Continuing to implement ReferencePlatform (implemented GBSA kernels, added...

Continuing to implement ReferencePlatform (implemented GBSA kernels, added test case for SHAKE and fixed some bugs in it)

olla/include/kernels.h

@@ -106,13 +106,11 @@ public:
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
      * 
-     * @param bornRadii           the initial value of the Born radius for each atom
      * @param atomParameters      the force parameters (charge, atomic radius, scaling factor) for each atom
      * @param solventDielectric   the dielectric constant of the solvent
      * @param soluteDielectric    the dielectric constant of the solute
      */
-    virtual void initialize(const std::vector<double>& bornRadii, const std::vector<std::vector<double> >& atomParameters,
-            double solventDielectric, double soluteDielectric) = 0;
+    virtual void initialize(const std::vector<std::vector<double> >& atomParameters, double solventDielectric, double soluteDielectric) = 0;
     /**
      * Execute the kernel to calculate the forces.
      * 

openmmapi/src/GBSAOBCForceField.cpp

@@ -36,7 +36,7 @@
 
 using namespace OpenMM;
 
-GBSAOBCForceField::GBSAOBCForceField(int numAtoms) : atoms(numAtoms) {
+GBSAOBCForceField::GBSAOBCForceField(int numAtoms) : atoms(numAtoms), solventDielectric(78.3), soluteDielectric(1.0) {
 }
 
 void GBSAOBCForceField::getAtomParameters(int index, double& charge, double& radius, double& scalingFactor) const {

openmmapi/src/GBSAOBCForceFieldImpl.cpp

@@ -43,9 +43,7 @@ GBSAOBCForceFieldImpl::GBSAOBCForceFieldImpl(GBSAOBCForceField& owner, OpenMMCon
 void GBSAOBCForceFieldImpl::initialize(OpenMMContextImpl& context) {
     hasInitialized = true;
     kernel = context.getPlatform().createKernel(CalcGBSAOBCForceFieldKernel::Name());
-    std::vector<double> bornRadii;
-    // TODO calculate the initial Born radii.
-    vector<vector<double> > atomParameters;
+    vector<vector<double> > atomParameters(owner.getNumAtoms());
     for (int i = 0; i < owner.getNumAtoms(); ++i) {
         double charge, radius, scalingFactor;
         owner.getAtomParameters(i, charge, radius, scalingFactor);
@@ -53,8 +51,7 @@ void GBSAOBCForceFieldImpl::initialize(OpenMMContextImpl& context) {
         atomParameters[i].push_back(radius);
         atomParameters[i].push_back(scalingFactor);
     }
-    dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).initialize(bornRadii, atomParameters,
-            owner.getSolventDielectric(), owner.getSoluteDielectric());
+    dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).initialize(atomParameters, owner.getSolventDielectric(), owner.getSoluteDielectric());
 }
 
 void GBSAOBCForceFieldImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {

platforms/reference/src/ReferenceKernels.cpp

@@ -31,6 +31,7 @@
 
 #include "ReferenceKernels.h"
 #include "ReferenceFloatStreamImpl.h"
+#include "gbsa/CpuObc.h"
 #include "SimTKReference/ReferenceAngleBondIxn.h"
 #include "SimTKReference/ReferenceBondForce.h"
 #include "SimTKReference/ReferenceHarmonicBondIxn.h"
@@ -209,17 +210,44 @@ double ReferenceCalcStandardMMForceFieldKernel::executeEnergy(const Stream& posi
     return energy;
 }
 
-void ReferenceCalcGBSAOBCForceFieldKernel::initialize(const vector<double>& bornRadii, const vector<vector<double> >& atomParameters,
-        double solventDielectric, double soluteDielectric) {
+ReferenceCalcGBSAOBCForceFieldKernel::~ReferenceCalcGBSAOBCForceFieldKernel() {
+    if (obc) {
+        delete obc->getObcParameters();
+        delete obc;
+    }
+}
 
+void ReferenceCalcGBSAOBCForceFieldKernel::initialize(const vector<vector<double> >& atomParameters, double solventDielectric, double soluteDielectric) {
+    int numAtoms = atomParameters.size();
+    charges.resize(numAtoms);
+    vector<RealOpenMM> atomicRadii(numAtoms);
+    vector<RealOpenMM> scaleFactors(numAtoms);
+    for (int i = 0; i < numAtoms; ++i) {
+        charges[i] = atomParameters[i][0];
+        atomicRadii[i] = atomParameters[i][1];
+        scaleFactors[i] = atomParameters[i][2];
+    }
+    ObcParameters* obcParameters  = new ObcParameters(numAtoms, ObcParameters::ObcTypeII);
+    obcParameters->setAtomicRadii(atomicRadii, SimTKOpenMMCommon::KcalAngUnits);
+    obcParameters->setScaledRadiusFactors(scaleFactors);
+    obcParameters->setSolventDielectric(solventDielectric);
+    obcParameters->setSoluteDielectric(soluteDielectric);
+    obc = new CpuObc(obcParameters);
+    obc->setIncludeAceApproximation(true);
 }
 
 void ReferenceCalcGBSAOBCForceFieldKernel::executeForces(const Stream& positions, Stream& forces) {
-    
+    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) positions.getImpl()).getData()); // Reference code needs to be made const correct
+    RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) forces.getImpl()).getData();
+    obc->computeImplicitSolventForces(posData, &charges[0], forceData, 0);
 }
 
 double ReferenceCalcGBSAOBCForceFieldKernel::executeEnergy(const Stream& positions) {
-    return 0.0; // TODO implement correctly
+    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) positions.getImpl()).getData()); // Reference code needs to be made const correct
+    RealOpenMM** forceData = allocateRealArray(positions.getSize(), 3);
+    obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
+    disposeRealArray(forceData, positions.getSize());
+    return obc->getEnergy();
 }
 
 void ReferenceIntegrateVerletStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,

platforms/reference/src/ReferenceKernels.h

@@ -35,6 +35,7 @@
 #include "kernels.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
+class CpuObc;
 class ReferenceStochasticDynamics;
 class ReferenceShakeAlgorithm;
 
@@ -102,16 +103,15 @@ class ReferenceCalcGBSAOBCForceFieldKernel : public CalcGBSAOBCForceFieldKernel
 public:
     ReferenceCalcGBSAOBCForceFieldKernel(std::string name, const Platform& platform) : CalcGBSAOBCForceFieldKernel(name, platform) {
     }
+    ~ReferenceCalcGBSAOBCForceFieldKernel();
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
      * 
-     * @param bornRadii           the initial value of the Born radius for each atom
      * @param atomParameters      the force parameters (charge, atomic radius, scaling factor) for each atom
      * @param solventDielectric   the dielectric constant of the solvent
      * @param soluteDielectric    the dielectric constant of the solute
      */
-    void initialize(const std::vector<double>& bornRadii, const std::vector<std::vector<double> >& atomParameters,
-            double solventDielectric, double soluteDielectric);
+    void initialize(const std::vector<std::vector<double> >& atomParameters, double solventDielectric, double soluteDielectric);
     /**
      * Execute the kernel to calculate the forces.
      * 
@@ -127,6 +127,9 @@ public:
      * @return the potential energy due to the GBSAOBCForceField
      */
     double executeEnergy(const Stream& positions);
+private:
+    CpuObc* obc;
+    std::vector<RealOpenMM> charges;
 };
 
 /**

platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp

@@ -65,6 +65,7 @@ ReferenceShakeAlgorithm::ReferenceShakeAlgorithm( int numberOfConstraints,
 
    _maximumNumberOfIterations  = 15;
    _tolerance                  = (RealOpenMM) 1.0e-04;
+   _hasInitializedMasses       = false;
 
    // work arrays
 
@@ -237,7 +238,6 @@ int ReferenceShakeAlgorithm::applyShake( int numberOfAtoms, RealOpenMM** atomCoo
 
    static const RealOpenMM epsilon6    = (RealOpenMM) 1.0e-06;
 
-   static int firstPass                = 1;
    static int debug                    = 0;
 
    // ---------------------------------------------------------------------------------------
@@ -253,8 +253,8 @@ int ReferenceShakeAlgorithm::applyShake( int numberOfAtoms, RealOpenMM** atomCoo
 
    // calculate reduced masses on 1st pass
 
-   if( firstPass ){
-      firstPass = 0;
+   if( !_hasInitializedMasses ){
+      _hasInitializedMasses = true;
       for( int ii = 0; ii < _numberOfConstraints; ii++ ){
          int atomI          = _atomIndices[ii][0];
          int atomJ          = _atomIndices[ii][1];
@@ -298,7 +298,8 @@ int ReferenceShakeAlgorithm::applyShake( int numberOfAtoms, RealOpenMM** atomCoo
          }
 
          RealOpenMM rp2  = DOT3( rp_ij, rp_ij );
-         RealOpenMM diff = d_ij2[ii] - rp2;
+         RealOpenMM dist2= _shakeParameters[ii][0]*_shakeParameters[ii][0];
+         RealOpenMM diff = dist2 - rp2;
          int iconv       = (int) ( FABS( diff )*distanceTolerance[ii] );
          if( iconv ){
             RealOpenMM rrpr  = DOT3(  rp_ij, r_ij[ii] );

platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.h

@@ -42,6 +42,7 @@ class ReferenceShakeAlgorithm {
       RealOpenMM* _d_ij2;
       RealOpenMM* _distanceTolerance;
       RealOpenMM* _reducedMasses;
+      bool _hasInitializedMasses;
       
    public:
 

platforms/reference/src/gbsa/CpuObc.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef __CpuObc_H__
+#define __CpuObc_H__
+
+#include "ObcParameters.h"
+#include "CpuImplicitSolvent.h"
+
+// ---------------------------------------------------------------------------------------
+
+class CpuObc : public CpuImplicitSolvent {
+
+   private:
+
+      // GBSA/OBC parameters
+
+      ObcParameters* _obcParameters;
+
+      // arrays containing OBC chain derivative 
+
+      RealOpenMM* _obcChain;
+      RealOpenMM* _obcChainTemp;
+
+      // initialize data members (more than
+      // one constructor, so centralize intialization here)
+
+      void _initializeObcDataMembers( void );
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         @param implicitSolventParameters    ImplicitSolventParameters reference
+      
+         @return CpuImplicitSolvent object
+      
+         --------------------------------------------------------------------------------------- */
+
+       CpuObc( ImplicitSolventParameters* obcParameters );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~CpuObc( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Return ObcParameters
+      
+         @return ObcParameters
+      
+         --------------------------------------------------------------------------------------- */
+
+      ObcParameters* getObcParameters( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set ImplicitSolventParameters
+      
+         @param ImplicitSolventParameters
+      
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+
+      int setObcParameters( ObcParameters* obcParameters );
+ 
+      /**---------------------------------------------------------------------------------------
+      
+         Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
+         On first call, memory for array is allocated if not set
+      
+         @return array
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM* getObcChain( void );
+      RealOpenMM* getObcChainConst( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Return OBC chain temp work array of size=_implicitSolventParameters->getNumberOfAtoms()
+         On first call, memory for array is allocated if not set
+      
+         @return array
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM* getObcChainTemp( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get Born radii based on OBC 
+
+         @param atomCoordinates   atomic coordinates
+         @param bornRadii         output array of Born radii
+         @param obcChain          output array of OBC chain derivative factors; if NULL,
+                                  then ignored
+      
+         @return array of Born radii
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int computeBornRadii( RealOpenMM** atomCoordinates, RealOpenMM* bornRadii,
+                            RealOpenMM* obcChain = NULL );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get Born energy and forces based on OBC 
+      
+         @param bornRadii         Born radii
+         @param atomCoordinates   atomic coordinates
+         @param partialCharges    partial charges
+         @param forces            forces
+      
+         @return force array
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoordinates,
+                                   const RealOpenMM* partialCharges, RealOpenMM** forces );
+      
+      int computeBornEnergyForcesPrint( RealOpenMM* bornRadii, RealOpenMM** atomCoordinates,
+                                        const RealOpenMM* partialCharges, RealOpenMM** forces );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get state 
+      
+         title             title (optional)
+      
+         @return state string
+      
+         --------------------------------------------------------------------------------------- */
+      
+      std::string getStateString( const char* title ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Write Born energy and forces (Simbios)
+      
+         @param atomCoordinates   atomic coordinates
+         @param partialCharges    partial atom charges
+         @param forces            force array
+         @param resultsFileName   output file name
+      
+         @return SimTKOpenMMCommon::DefaultReturn if file opened; else return SimTKOpenMMCommon::ErrorReturn
+      
+         --------------------------------------------------------------------------------------- */
+          
+      int writeBornEnergyForces( RealOpenMM** atomCoordinates,
+                                 const RealOpenMM* partialCharges, RealOpenMM** forces,
+                                 const std::string& resultsFileName ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Write  results from first loop
+      
+         @param atomCoordinates     atomic coordinates
+         @param RealOpenMM forces         forces
+         @param outputFileName      output file name
+      
+         @return SimTKOpenMMCommon::DefaultReturn unless
+                 file cannot be opened
+                 in which case return SimTKOpenMMCommon::ErrorReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int writeForceLoop1( int numberOfAtoms, RealOpenMM** forces, const RealOpenMM* bornForce,
+                                  const std::string& outputFileName );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Write results
+      
+         @param numberOfAtoms       number of atoms
+         @param chunkSizes          vector of chunk sizes for realRealOpenMMVector
+         @param realRealOpenMMVector      vector of RealOpenMM**
+         @param realVector          vector of RealOpenMM*
+         @param outputFileName      output file name
+      
+         @return SimTKOpenMMCommon::DefaultReturn unless
+                 file cannot be opened
+                 in which case return SimTKOpenMMCommon::ErrorReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int writeForceLoop( int numberOfAtoms, const IntVector& chunkSizes,
+                                 const RealOpenMMPtrPtrVector& realRealOpenMMVector, 
+                                 const RealOpenMMPtrVector& realVector,
+                                 const std::string& outputFileName );
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __CpuObc_H__

platforms/reference/src/gbsa/ImplicitSolventParameters.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef __ImplicitSolventParameters_H__
+#define __ImplicitSolventParameters_H__
+
+#include "../SimTKUtilities/SimTKOpenMMRealType.h"
+#include <string>
+
+// ---------------------------------------------------------------------------------------
+
+class ImplicitSolventParameters {
+
+   protected:
+
+      // parameters common to implicit solvent models
+   
+      RealOpenMM _solventDielectric;
+      RealOpenMM _soluteDielectric;
+      RealOpenMM _kcalA_To_kJNm;
+      RealOpenMM _electricConstant;
+      RealOpenMM _probeRadius;
+      RealOpenMM _pi4Asolv;
+
+      RealOpenMM _preFactor;
+   
+      // ---------------------------------------------------------------------------------------
+
+      // atom count
+
+      int _numberOfAtoms;
+
+      // flag signalling whether arrays are to be freed
+
+      int _freeArrays;
+
+      // atomic radii
+
+      int _ownAtomicRadii;
+      RealOpenMM* _atomicRadii;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Initialize ImplicitSolvent Parameters (Simbios) 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void _initializeImplicitSolventConstants( void );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set KcalA_To_kJNm
+      
+         @param kcalA_To_kJNm probe radius
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setKcalA_To_kJNm( RealOpenMM kcalA_To_kJNm );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set free array flag -- if set then work arrays are freed when destructor is called
+      
+         @param freeArrays flag
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+
+      int setFreeArrays( int freeArrays );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Reset prefactor (Simbios) 
+      
+         called when _electricConstant, _soluteDielectric, or _solventDielectric are modified
+      
+         --------------------------------------------------------------------------------------- */
+      
+      void _resetPreFactor( void );
+      
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         ImplicitSolventParameters constructor (Simbios) 
+      
+         @param numberOfAtoms       number of atoms
+      
+         --------------------------------------------------------------------------------------- */
+    
+       ImplicitSolventParameters( int numberOfAtoms );
+
+      /**---------------------------------------------------------------------------------------
+      
+         ImplicitSolventParameters destructor (Simbios) 
+      
+         --------------------------------------------------------------------------------------- */
+    
+       ~ImplicitSolventParameters( );
+
+      // override of new/delete
+
+      //static void* operator new( size_t size );
+      //static void  operator delete( void *p );
+
+      //static void* operator new[]( size_t size );
+      //static void  operator delete[]( void *p );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get number of atoms
+      
+         @return number of atoms
+      
+         --------------------------------------------------------------------------------------- */
+    
+      int getNumberOfAtoms( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get free array flag -- if set then work arrays are freed when destructor is called
+      
+         @return freeArrays flag
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getFreeArrays( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get solvent dielectric
+      
+         @return solvent dielectric
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getSolventDielectric( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set solvent dielectric
+      
+         @param solventDielectric solvent dielectric
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setSolventDielectric( RealOpenMM solventDielectric );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get solute dielectric
+      
+         @return soluteDielectric
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getSoluteDielectric( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set solute dielectric
+      
+         @param soluteDielectric solute dielectric
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setSoluteDielectric( RealOpenMM soluteDielectric );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get conversion factor for kcal/A -> kJ/nm (Simbios) 
+      
+         @return kcalA_To_kJNm factor
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getKcalA_To_kJNm( void ) const;
+      
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get electric constant (Simbios) 
+      
+         @return electricConstant
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getElectricConstant( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set electric constant (Simbios) 
+      
+         @param electricConstant       electric constant
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setElectricConstant( RealOpenMM electricConstant );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get probe radius (Simbios) 
+      
+         @return probeRadius
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getProbeRadius( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set probe radius (Simbios) 
+      
+         @param probeRadius   probe radius
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setProbeRadius( RealOpenMM probeRadius );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get pi4Asolv:  used in ACE approximation for nonpolar term  
+            ((RealOpenMM) M_PI)*4.0f*0.0049f*1000.0f; (Simbios) 
+      
+         @return pi4Asolv
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getPi4Asolv( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get prefactor
+      
+         @returnpreFactor 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getPreFactor( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set values used in ACE approximation for nonpolar term
+            ((RealOpenMM) M_PI)*4.0f*0.0049f*1000.0f; (Simbios) 
+      
+         @param pi4Asolv   see above
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setPi4Asolv( RealOpenMM pi4Asolv );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get AtomicRadii array
+      
+         @return array of atom volumes
+      
+         --------------------------------------------------------------------------------------- */
+
+      virtual RealOpenMM* getAtomicRadii( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set AtomicRadii array
+      
+         @param atomicRadii array of atomic radii
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+
+      virtual int setAtomicRadii( RealOpenMM* atomicRadii );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Set AtomicRadii array
+      
+         @param atomicRadii vector of atomic radii
+         @param units       units flag SimTKOpenMMCommon::MdUnits or
+                                       SimTKOpenMMCommon::KcalAngUnits
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+
+      virtual int setAtomicRadii( const RealOpenMMVector& atomicRadii,
+                                  int units = SimTKOpenMMCommon::MdUnits );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set AtomicRadii array
+      
+         @param atomicRadii array of atomic radii
+         @param units       units flag: SimTKOpenMMCommon::KcalAngUnits or
+                                        SimTKOpenMMCommon::MdUnits 
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual int setAtomicRadii( RealOpenMM* atomicRadii, int units );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set flag indicating whether AtomicRadii array is owned by
+         object; if flag is set, then when the object is deleted,
+         the array will be freed
+      
+         @param ownAtomicRadii flag indicating whether array of atomic radii
+                               should be freed
+      
+         @return SimTKOpenMMCommon::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+
+      int setOwnAtomicRadii( int ownAtomicRadii );
+
+      /**---------------------------------------------------------------------------------------
+            
+         Print state to log file (Simbios)
+         
+         @param title               title (optional)
+         @param log                 print state to log file
+            
+         @return SimTKOpenMMCommon::DefaultReturn
+            
+         --------------------------------------------------------------------------------------- */
+      
+      virtual std::string getStateString( const char* title ) const;
+
+      /**---------------------------------------------------------------------------------------
+            
+         Get string tab -- centralized
+         
+         @return tab string
+            
+         --------------------------------------------------------------------------------------- */
+      
+      std::string getStringTab( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+            
+         Return nonzero value errors
+         
+         @return ready status
+            
+         --------------------------------------------------------------------------------------- */
+      
+      virtual int isNotReady( void ) const;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ImplicitSolventParameters_H__

platforms/reference/src/gbsa/ObcReadme.txt

+
+
+The OBC Generalized Born model is based on the following papers:
+ 
+      J. Phys. Chem. 1996 100, 19824-19839 (HCT paper)
+
+      Proteins: Structure, Function, and Bioinformatics 55:383-394 (2004) (OBC paper)
+
+---------------------------------------------------------------------------------------
+
+The two main interface methods perform the following tasks: 
+
+	(1) set the GBSA parameters; this method is called once prior to execution of
+       the main simulation loop
+
+	(2) calculate the GBSA forces/energy given the atom coordinates and charges
+       for each simulation step
+
+The two methods and helper methods are in the file cpuObcInterface.cpp
+
+---------------------------------------------------------------------------------------
+
+The setup call is
+
+   cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obcScaleFactors,
+                        int includeAceApproximation,
+                        RealOpenMM soluteDielectric, RealOpenMM solventDielectric, FILE* log );
+
+The parameters include the following:
+
+	(1)   number of atoms
+	(2)   the OBC atomic radii (akin to VDW radii, but optimized for GBSA calculations)
+	(3)   the OBC scale factors for each atom
+	(4)   a flag indicating whether the nonpolar ACE approximation is to be included 
+         in calculating the forces and energy: I do not have a reference for this term
+	(5-6) the solute and solvent dielectric (typically 1.0 & 78.3)
+	(7)   a log file reference; the reference may be set to NULL,
+         if logging is unwanted. Note: if the reference is NULL, warnings, ... will be output to stderr
+
+  cpuSetObcParameters() creates a static CpuObc object which is then referenced when the
+  GBSA forces and energy are to be calculated
+
+  The default OBC model is the Type II model: Eq. 8 in the 2004 OBC paper; 
+  for the Type I model, replace the call
+
+     ObcParameters* obcParameters  = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeII );
+
+   with 
+
+     ObcParameters* obcParameters  = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeI );
+
+---------------------------------------------------------------------------------------
+
+The OBC scale factors may be obtained via calls to either of the following 'helper' methods
+
+      getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, RealOpenMM* scaleFactors )
+
+   or
+
+      getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealOpenMM* masses, RealOpenMM* scaleFactors )
+
+Documentation for the inputs to these routines is contained in the file, cpuObcInterface.cpp.
+The scale factors are those used in Tinker5, and are based on the element type
+of each atom (H, C, N, O, ...).
+
+---------------------------------------------------------------------------------------
+
+The OBC radii may be obtained via the helper method:
+
+      getGbsaRadii( int numberOfAtoms, const int* atomicNumber, 
+                    const int* numberOfCovalentPartners, const int* indexOfCovalentPartner,
+                    RealOpenMM* gbsaRadii );
+
+Documentation for the inputs to this routine is contained in the file, cpuObcInterface.cpp.
+The radii are based on the atom type (methyl C, carbonyl C, ...). The value for a hydrogen
+depends on its covalent heavy atom partner. As for the OBC scale factors, the values 
+hardwired into the method are the same as those used in Tinker5.
+ 
+---------------------------------------------------------------------------------------
+
+The energy/forces are calculated via the call
+
+   cpuCalculateImplicitSolventForces( RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges,
+                                      RealOpenMM** forces, RealOpenMM* energy, int updateBornRadii );
+
+	The coordinate and force arrays should have the layout: atomCoordinates[atomIndex][3] &  
+                                                                    forces[atomIndex][3]
+
+   If updateBornRadii = 0, then the Born radii from the previous iteration are used; this reduces the
+   number of O(N**2) loops from 3 to 2.
+
+   If updateBornRadii != 0, then the Born radii are calculated for the input configuration. 
+
+   For MD runs, setting updateBornRadii = 0 is relatively safe since the radii change little 
+   from one iteration to the next. However, for minimization techniques updateBornRadii 
+   should probably be set to a nonzero value since the configuarations can change significantly
+   between adjacent calls.
+
+---------------------------------------------------------------------------------------
+ 
+Notes:
+
+	(1) The type (float or double) for floating-point numbers is set in the file SimTKOpenMMRealType.h.
+       If 'RealOpenMMType' is set to 1 in the file, the calculations are performed in
+       single-precision; otherwise they are performed in double-precision
+
+   (2) The units are Angstroms for the spatial dimensions, kcal/mol for energy, and kcal/mol.A for the forces
+
+   (3) The code in gromacsCpuObcInterface.cpp provides an example of the parameter setup, ... used for
+       interfacing w/ Gromacs; the details are somewhat different from the code in cpuObcInterface.cpp
+
+   (4) Output from Tinker for a singles ubiquitin configuration are in the directory 'Examples'.
+
+       The xyz file gives the coordinates and atom types (Amber99 -- note the charge for atom type 268
+      (line 2008 in the Tinker amber99.prm file) was changed from -0.2737 to -0.2774 to agree w/ 
+      the value used in the version of Gromacs we have access to.) 
+
+       The key file specifies that OBC should be used for the implicit solvent.
+
+       The results are in the files 111UBQ.gbsaAce and 111UBQ.gbsaNoAce. The first file includes the
+       ACE approximation, while the second does not. On the first line of each file, the number of atoms
+       and GBSA energy are reported. The remaining lines (one for each atom) give the coordinates (3 entries),
+       Born radius, partial charge, GBSA radius (rsolv in Tinker), the OBC scaling factor, and the forces (3). The
+       last three fields give the atomic number, Tinker Amber99 atom name and type.
+
+---------------------------------------------------------------------------------------

platforms/reference/src/gbsa/SimTKOpenMMWindowLinux.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+
+#ifndef __SimTKOpenMMWindowLinux_H_
+#define __SimTKOpenMMWindowLinux_H__
+
+#ifdef WIN32
+#define FOPEN fopen_s
+#else
+#define FOPEN fopen
+#endif
+
+
+#endif // __SimTKOpenMMWindowLinux_H__

platforms/reference/tests/TestReferenceGBSAOBCForceField.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of GBSAOBCForceField.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "OpenMMContext.h"
+#include "ReferencePlatform.h"
+#include "GBSAOBCForceField.h"
+#include "System.h"
+#include "LangevinIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleAtom() {
+    ReferencePlatform platform;
+    System system(1, 0);
+    system.setAtomMass(0, 2.0);
+    LangevinIntegrator integrator(0, 0.1, 0.01);
+    GBSAOBCForceField* forceField = new GBSAOBCForceField(1);
+    forceField->setAtomParameters(0, 0.5, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    positions[0] = Vec3(0, 0, 0);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy);
+    double bornRadius = 1.5-0.09; // dielectric offset
+    double eps0 = EPSILON0*A2NM*CAL2JOULE;
+    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
+    double extendedRadius = bornRadius+1.4; // probe radius
+    double nonpolarEnergy = PI_M*0.0216*extendedRadius*extendedRadius*std::pow(1.5/bornRadius, 6.0); // Where did this formula come from?  Just copied it from CpuImplicitSolvent.cpp
+    ASSERT_EQUAL_TOL(bornEnergy+nonpolarEnergy, state.getPotentialEnergy(), 0.01);
+}
+
+void testForce() {
+    ReferencePlatform platform;
+    const int numAtoms = 10;
+    System system(numAtoms, 0);
+    LangevinIntegrator integrator(0, 0.1, 0.01);
+    GBSAOBCForceField* forceField = new GBSAOBCForceField(numAtoms);
+    for (int i = 0; i < numAtoms; ++i)
+        forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    
+    // Set random positions for all the atoms.
+    
+    vector<Vec3> positions(numAtoms);
+    init_gen_rand(0);
+    for (int i = 0; i < numAtoms; ++i)
+        positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    
+    // Take a small step in the direction of the energy gradient.
+    
+    double norm = 0.0;
+    for (int i = 0; i < numAtoms; ++i) {
+        Vec3 f = state.getForces()[i];
+        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
+    }
+    norm = std::sqrt(norm);
+    const double delta = 1e-3;
+    double step = delta/norm;
+    for (int i = 0; i < numAtoms; ++i) {
+        Vec3 p = positions[i];
+        Vec3 f = state.getForces()[i];
+        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
+    }
+    context.setPositions(positions);
+    
+    // See whether the potential energy changed by the expected amount.
+    
+    State state2 = context.getState(State::Energy);
+    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
+}
+
+int main() {
+    try {
+        testSingleAtom();
+        testForce();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}