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"examples/cpp-examples/Makefile" did not exist on "346d3ce3244e9af797a12002ced79cbcb5190a5b"
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
--------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& CpuGBVISoftcore::getSwitchDeriviative( void ){
RealOpenMMVector& CpuGBVISoftcore::getSwitchDeriviative( void ){
return _switchDeriviative;
}
......@@ -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 ){
// ---------------------------------------------------------------------------------------
......@@ -226,13 +226,13 @@ void CpuGBVISoftcore::computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordi
// ---------------------------------------------------------------------------------------
GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii();
const std::vector<RealOpenMM>& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const RealOpenMMVector& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
std::vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative();
RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
// ---------------------------------------------------------------------------------------
......@@ -475,8 +475,8 @@ RealOpenMM CpuGBVISoftcore::computeBornEnergy( const vector<RealOpenMM>& bornRad
const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
const RealOpenMM preFactor = gbviParameters->getElectricConstant();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
// ---------------------------------------------------------------------------------------
......@@ -556,15 +556,15 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve
const GBVISoftcoreParameters* gbviParameters = getGBVISoftcoreParameters();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const std::vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const std::vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
const RealOpenMM preFactor = two*gbviParameters->getElectricConstant();
// ---------------------------------------------------------------------------------------
// set energy/forces to zero
std::vector<RealOpenMM> bornForces( numberOfAtoms, 0.0 );
RealOpenMMVector bornForces( numberOfAtoms, 0.0 );
std::vector<RealVec> forces( numberOfAtoms );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
forces[atomI][0] = zero;
......@@ -638,9 +638,9 @@ void CpuGBVISoftcore::computeBornForces( const vector<RealOpenMM>& bornRadii, ve
// dGpol/dBornRadius) = bornForces[]
// dBornRadius/dr = (1/3)*(bR**4)*(dV/dr)
const std::vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii();
std::vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative();
const std::vector<RealOpenMM>& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
const RealOpenMMVector& bornRadiusScaleFactors = gbviParameters->getBornRadiusScaleFactors();
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
RealOpenMM R = atomicRadii[atomI];
......
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
View file @ 7f561d68
......@@ -39,7 +39,7 @@ class CpuGBVISoftcore {
// vector containing switching function derivative
std::vector<RealOpenMM> _switchDeriviative;
RealOpenMMVector _switchDeriviative;
public:
......@@ -92,7 +92,7 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getSwitchDeriviative( void );
RealOpenMMVector& getSwitchDeriviative( void );
/**---------------------------------------------------------------------------------------
......@@ -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 {
--------------------------------------------------------------------------------------- */
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 );
/**---------------------------------------------------------------------------------------
......@@ -212,8 +212,8 @@ class CpuGBVISoftcore {
--------------------------------------------------------------------------------------- */
void computeBornForces( const std::vector<RealOpenMM>& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMM* partialCharges, std::vector<OpenMM::RealVec>& inputForces );
void computeBornForces( const RealOpenMMVector& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
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 {
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& GBVISoftcoreParameters::getAtomicRadii( void ) const {
const RealOpenMMVector& GBVISoftcoreParameters::getAtomicRadii( void ) const {
return _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;
}
......@@ -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;
}
......@@ -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;
}
......
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
View file @ 7f561d68
......@@ -56,10 +56,10 @@ class GBVISoftcoreParameters {
// gamma parameters
// BornRadiusScaleFactors parameters
std::vector<RealOpenMM> _scaledRadii;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _gammaParameters;
std::vector<RealOpenMM> _bornRadiusScaleFactors;
RealOpenMMVector _scaledRadii;
RealOpenMMVector _atomicRadii;
RealOpenMMVector _gammaParameters;
RealOpenMMVector _bornRadiusScaleFactors;
RealOpenMM _solventDielectric;
RealOpenMM _soluteDielectric;
......@@ -168,7 +168,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getScaledRadii( void ) const;
const RealOpenMMVector& getScaledRadii( void ) const;
/**---------------------------------------------------------------------------------------
......@@ -178,7 +178,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadii( const std::vector<RealOpenMM>& radii );
void setScaledRadii( const RealOpenMMVector& radii );
/**---------------------------------------------------------------------------------------
......@@ -188,7 +188,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getAtomicRadii( void ) const;
const RealOpenMMVector& getAtomicRadii( void ) const;
/**---------------------------------------------------------------------------------------
......@@ -208,7 +208,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getGammaParameters( void ) const;
const RealOpenMMVector& getGammaParameters( void ) const;
/**---------------------------------------------------------------------------------------
......@@ -228,7 +228,7 @@ class GBVISoftcoreParameters {
--------------------------------------------------------------------------------------- */
const std::vector<RealOpenMM>& getBornRadiusScaleFactors( void ) const;
const RealOpenMMVector& getBornRadiusScaleFactors( void ) const;
/**---------------------------------------------------------------------------------------
......
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