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Commit 4d499572 authored by Mark Friedrichs's avatar Mark Friedrichs
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Cleaned up code

parent e9505f5b
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Showing with 645 additions and 1470 deletions
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
View file @ 4d499572
......@@ -26,11 +26,10 @@
#define __CpuGBVISoftcore_H__
#include "GBVISoftcoreParameters.h"
#include "gbsa/CpuImplicitSolvent.h"
// ---------------------------------------------------------------------------------------
class CpuGBVISoftcore : public CpuImplicitSolvent {
class CpuGBVISoftcore {
private:
......@@ -38,14 +37,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
GBVISoftcoreParameters* _gbviParameters;
// arrays containing switching function derivative
// vector containing switching function derivative
RealOpenMM* _switchDeriviative;
// initialize data members (more than
// one constructor, so centralize intialization here)
void _initializeGBVISoftcoreDataMembers( void );
std::vector<RealOpenMM> _switchDeriviative;
public:
......@@ -59,7 +53,7 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
CpuGBVISoftcore( ImplicitSolventParameters* gbviParameters );
CpuGBVISoftcore( GBVISoftcoreParameters* gbviParameters );
/**---------------------------------------------------------------------------------------
......@@ -98,8 +92,7 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
RealOpenMM* getSwitchDeriviative( void );
RealOpenMM* getSwitchDeriviativeConst( void ) const;
std::vector<RealOpenMM>& getSwitchDeriviative( void );
/**---------------------------------------------------------------------------------------
......@@ -111,8 +104,6 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii,
RealOpenMM* switchDeriviative = NULL );
void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii );
/**---------------------------------------------------------------------------------------
......
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
View file @ 4d499572
......@@ -26,11 +26,10 @@
#define __GBVISoftcoreParameters_H__
#include "SimTKUtilities/SimTKOpenMMCommon.h"
#include "gbsa/ImplicitSolventParameters.h"
// ---------------------------------------------------------------------------------------
class GBVISoftcoreParameters : public ImplicitSolventParameters {
class GBVISoftcoreParameters {
public:
......@@ -42,41 +41,41 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
* No scaling method is applied.
*/
NoScaling = 0,
/**
* Use the method outlined in Proteins 55, 383-394 (2004), Eq. 6
*/
Tanh = 1,
/**
* Use quintic spline scaling function
*/
QuinticSpline = 2
QuinticSpline = 1
};
private:
// scaled radii
int _ownScaledRadii;
RealOpenMM* _scaledRadii;
int _numberOfAtoms;
// parameters:
// scaled radii
// gamma parameters
int _ownGammaParameters;
RealOpenMM* _gammaParameters;
// BornRadiusScaleFactors parameters
int _ownBornRadiusScaleFactors;
RealOpenMM* _bornRadiusScaleFactors;
std::vector<RealOpenMM> _scaledRadii;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _gammaParameters;
std::vector<RealOpenMM> _bornRadiusScaleFactors;
RealOpenMM _solventDielectric;
RealOpenMM _soluteDielectric;
RealOpenMM _electricConstant;
// cutoff and periodic boundary conditions
bool cutoff;
bool periodic;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
bool _cutoff;
bool _periodic;
RealOpenMM _periodicBoxSize[3];
RealOpenMM _cutoffDistance;
// Born radii switching function params
BornRadiusScalingSoftcoreMethod _bornRadiusScalingSoftcoreMethod;
RealOpenMM _quinticLowerLimitFactor;
RealOpenMM _quinticUpperBornRadiusLimit;
RealOpenMM _quinticUpperSplineLimit;
......@@ -103,140 +102,133 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
/**---------------------------------------------------------------------------------------
Return scaled radii
Get number of atoms
@return array
@return number of atoms
--------------------------------------------------------------------------------------- */
const RealOpenMM* getScaledRadii( void ) const;
int getNumberOfAtoms( void ) const;
/**---------------------------------------------------------------------------------------
Return scaled radii
Get electric constant
@return array
@return electric constant
--------------------------------------------------------------------------------------- */
void setScaledRadii( RealOpenMM* scaledRadii );
#if RealOpenMMType == 0
void setScaledRadii( float* scaledRadii );
#endif
void setScaledRadii( const RealOpenMMVector& scaledRadii );
RealOpenMM getElectricConstant( void ) const;
/**---------------------------------------------------------------------------------------
Set flag indicating whether scaled radii array should be deleted
Get solvent dielectric
@param ownScaledRadiusFactors flag indicating whether scaled radii
array should be deleted
@return solvent dielectric
--------------------------------------------------------------------------------------- */
void setOwnScaledRadii( int ownScaledRadii );
RealOpenMM getSolventDielectric( void ) const;
/**---------------------------------------------------------------------------------------
Get AtomicRadii array w/ dielectric offset applied
Set solvent dielectric
@return array of atom volumes
@param solventDielectric solvent dielectric
--------------------------------------------------------------------------------------- */
RealOpenMM* getAtomicRadii( void ) const;
void setSolventDielectric( RealOpenMM solventDielectric );
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
Get solute dielectric
@param atomicRadii array of atomic radii
@return soluteDielectric
--------------------------------------------------------------------------------------- */
void setAtomicRadii( RealOpenMM* atomicRadii );
RealOpenMM getSoluteDielectric( void ) const;
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
Set solute dielectric
@param atomicRadii vector of atomic radii
@param soluteDielectric solute dielectric
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
void setSoluteDielectric( RealOpenMM soluteDielectric );
/**---------------------------------------------------------------------------------------
Set flag indicating whether gamma parameter array should be deleted
Return scaled radii
@param ownGammaParameters flag indicating whether gamma parameter
array should be deleted
@return array
--------------------------------------------------------------------------------------- */
void setOwnGammaParameters( int ownGammaParameters );
const std::vector<RealOpenMM>& getScaledRadii( void ) const;
/**---------------------------------------------------------------------------------------
Get GammaParameters array
Set scaled radii
@return array of gamma values
@param vector of scaled radii
--------------------------------------------------------------------------------------- */
RealOpenMM* getGammaParameters( void ) const;
void setScaledRadii( const std::vector<RealOpenMM>& radii );
/**---------------------------------------------------------------------------------------
Set GammaParameters array
Get AtomicRadii array w/ dielectric offset applied
@param gammaParameters array of gamma parameters
@return array of atom volumes
--------------------------------------------------------------------------------------- */
void setGammaParameters( RealOpenMM* gammaParameters );
const std::vector<RealOpenMM>& getAtomicRadii( void ) const;
/**---------------------------------------------------------------------------------------
Set GammaParameters array
Set AtomicRadii array
@param gammaParameters array of gamma parameters
@param atomicRadii vector of atomic radii
--------------------------------------------------------------------------------------- */
void setGammaParameters( const RealOpenMMVector& gammaParameters );
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
/**---------------------------------------------------------------------------------------
Set flag indicating whether bornRadiusScaleFactor parameter array should be deleted
Get GammaParameters array
@param ownBornRadiusScaleFactors flag indicating whether bornRadiusScaleFactor parameter
array should be deleted
@return array of gamma values
--------------------------------------------------------------------------------------- */
void setOwnBornRadiusScaleFactors( int ownBornRadiusScaleFactors );
const std::vector<RealOpenMM>& getGammaParameters( void ) const;
/**---------------------------------------------------------------------------------------
Get BornRadiusScaleFactors array
Set GammaParameters array
@return array of bornRadiusScaleFactor values
@param gammaParameters array of gamma parameters
--------------------------------------------------------------------------------------- */
RealOpenMM* getBornRadiusScaleFactors( void ) const;
void setGammaParameters( const RealOpenMMVector& gammaParameters );
/**---------------------------------------------------------------------------------------
Set BornRadiusScaleFactors array
Get BornRadiusScaleFactors array
@param bornRadiusScaleFactors array of bornRadiusScaleFactor parameters
@return array of bornRadiusScaleFactor values
--------------------------------------------------------------------------------------- */
void setBornRadiusScaleFactors( RealOpenMM* bornRadiusScaleFactors );
const std::vector<RealOpenMM>& getBornRadiusScaleFactors( void ) const;
/**---------------------------------------------------------------------------------------
......@@ -248,18 +240,6 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
void setBornRadiusScaleFactors( const RealOpenMMVector& bornRadiusScaleFactors );
/**---------------------------------------------------------------------------------------
Get string w/ state
@param title title (optional)
@return string
--------------------------------------------------------------------------------------- */
std::string getStateString( const char* title ) const;
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
......@@ -276,7 +256,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
bool getUseCutoff();
bool getUseCutoff( void );
/**---------------------------------------------------------------------------------------
......@@ -284,7 +264,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getCutoffDistance();
RealOpenMM getCutoffDistance( void );
/**---------------------------------------------------------------------------------------
......@@ -304,7 +284,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
bool getPeriodic();
bool getPeriodic( void );
/**---------------------------------------------------------------------------------------
......@@ -312,7 +292,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMM* getPeriodicBox();
const RealOpenMM* getPeriodicBox( void );
/**---------------------------------------------------------------------------------------
......
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