Code cleanup

plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp

@@ -23,15 +23,13 @@
  */
 
 #include <string.h>
+#include <math.h>
 #include <sstream>
 #include <vector>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "CpuGBVISoftcore.h"
 #include "../SimTKReference/ReferenceForce.h"
-#include <math.h>
+#include "CpuGBVISoftcore.h"
 
 using std::vector;
 using OpenMM::RealVec;

plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h

@@ -30,7 +30,7 @@
 
 // ---------------------------------------------------------------------------------------
 
-class CpuObcSoftcore : public CpuImplicitSolvent {
+class CpuObcSoftcore {
 
    private:
 
@@ -40,13 +40,12 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
 
       // arrays containing OBC chain derivative 
 
-      std::vector<RealOpenMM> _obcChain;
-      std::vector<RealOpenMM> _obcChainTemp;
+      RealOpenMMVector _obcChain;
 
-      // initialize data members (more than
-      // one constructor, so centralize intialization here)
+      // flag to signal whether ACE approximation
+      // is to be included
 
-      void _initializeObcDataMembers( void );
+      int _includeAceApproximation;
 
    public:
 
@@ -60,7 +59,7 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
       
          --------------------------------------------------------------------------------------- */
 
-       CpuObcSoftcore( ImplicitSolventParameters* obcSoftcoreParameters );
+       CpuObcSoftcore( ObcSoftcoreParameters* obcSoftcoreParameters );
 
       /**---------------------------------------------------------------------------------------
       
@@ -92,26 +91,45 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
  
       /**---------------------------------------------------------------------------------------
       
-         Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
-         On first call, memory for array is allocated if not set
+         Return flag signalling whether AceApproximation for nonpolar term is to be included
       
-         @return array
+         @return flag
       
          --------------------------------------------------------------------------------------- */
 
-      std::vector<RealOpenMM>& getObcChain( void );
-      const std::vector<RealOpenMM>& getObcChainConst( void ) const;
+      int includeAceApproximation( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set flag indicating whether AceApproximation is to be included
+      
+         @param includeAceApproximation new includeAceApproximation value
+      
+         --------------------------------------------------------------------------------------- */
+
+      void setIncludeAceApproximation( int includeAceApproximation );
+
 
       /**---------------------------------------------------------------------------------------
       
-         Return OBC chain temp work array of size=_implicitSolventParameters->getNumberOfAtoms()
+         Get energy 
+      
+         @return energy
+      
+         --------------------------------------------------------------------------------------- */
+
+      RealOpenMM getEnergy( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
          On first call, memory for array is allocated if not set
       
          @return array
       
          --------------------------------------------------------------------------------------- */
       
-      std::vector<RealOpenMM>& getObcChainTemp( void );
+      RealOpenMMVector& getObcChain( void );
       
       /**---------------------------------------------------------------------------------------
       
@@ -124,7 +142,7 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates,  std::vector<RealOpenMM>& bornRadii );
+      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates,  RealOpenMMVector& bornRadii );
       
       /**---------------------------------------------------------------------------------------
       
@@ -139,22 +157,23 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
          --------------------------------------------------------------------------------------- */
       
       void computeAceNonPolarForce( const ObcSoftcoreParameters* obcSoftcoreParameters,
-                                   const std::vector<RealOpenMM>& bornRadii, RealOpenMM* energy,
-                                   std::vector<RealOpenMM>& forces ) const;
+                                    const RealOpenMMVector& bornRadii, RealOpenMM* energy,
+                                    RealOpenMMVector& forces ) const;
       
       /**---------------------------------------------------------------------------------------
       
          Get Born energy and forces based on OBC 
       
-         @param bornRadii         Born radii
          @param atomCoordinates   atomic coordinates
          @param partialCharges    partial charges
          @param forces            forces
 
+         @return energy
+      
          --------------------------------------------------------------------------------------- */
       
-      void computeBornEnergyForces( std::vector<RealOpenMM>& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
-                                   const RealOpenMM* partialCharges, std::vector<OpenMM::RealVec>& forces );
+      RealOpenMM computeBornEnergyForces( std::vector<OpenMM::RealVec>& atomCoordinates,
+                                          const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces );
 };
 
 // ---------------------------------------------------------------------------------------

plugins/freeEnergy/platforms/reference/src/gbsa/ObcSoftcoreParameters.h

-
 /* Portions copyright (c) 2006-2009 Stanford University and Simbios.
  * Contributors: Pande Group
  *
@@ -26,11 +25,10 @@
 #define __ObcSoftcoreParameters_H__
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "gbsa/ImplicitSolventParameters.h"
 
 // ---------------------------------------------------------------------------------------
 
-class ObcSoftcoreParameters : public ImplicitSolventParameters {
+class ObcSoftcoreParameters {
 
    public:
 
@@ -38,37 +36,42 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
        enum ObcType { ObcTypeI, ObcTypeII };
 
-       static const std::string ParameterFileName;
-
    private:
 
+      int _numberOfAtoms;
+
       // OBC constants & parameters
    
       RealOpenMM _dielectricOffset;
       RealOpenMM _alphaObc;
       RealOpenMM _betaObc;
       RealOpenMM _gammaObc;
+      RealOpenMM _probeRadius;
+      RealOpenMM _pi4Asolv;
 
       ObcType _obcType;
 
       RealOpenMM _nonPolarPreFactor;
 
+      RealOpenMM _solventDielectric;
+      RealOpenMM _soluteDielectric;
+      RealOpenMM _electricConstant;
+
      // scaling factors for nonpolar term
 
-      int _ownNonPolarScaleFactors;
-      RealOpenMM* _nonPolarScaleFactors;
+      RealOpenMMVector _atomicRadii;
+      RealOpenMMVector _nonPolarScaleFactors;
 
       // scaled radius factors (S_kk in HCT paper)
 
-      int _ownScaledRadiusFactors;
-      RealOpenMM* _scaledRadiusFactors;
+      RealOpenMMVector _scaledRadiusFactors;
 
       // cutoff and periodic boundary conditions
       
-      bool cutoff;
-      bool periodic;
-      RealOpenMM periodicBoxSize[3];
-      RealOpenMM cutoffDistance;
+      bool _cutoff;
+      bool _periodic;
+      RealOpenMM _periodicBoxSize[3];
+      RealOpenMM _cutoffDistance;
 
    public:
 
@@ -92,153 +95,194 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
       /**---------------------------------------------------------------------------------------
       
-         Get OBC type
+         Get number of atoms
       
-         @return OBC type
+         @return number of atoms
       
          --------------------------------------------------------------------------------------- */
 
-      ObcSoftcoreParameters::ObcType getObcType( void ) const;
+      int getNumberOfAtoms( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Set OBC type specific parameters
+         Get electric constant
       
-         @param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
+         @return electric constant
       
          --------------------------------------------------------------------------------------- */
 
-      void setObcTypeParameters( ObcSoftcoreParameters::ObcType obcType );
+      RealOpenMM getElectricConstant( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Get alpha OBC (Eqs. 6 & 7) in Proteins paper
+         Get probe radius (Simbios) 
       
-         @return alphaObc
+         @return probeRadius
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getAlphaObc( void ) const;
+      RealOpenMM getProbeRadius( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Get beta OBC (Eqs. 6 & 7) in Proteins paper
+         Set probe radius (Simbios) 
       
-         @return betaObc
+         @param probeRadius   probe radius
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getBetaObc( void ) const;
+      void setProbeRadius( RealOpenMM probeRadius );
 
       /**---------------------------------------------------------------------------------------
       
-         Get gamma OBC (Eqs. 6 & 7) in Proteins paper
+         Get pi4Asolv:  used in ACE approximation for nonpolar term  
+            ((RealOpenMM) M_PI)*4.0f*0.0049f*1000.0f; (Simbios) 
       
-         @return gammaObc
+         @return pi4Asolv
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getGammaObc( void ) const;
+      RealOpenMM getPi4Asolv( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Get solvent dielectric (Simbios) 
+         Get solvent dielectric
       
-         @return dielectricOffset dielectric offset
+         @return solvent dielectric
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getDielectricOffset( void ) const;
+      RealOpenMM getSolventDielectric( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Return OBC scale factors
+         Set solvent dielectric
       
-         @return array
+         @param solventDielectric solvent dielectric
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMM* getScaledRadiusFactors( void ) const;
+      void setSolventDielectric( RealOpenMM solventDielectric );
 
       /**---------------------------------------------------------------------------------------
       
-         Return OBC scale factors
+         Get solute dielectric
       
-         @return array
+         @return soluteDielectric
       
          --------------------------------------------------------------------------------------- */
 
-      void setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors );
-#if RealOpenMMType == 0
-      void setScaledRadiusFactors( float* scaledRadiusFactors );
-#endif
-      void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
+      RealOpenMM getSoluteDielectric( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
-         Set flag indicating whether scale factors arra should be deleted
+         Set solute dielectric
       
-         @param ownScaledRadiusFactors flag indicating whether scale factors 
-                                       array should be deleted
+         @param soluteDielectric solute dielectric
       
          --------------------------------------------------------------------------------------- */
 
-      void setOwnScaleFactors( int ownScaledRadiusFactors );
+      void setSoluteDielectric( RealOpenMM soluteDielectric );
 
       /**---------------------------------------------------------------------------------------
       
-         Get AtomicRadii array w/ dielectric offset applied
+         Get OBC type
       
-         @return array of atom volumes
+         @return OBC type
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM* getAtomicRadii( void ) const;
+      ObcSoftcoreParameters::ObcType getObcType( void ) const;
       
       /**---------------------------------------------------------------------------------------
       
-         Set AtomicRadii array
+         Set OBC type specific parameters
       
-         @param atomicRadii array of atomic radii
+         @param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
       
          --------------------------------------------------------------------------------------- */
       
-      void setAtomicRadii( RealOpenMM* atomicRadii );
+      void setObcTypeParameters( ObcSoftcoreParameters::ObcType obcType );
       
       /**---------------------------------------------------------------------------------------
       
-         Set AtomicRadii array
+         Get alpha OBC (Eqs. 6 & 7) in Proteins paper
       
-         @param atomicRadii vector of atomic radii
+         @return alphaObc
       
          --------------------------------------------------------------------------------------- */
       
-      void setAtomicRadii( const RealOpenMMVector& atomicRadii );
+      RealOpenMM getAlphaObc( void ) const;
       
       /**---------------------------------------------------------------------------------------
       
-         Map Gmx atom name to Tinker atom number (Simbios)
+         Get beta OBC (Eqs. 6 & 7) in Proteins paper
       
-         @param atomName            atom name (CA, HA, ...); upper and lower case should both work
-         @param log                 if set, then print error messages to log file
+         @return betaObc
       
-         return Tinker atom number if atom name is valid; else return -1
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getBetaObc( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get gamma OBC (Eqs. 6 & 7) in Proteins paper
+      
+         @return gammaObc
       
          --------------------------------------------------------------------------------------- */
       
-      int mapGmxAtomNameToTinkerAtomNumber( const char* atomName, FILE* log ) const;
+      RealOpenMM getGammaObc( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get solvent dielectric (Simbios) 
+      
+         @return dielectricOffset dielectric offset
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getDielectricOffset( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Return OBC scale factors
+      
+         @return array
+      
+         --------------------------------------------------------------------------------------- */
+      
+      const RealOpenMMVector& getScaledRadiusFactors( void ) const;
+        
+      /**---------------------------------------------------------------------------------------
+      
+         Set OBC scale factors
+      
+         @param input vector of radius factors
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
         
       /**---------------------------------------------------------------------------------------
       
-         Get string w/ state
+         Get AtomicRadii array w/ dielectric offset applied
       
-         @param title               title (optional)
+         @return array of atom volumes
       
-         @return string
+         --------------------------------------------------------------------------------------- */
+
+      const RealOpenMMVector& getAtomicRadii( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set AtomicRadii array
+      
+         @param atomicRadii vector of atomic radii
       
          --------------------------------------------------------------------------------------- */
 
-      std::string getStateString( const char* title ) const;
+      void setAtomicRadii( const RealOpenMMVector& atomicRadii );
 
       /**---------------------------------------------------------------------------------------
 
@@ -256,7 +300,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      bool getUseCutoff();
+      bool getUseCutoff( void );
 
       /**---------------------------------------------------------------------------------------
 
@@ -264,7 +308,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getCutoffDistance();
+      RealOpenMM getCutoffDistance( void );
 
       /**---------------------------------------------------------------------------------------
 
@@ -284,7 +328,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      bool getPeriodic();
+      bool getPeriodic( void );
 
       /**---------------------------------------------------------------------------------------
 
@@ -292,29 +336,17 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMM* getPeriodicBox();
-
-      /**---------------------------------------------------------------------------------------
-      
-         Set flag indicating whether scale factors array should be deleted
-      
-         @param ownNonPolarScaleFactors flag indicating whether scale factors 
-                                       array should be deleted
-      
-         --------------------------------------------------------------------------------------- */
-      
-      void setOwnNonPolarScaleFactors( int ownNonPolarScaleFactors );
+      const RealOpenMM* getPeriodicBox( void );
 
       /**---------------------------------------------------------------------------------------
       
          Return non-polar scale factors
-         If not previously set, allocate space
       
          @return array 
       
          --------------------------------------------------------------------------------------- */
       
-      const RealOpenMM* getNonPolarScaleFactors( void ) const;
+      const RealOpenMMVector& getNonPolarScaleFactors( void ) const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -338,19 +370,6 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
 
 };
    
-/**---------------------------------------------------------------------------------------
-      
-   Qsort/heapsort integer comparison (Simbios) 
-      
-   @parma a first value to compare
-   @param b second value to compare
-
-   @return -1, 0, 1
-      
---------------------------------------------------------------------------------------- */
-
-int integerComparison( const void *a, const void *b);
-
 // ---------------------------------------------------------------------------------------
 
 #endif // __ObcSoftcoreParameters_H__