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Commit 08c2e027 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods

parent 9936ec46
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Showing with 265 additions and 33 deletions
platforms/brook/src/BrookBondParameters.cpp
View file @ 08c2e027
......@@ -48,6 +48,7 @@ using namespace std;
BrookBondParameters::BrookBondParameters( std::string bondName, int numberOfParticlesInBond,
int numberOfParametersInBond, int numberOfBonds, FILE* log = NULL ) :
_bondName( bondName ), _numberOfParticlesInBond( numberOfParticlesInBond ),
_numberOfParametersInBond( numberOfParametersInBond ), _numberOfBonds( numberOfBonds ), _log( log ){
......@@ -212,21 +213,13 @@ int BrookBondParameters::setBond( int bondIndex, int* particleIndices, double* b
// load'em up
int numberOfParticlesInBond = getNumberOfParticlesInBond();
std::vector<int> indices;
_particleIndices[bondIndex] = indices;
indices.resize( numberOfParticlesInBond );
for( int ii = 0; ii < numberOfParticlesInBond; ii++ ){
indices[ii] = particleIndices[ii];
_particleIndices[bondIndex].push_back( particleIndices[ii] );
}
int numberOfParametersInBond = getNumberOfParametersInBond();
std::vector<double> parameters;
_bondParameters[bondIndex] = parameters;
parameters.resize( numberOfParametersInBond );
for( int ii = 0; ii < numberOfParametersInBond; ii++ ){
parameters[ii] = bondParameters[ii];
_bondParameters[bondIndex].push_back( bondParameters[ii] );
}
// ---------------------------------------------------------------------------------------
......@@ -317,16 +310,19 @@ std::string BrookBondParameters::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( value, "%d", getNumberOfParametersInBond() );
message << _getLine( tab, "Parameters/bond:", value );
//(void) fprintf( getLog(), "%s %s QQQ1\n", methodName.c_str(), message.str().c_str() ); (void) fflush( getLog() );
message << "Bonds:" << std::endl;
for( int ii = 0; ii < getNumberOfBonds(); ii++ ){
const static size_t descriptionSz = 256;
char description[256];
char buffer[256];
const static size_t descriptionSz = 1024;
char description[1024];
char buffer[1024];
(void) LOCAL_SPRINTF( description, "%6d [", ii );
#ifdef WIN32
// particle indices
#ifdef WIN32
for( int jj = 0; jj < getNumberOfParticlesInBond(); jj++ ){
(void) LOCAL_SPRINTF( buffer, "%6d ", _particleIndices[ii][jj] );
(void) strcat_s( description, descriptionSz, buffer );
......@@ -339,8 +335,12 @@ std::string BrookBondParameters::getContentsString( int level ) const {
(void) LOCAL_SPRINTF( buffer, "%18.10e ", _bondParameters[ii][jj] );
(void) strcat_s( description, descriptionSz, buffer );
}
(void) strcat_s( description, descriptionSz, "]" );
#else
// particle indices
for( int jj = 0; jj < getNumberOfParticlesInBond(); jj++ ){
(void) LOCAL_SPRINTF( buffer, "%6d ", _particleIndices[ii][jj] );
(void) strcat( description, buffer );
......
platforms/brook/src/BrookCalcHarmonicBondForceKernel.cpp
View file @ 08c2e027
......@@ -131,6 +131,8 @@ void BrookCalcHarmonicBondForceKernel::initialize( const System& system, const H
// ---------------------------------------------------------------------------------------
//(void) fprintf( getLog(), "%s\n", methodName.c_str() ); (void) fflush( getLog() );
// create _brookBondParameters object containing particle indices/parameters
int numberOfBonds = force.getNumBonds();
......@@ -182,7 +184,7 @@ void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "BrookCalcHarmonicBondForceKernel::executeForces";
static const std::string methodName = "BrookCalcHarmonicBondForceKernel::executeForces";
// ---------------------------------------------------------------------------------------
......
platforms/brook/src/BrookCalcNonbondedForceKernel.cpp
View file @ 08c2e027
......@@ -251,7 +251,7 @@ void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& syst
_brookBondParameters->setBond( ii, particles, parameters );
}
_openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters );
_openMMBrookInterface.setNonBonded14ForceParameters( _brookBondParameters, 1.0, 1.0 );
if( log ){
std::string contents = _brookBondParameters->getContentsString( );
......
platforms/brook/src/BrookPlatform.cpp
View file @ 08c2e027
......@@ -345,6 +345,16 @@ double BrookPlatform::getSpeed() const {
return 10.0;
}
/**
* Return particle stream width
*
* @return particle stream width
*/
int BrookPlatform::getParticleStreamWidth() const {
return _particleStreamWidth;
}
/**
* Return true if BrookPlatform supports double precison
*
......@@ -393,7 +403,7 @@ int BrookPlatform::getStreamSize( int size, int streamWidth, int* outputHeight )
// ---------------------------------------------------------------------------------------
if( streamWidth < 1 || size < 1){
if( streamWidth < 1 || size < 1 ){
return -1;
}
......@@ -446,7 +456,7 @@ void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const {
// ---------------------------------------------------------------------------------------
context.setPlatformData( new OpenMMBrookInterface() );
context.setPlatformData( new OpenMMBrookInterface( getParticleStreamWidth() ) );
}
/**
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ 08c2e027
......@@ -46,7 +46,7 @@ using namespace std;
*
*/
OpenMMBrookInterface::OpenMMBrookInterface( void ){
OpenMMBrookInterface::OpenMMBrookInterface( int streamWidth ) : _particleStreamWidth(streamWidth){
// ---------------------------------------------------------------------------------------
......@@ -76,6 +76,14 @@ OpenMMBrookInterface::OpenMMBrookInterface( void ){
_referencePlatform = NULL;
_refVerletIntegrator = NULL;
_lj14Scale = 1.0;
_coulomb14Scale = 1.0;
_particleStreamSize = -1;
for( int ii = 0; ii < LastBondForce; ii++ ){
_bondParameters[ii] = NULL;
}
}
/**
......@@ -93,6 +101,10 @@ OpenMMBrookInterface::~OpenMMBrookInterface( ){
delete _brookBonded;
delete _brookNonBonded;
delete _brookGbsa;
for( int ii = 0; ii < LastBondForce; ii++ ){
delete _bondParameters[ii];
}
// deleted w/ kernel delete? If activated, program crashes
......@@ -105,6 +117,65 @@ OpenMMBrookInterface::~OpenMMBrookInterface( ){
*/
}
/**
* Get number of particles
*
* @return number of particles
*
*/
int OpenMMBrookInterface::getNumberOfParticles( void ) const {
return _numberOfParticles;
}
/**
* Get particle stream width
*
* @return particle stream width
*
*/
int OpenMMBrookInterface::getParticleStreamWidth( void ) const {
return _particleStreamWidth;
}
/**
* Get particle stream size
*
* @return particle stream size
*
*/
int OpenMMBrookInterface::getParticleStreamSize( void ) const {
if( _particleStreamSize < 0 && _numberOfParticles > 0 ){
OpenMMBrookInterface* localThis = const_cast<OpenMMBrookInterface* const>(this);
localThis->_particleStreamSize = BrookPlatform::getStreamSize( _numberOfParticles, _particleStreamWidth, NULL );
}
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
*
......@@ -130,6 +201,19 @@ int OpenMMBrookInterface::setLog( FILE* log ){
return BrookCommon::DefaultReturnValue;
}
/**
* Get BrookBondParameters at specified index
*
* @param index
*
* @return BrookBondParameters* object
*
*/
BrookBondParameters* OpenMMBrookInterface::_getBondParameters( BondParameterIndices index ) const {
return _bondParameters[index];
}
/**
* Set BrookBondParameters at specified index
*
......@@ -145,6 +229,17 @@ int OpenMMBrookInterface::_setBondParameters( BondParameterIndices index, BrookB
return BrookCommon::DefaultReturnValue;
}
/**
* Get BrookBondParameters for harmonic bond force
*
* @return brookBondParameters for harmonic bond force
*
*/
BrookBondParameters* OpenMMBrookInterface::getHarmonicBondForceParameters( void ) const {
return _getBondParameters( HarmonicBondIndex );
}
/**
* Set BrookBondParameters for harmonic bond force
*
......@@ -155,7 +250,18 @@ int OpenMMBrookInterface::_setBondParameters( BondParameterIndices index, BrookB
*/
int OpenMMBrookInterface::setHarmonicBondForceParameters( BrookBondParameters* brookBondParameters ){
return _setBondParameters( HarmonicAngleIndex, brookBondParameters );
return _setBondParameters( HarmonicBondIndex, brookBondParameters );
}
/**
* Get BrookBondParameters for harmonic angle force
*
* @return brookBondParameters for harmonic angle force
*
*/
BrookBondParameters* OpenMMBrookInterface::getHarmonicAngleForceParameters( void ) const {
return _getBondParameters( HarmonicAngleIndex );
}
/**
......@@ -172,9 +278,20 @@ int OpenMMBrookInterface::setHarmonicAngleForceParameters( BrookBondParameters*
}
/**
* Set BrookBondParameters for proper dihedral force
* Get BrookBondParameters for periodic torsion force
*
* @return brookBondParameters for periodic torsion force
*
*/
BrookBondParameters* OpenMMBrookInterface::getPeriodicTorsionForceParameters( void ) const {
return _getBondParameters( PeriodicTorsionForceIndex );
}
/**
* Set BrookBondParameters for periodic torsion force
*
* @param brookBondParameters brookBondParameters for proper dihedral force
* @param brookBondParameters brookBondParameters for periodic torsion force
*
* @return DefaultReturnValue
*
......@@ -185,9 +302,20 @@ int OpenMMBrookInterface::setPeriodicTorsionForceParameters( BrookBondParameters
}
/**
* Set BrookBondParameters for RB dihedral force
* Get BrookBondParameters for rb torsion force
*
* @return brookBondParameters for rb torsion force
*
*/
BrookBondParameters* OpenMMBrookInterface::getRBTorsionForceParameters( void ) const {
return _getBondParameters( RbTorsionForceIndex );
}
/**
* Set BrookBondParameters for RB torsion force
*
* @param brookBondParameters brookBondParameters for RB force
* @param brookBondParameters brookBondParameters for RB torsion force
*
* @return DefaultReturnValue
*
......@@ -197,16 +325,32 @@ int OpenMMBrookInterface::setRBTorsionForceParameters( BrookBondParameters* broo
return _setBondParameters( RbTorsionForceIndex, brookBondParameters );
}
/**
* Get BrookBondParameters for LJ 14 force
*
* @return brookBondParameters for LJ 14 force
*
*/
BrookBondParameters* OpenMMBrookInterface::getNonBonded14ForceParameters( void ) const {
return _getBondParameters( LJ14Index );
}
/**
* 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 ){
int OpenMMBrookInterface::setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters,
double lj14Scale, double coulomb14Scale ){
_lj14Scale = lj14Scale;
_coulomb14Scale = coulomb14Scale;
return _setBondParameters( LJ14Index, brookBondParameters );
}
......@@ -373,6 +517,8 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// static const int debug = 1;
(void) fprintf( stderr, "%s ", methodName.c_str() ); (void) fflush( stderr );
// ---------------------------------------------------------------------------------------
// nonbonded forces
......@@ -390,6 +536,16 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
if( _brookBonded ){
(void) fprintf( stderr, "%s Bonded", methodName.c_str() ); (void) fflush( stderr );
// perform setup first time through
if( _brookBonded->isSetupCompleted() == 0 ){
_brookBonded->setup( getNumberOfParticles(), getHarmonicBondForceParameters(), getHarmonicAngleForceParameters(),
getPeriodicTorsionForceParameters(), getRBTorsionForceParameters(),
getNonBonded14ForceParameters(),
getLj14Scale(), getCoulomb14Scale(), getParticleStreamWidth(), getParticleStreamSize() );
}
_brookBonded->computeForces( *positions, *forces );
// diagnostics
......
platforms/brook/src/OpenMMBrookInterface.h
View file @ 08c2e027
......@@ -53,7 +53,7 @@ class OpenMMBrookInterface {
public:
OpenMMBrookInterface( void );
OpenMMBrookInterface( int streamWidth );
~OpenMMBrookInterface();
......@@ -90,6 +90,51 @@ class OpenMMBrookInterface {
std::string getContents( int level ) const;
/**
* Get number of particles
*
* @return number of particles
*
*/
int getNumberOfParticles( void ) const;
/**
* Get particle stream width
*
* @return particle stream width
*
*/
int getParticleStreamWidth( void ) const;
/**
* Get particle stream size
*
* @return particle stream size
*
*/
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
*
......@@ -169,7 +214,7 @@ class OpenMMBrookInterface {
*
*/
BrookBondParameters* getHarmonicBondForceParameters( void );
BrookBondParameters* getHarmonicBondForceParameters( void ) const;
/**
* Set BrookBondParameters for harmonic bond force
......@@ -189,7 +234,7 @@ class OpenMMBrookInterface {
*
*/
BrookBondParameters* getHarmonicAngleForceParameters( void );
BrookBondParameters* getHarmonicAngleForceParameters( void ) const;
/**
* Set BrookBondParameters for harmonic angle force
......@@ -209,7 +254,7 @@ class OpenMMBrookInterface {
*
*/
BrookBondParameters* getPeriodicTorsionForceParameters( void );
BrookBondParameters* getPeriodicTorsionForceParameters( void ) const;
/**
* Set BrookBondParameters for periodic torsion force
......@@ -229,7 +274,7 @@ class OpenMMBrookInterface {
*
*/
BrookBondParameters* getRBTorsionForceParameters( void );
BrookBondParameters* getRBTorsionForceParameters( void ) const;
/**
* Set BrookBondParameters for RB torsion force
......@@ -249,18 +294,20 @@ class OpenMMBrookInterface {
*
*/
BrookBondParameters* getNonBonded14ForceParameters( void );
BrookBondParameters* getNonBonded14ForceParameters( void ) const;
/**
* 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 );
int setNonBonded14ForceParameters( BrookBondParameters* brookBondParameters, double lj14Scale, double coulomb14Scale );
/**
* Get positions stream
......@@ -333,10 +380,16 @@ class OpenMMBrookInterface {
FILE* _log;
int _particleStreamWidth;
int _particleStreamSize;
// number of particles
int _numberOfParticles;
double _lj14Scale;
double _coulomb14Scale;
// Brook bonded, nonbonded, Gbsa
BrookBonded* _brookBonded;
......@@ -374,6 +427,17 @@ class OpenMMBrookInterface {
int _setBondParameters( BondParameterIndices index, BrookBondParameters* brookBondParameters );
/**
* Get BrookBondParameters at specified index
*
* @param index
*
* @return BrookBondParameters* object
*
*/
BrookBondParameters* _getBondParameters( BondParameterIndices index ) const;
};
} // namespace OpenMM
......
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