );
// _brookRandomNumberGenerator->setVerbosity( 1 );
}
/**
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp
View file @ 7ed51ce4
......@@ -141,7 +141,7 @@ void BrookIntegrateLangevinStepKernel::initialize( const System& system, const L
_brookRandomNumberGenerator = new BrookRandomNumberGenerator( );
_brookRandomNumberGenerator->setup( (int) masses.size(), getPlatform() );
_brookRandomNumberGenerator->setVerbosity( 1 );
// _brookRandomNumberGenerator->setVerbosity( 1 );
}
......
platforms/brook/src/BrookPlatform.cpp
View file @ 7ed51ce4
......@@ -456,7 +456,9 @@ void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const {
// ---------------------------------------------------------------------------------------
context.setPlatformData( new OpenMMBrookInterface( getParticleStreamWidth() ) );
OpenMMBrookInterface* openMMBrookInterface = new OpenMMBrookInterface( getParticleStreamWidth() );
openMMBrookInterface->setLog( stderr );
context.setPlatformData( openMMBrookInterface );
}
/**
......
platforms/brook/src/BrookRandomNumberGenerator.cpp
View file @ 7ed51ce4
......@@ -375,7 +375,7 @@ int BrookRandomNumberGenerator::_loadRandomNumberStreamsKiss( void ){
state[2] = rand();
state[3] = rand();
if( getVerbosity() && getLog() ){
if( getLog() ){
(void) fprintf( getLog(), "LoadGVStreamsKiss: reset state seeds stateInitialized=%d reseed=%d\n",
stateInitialized, reseed );
(void) fflush( getLog() );
......@@ -395,7 +395,7 @@ state[3] = 27587;
float* loadBuffer = _getLoadBuffer();
if( getVerbosity() && getLog() ){
if( getLog() ){
static float count = 0.0f;
float block = (float) (3*getRandomNumberStreamSize() );
count += 1.0f;
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ 7ed51ce4
......@@ -34,6 +34,12 @@
#include "OpenMMException.h"
#include <sstream>
// used for energy calculartion
#include "LangevinIntegrator.h"
#include "ReferencePlatform.h"
#include "internal/OpenMMContextImpl.h"
#include "BrookStreamImpl.h"
#include "OpenMMBrookInterface.h"
#include "gpu/kcommon.h"
......@@ -56,10 +62,6 @@ OpenMMBrookInterface::OpenMMBrookInterface( int streamWidth ) : _particleStreamW
_numberOfParticles = 0;
_brookBonded = NULL;
_brookNonBonded = NULL;
_brookGbsa = NULL;
_triggerForceKernel = NULL;
_triggerEnergyKernel = NULL;
......@@ -99,9 +101,6 @@ OpenMMBrookInterface::~OpenMMBrookInterface( ){
// ---------------------------------------------------------------------------------------
delete _brookBonded;
delete _brookNonBonded;
delete _brookGbsa;
for( int ii = 0; ii < LastBondForce; ii++ ){
delete _bondParameters[ii];
}
......@@ -128,6 +127,18 @@ int OpenMMBrookInterface::getNumberOfParticles( void ) const {
return _numberOfParticles;
}
/**
* Set number of particles
*
* @param numberOfParticles number of particles
*
*/
int OpenMMBrookInterface::setNumberOfParticles( int numberOfParticles ){
_numberOfParticles = numberOfParticles;
return BrookCommon::DefaultReturnValue;
}
/**
* Get particle stream width
*
......@@ -198,6 +209,9 @@ FILE* OpenMMBrookInterface::getLog( void ) const {
int OpenMMBrookInterface::setLog( FILE* log ){
_log = log;
_brookBonded.setLog( log );
_brookNonBonded.setLog( log );
_brookGbsa.setLog( log );
return BrookCommon::DefaultReturnValue;
}
......@@ -225,7 +239,20 @@ BrookBondParameters* OpenMMBrookInterface::_getBondParameters( BondParameterIndi
*/
int OpenMMBrookInterface::_setBondParameters( BondParameterIndices index, BrookBondParameters* brookBondParameters ){
if( brookBondParameters && brookBondParameters->getNumberOfBonds() > 0 ){
_brookBonded.setIsActive( 1 );
}
_bondParameters[index] = brookBondParameters;
if( !brookBondParameters || brookBondParameters->getNumberOfBonds() < 1 ){
int isActive = 0;
for( int ii = 0; ii < LastBondForce && !isActive; ii++ ){
isActive = (_bondParameters[ii] != NULL && brookBondParameters->getNumberOfBonds() > 0) ? 1 : 0;
}
_brookBonded.setIsActive( isActive );
}
return BrookCommon::DefaultReturnValue;
}
......@@ -473,6 +500,28 @@ void* OpenMMBrookInterface::getTriggerEnergyKernel( void ) const {
return _triggerEnergyKernel;
}
/**
* Get Brook non bonded
*
* @return BrookNonBonded reference
*
*/
BrookNonBonded& OpenMMBrookInterface::getBrookNonBonded( void ){
return _brookNonBonded;
}
/**
* Get Brook GBSA
*
* @return BrookGbsa reference
*
*/
BrookGbsa& OpenMMBrookInterface::getBrookGbsa( void ){
return _brookGbsa;
}
/**
* Zero forces
*
......@@ -517,8 +566,6 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// static const int debug = 1;
(void) fprintf( stderr, "%s ", methodName.c_str() ); (void) fflush( stderr );
// ---------------------------------------------------------------------------------------
// nonbonded forces
......@@ -526,27 +573,27 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
BrookStreamImpl* positions = getParticlePositions();
BrookStreamImpl* forces = getParticleForces();
if( _brookNonBonded ){
_brookNonBonded->computeForces( *positions, *forces );
if( _brookNonBonded.isActive() ){
_brookNonBonded.computeForces( *positions, *forces );
}
// ---------------------------------------------------------------------------------------
// bonded forces
if( _brookBonded ){
if( _brookBonded.isActive() ){
(void) fprintf( stderr, "%s Bonded", methodName.c_str() ); (void) fflush( stderr );
//(void) fprintf( stderr, "%s Bonded\n", methodName.c_str() ); (void) fflush( stderr );
// perform setup first time through
if( _brookBonded->isSetupCompleted() == 0 ){
_brookBonded->setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
if( _brookBonded.isSetupCompleted() == 0 ){
_brookBonded.setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
getPeriodicTorsionForceParameters(), getRBTorsionForceParameters(),
getNonBonded14ForceParameters(),
getLj14Scale(), getCoulomb14Scale(), getParticleStreamWidth(), getParticleStreamSize() );
}
_brookBonded->computeForces( *positions, *forces );
_brookBonded.computeForces( *positions, *forces );
// diagnostics
......@@ -569,8 +616,8 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// GBSA OBC forces
if( _brookGbsa ){
_brookGbsa->computeForces( *positions, *forces );
if( _brookGbsa.isActive() ){
_brookGbsa.computeForces( *positions, *forces );
}
// ---------------------------------------------------------------------------------------
......@@ -580,25 +627,36 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
* Compute energy
*
* @param context context
* @param system system reference
*
*/
double OpenMMBrookInterface::computeEnergy( OpenMMContextImpl& context ){
double OpenMMBrookInterface::computeEnergy( OpenMMContextImpl& context, System& system ){
// ---------------------------------------------------------------------------------------
/*
static const std::string methodName = "OpenMMBrookInterface::computeEnergy";
static const int PrintOn = 0;
static const int MaxErrorMessages = 2;
static int ErrorMessages = 0;
*/
// static const int debug = 1;
//static const std::string methodName = "OpenMMBrookInterface::computeEnergy";
// ---------------------------------------------------------------------------------------
return 0.0;
// We don't currently have GPU kernels to calculate energy, so instead we have the reference
// platform do it. This is VERY slow.
LangevinIntegrator integrator(0.0, 1.0, 0.0);
ReferencePlatform platform;
OpenMMContext refContext( system, integrator, platform );
const Stream& positions = context.getPositions();
double* posData = new double[positions.getSize()*3];
positions.saveToArray(posData);
vector<Vec3> pos(positions.getSize());
for( int ii = 0; ii < pos.size(); ii++ ){
pos[ii] = Vec3(posData[3*ii], posData[3*ii+1], posData[3*ii+2]);
}
delete[] posData;
refContext.setPositions(pos);
return refContext.getState(State::Energy).getPotentialEnergy();
// ---------------------------------------------------------------------------------------
}
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