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Commit 7f561d68 authored by Mark Friedrichs's avatar Mark Friedrichs
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Cosmetic changes

parent b64535d8
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Showing with 35 additions and 35 deletions
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
View file @ 7f561d68
...@@ -96,7 +96,7 @@ void CpuGBVISoftcore::setGBVISoftcoreParameters( GBVISoftcoreParameters* gbviPar ...@@ -96,7 +96,7 @@ void CpuGBVISoftcore::setGBVISoftcoreParameters( GBVISoftcoreParameters* gbviPar
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& CpuGBVISoftcore::getSwitchDeriviative( void ){ RealOpenMMVector& CpuGBVISoftcore::getSwitchDeriviative( void ){
return _switchDeriviative; return _switchDeriviative;
} }
...@@ -213,7 +213,7 @@ void CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadiu ...@@ -213,7 +213,7 @@ void CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadiu
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void CpuGBVISoftcore::computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii ){ void CpuGBVISoftcore::computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -228,11 +228,11 @@ void CpuGBVISoftcore::computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordi ...@@ -228,11 +228,11 @@ void CpuGBVISoftcore::computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordi
GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters(); GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
int numberOfAtoms = gbviParameters->getNumberOfAtoms(); int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii(); const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii(); const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const std::vector<RealOpenMM>& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors(); const RealOpenMMVector& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
std::vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative(); RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -475,8 +475,8 @@ RealOpenMM CpuGBVISoftcore::computeBornEnergy( const vector<RealOpenMM>& bornRad ...@@ -475,8 +475,8 @@ RealOpenMM CpuGBVISoftcore::computeBornEnergy( const vector<RealOpenMM>& bornRad
const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters(); const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
const RealOpenMM preFactor = gbviParameters->getElectricConstant(); const RealOpenMM preFactor = gbviParameters->getElectricConstant();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms(); const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii(); const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters(); const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -556,15 +556,15 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve ...@@ -556,15 +556,15 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve
const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters(); const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms(); const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii(); const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters(); const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
const RealOpenMM preFactor = two*gbviParameters->getElectricConstant(); const RealOpenMM preFactor = two*gbviParameters->getElectricConstant();
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// set energy/forces to zero // set energy/forces to zero
std::vector<RealOpenMM> bornForces( numberOfAtoms, 0.0 ); RealOpenMMVector bornForces( numberOfAtoms, 0.0 );
std::vector<RealVec> forces( numberOfAtoms ); std::vector<RealVec> forces( numberOfAtoms );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){ for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
forces[atomI][0] = zero; forces[atomI][0] = zero;
...@@ -638,9 +638,9 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve ...@@ -638,9 +638,9 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve
// dGpol/dBornRadius) = bornForces[] // dGpol/dBornRadius) = bornForces[]
// dBornRadius/dr = (1/3)*(bR**4)*(dV/dr) // dBornRadius/dr = (1/3)*(bR**4)*(dV/dr)
const std::vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii(); const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
std::vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative(); RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
const std::vector<RealOpenMM>& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors(); const RealOpenMMVector& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){ for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
RealOpenMM R = atomicRadii[atomI]; RealOpenMM R = atomicRadii[atomI];
......
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
View file @ 7f561d68
...@@ -39,7 +39,7 @@ class CpuGBVISoftcore { ...@@ -39,7 +39,7 @@ class CpuGBVISoftcore {
// vector containing switching function derivative // vector containing switching function derivative
std::vector<RealOpenMM> _switchDeriviative; RealOpenMMVector _switchDeriviative;
public: public:
...@@ -92,7 +92,7 @@ class CpuGBVISoftcore { ...@@ -92,7 +92,7 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getSwitchDeriviative( void ); RealOpenMMVector& getSwitchDeriviative( void );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -104,7 +104,7 @@ class CpuGBVISoftcore { ...@@ -104,7 +104,7 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii ); void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -198,7 +198,7 @@ class CpuGBVISoftcore { ...@@ -198,7 +198,7 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergy( const std::vector<RealOpenMM>& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM computeBornEnergy( const RealOpenMMVector& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMM* partialCharges ); const RealOpenMM* partialCharges );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -212,7 +212,7 @@ class CpuGBVISoftcore { ...@@ -212,7 +212,7 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void computeBornForces( const std::vector<RealOpenMM>& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates, void computeBornForces( const RealOpenMMVector& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMM* partialCharges, std::vector<OpenMM::RealVec>& inputForces ); const RealOpenMM* partialCharges, std::vector<OpenMM::RealVec>& inputForces );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.cpp
View file @ 7f561d68
...@@ -205,7 +205,7 @@ RealOpenMM GBVISoftcoreParameters::getQuinticUpperSplineLimit( void ) const { ...@@ -205,7 +205,7 @@ RealOpenMM GBVISoftcoreParameters::getQuinticUpperSplineLimit( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& GBVISoftcoreParameters::getAtomicRadii( void ) const { const RealOpenMMVector& GBVISoftcoreParameters::getAtomicRadii( void ) const {
return _atomicRadii; return _atomicRadii;
} }
...@@ -242,7 +242,7 @@ void GBVISoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ...@@ -242,7 +242,7 @@ void GBVISoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& GBVISoftcoreParameters::getScaledRadii( void ) const { const RealOpenMMVector& GBVISoftcoreParameters::getScaledRadii( void ) const {
return _scaledRadii; return _scaledRadii;
} }
...@@ -279,7 +279,7 @@ void GBVISoftcoreParameters::setScaledRadii( const RealOpenMMVector& scaledRadii ...@@ -279,7 +279,7 @@ void GBVISoftcoreParameters::setScaledRadii( const RealOpenMMVector& scaledRadii
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& GBVISoftcoreParameters::getGammaParameters( void ) const { const RealOpenMMVector& GBVISoftcoreParameters::getGammaParameters( void ) const {
return _gammaParameters; return _gammaParameters;
} }
...@@ -316,7 +316,7 @@ void GBVISoftcoreParameters::setGammaParameters( const RealOpenMMVector& gammas ...@@ -316,7 +316,7 @@ void GBVISoftcoreParameters::setGammaParameters( const RealOpenMMVector& gammas
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& GBVISoftcoreParameters::getBornRadiusScaleFactors( void ) const { const RealOpenMMVector& GBVISoftcoreParameters::getBornRadiusScaleFactors( void ) const {
return _bornRadiusScaleFactors; return _bornRadiusScaleFactors;
} }
......
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
View file @ 7f561d68
...@@ -56,10 +56,10 @@ class GBVISoftcoreParameters { ...@@ -56,10 +56,10 @@ class GBVISoftcoreParameters {
// gamma parameters // gamma parameters
// BornRadiusScaleFactors parameters // BornRadiusScaleFactors parameters
std::vector<RealOpenMM> _scaledRadii; RealOpenMMVector _scaledRadii;
std::vector<RealOpenMM> _atomicRadii; RealOpenMMVector _atomicRadii;
std::vector<RealOpenMM> _gammaParameters; RealOpenMMVector _gammaParameters;
std::vector<RealOpenMM> _bornRadiusScaleFactors; RealOpenMMVector _bornRadiusScaleFactors;
RealOpenMM _solventDielectric; RealOpenMM _solventDielectric;
RealOpenMM _soluteDielectric; RealOpenMM _soluteDielectric;
...@@ -168,7 +168,7 @@ class GBVISoftcoreParameters { ...@@ -168,7 +168,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getScaledRadii( void ) const; const RealOpenMMVector& getScaledRadii( void ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -178,7 +178,7 @@ class GBVISoftcoreParameters { ...@@ -178,7 +178,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setScaledRadii( const std::vector<RealOpenMM>& radii ); void setScaledRadii( const RealOpenMMVector& radii );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -188,7 +188,7 @@ class GBVISoftcoreParameters { ...@@ -188,7 +188,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getAtomicRadii( void ) const; const RealOpenMMVector& getAtomicRadii( void ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -208,7 +208,7 @@ class GBVISoftcoreParameters { ...@@ -208,7 +208,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getGammaParameters( void ) const; const RealOpenMMVector& getGammaParameters( void ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -228,7 +228,7 @@ class GBVISoftcoreParameters { ...@@ -228,7 +228,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getBornRadiusScaleFactors( void ) const; const RealOpenMMVector& getBornRadiusScaleFactors( void ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
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