Added AMOEBA PME for Reference platoform

platforms/reference/src/SimTKUtilities/SimTKOpenMMRealType.h

@@ -53,6 +53,8 @@
 #define ATAN           atanf
 #define TANH           tanhf
 
+#define FLOOR          floorf
+
 #define ATOF           atoff
 
 #define PI_M               3.141592653589f
@@ -83,6 +85,8 @@
 #define ATAN           atan
 #define TANH           tanh
 
+#define FLOOR          floor
+
 #define ATOF           atof
 
 #define PI_M               3.141592653589

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -311,7 +311,6 @@ public:
     void getElectrostaticPotential(const std::vector< Vec3 >& inputGrid,
                                     Context& context, std::vector< double >& outputElectrostaticPotential);
 
-
     /**
      * Get the system multipole moments.
      * 
@@ -328,8 +327,7 @@ public:
                                       quadrupole_yx, quadrupole_yy, quadrupole_yz,
                                       quadrupole_zx, quadrupole_zy, quadrupole_zz)
      */
-
-    void getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMonents);
+    void getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -32,7 +32,6 @@
 #include "AmoebaReferenceStretchBendForce.h"
 #include "AmoebaReferenceOutOfPlaneBendForce.h"
 #include "AmoebaReferenceTorsionTorsionForce.h"
-#include "AmoebaReferenceMultipoleForce.h"
 #include "AmoebaReferenceVdwForce.h"
 #include "AmoebaReferenceWcaDispersionForce.h"
 #include "AmoebaReferenceGeneralizedKirkwoodForce.h"
@@ -44,6 +43,8 @@
 #include "openmm/internal/AmoebaMultipoleForceImpl.h"
 #include "openmm/internal/AmoebaVdwForceImpl.h"
 #include "openmm/internal/AmoebaGeneralizedKirkwoodForceImpl.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/internal/NonbondedForceImpl.h"
 
 #include <cmath>
 #ifdef _MSC_VER
@@ -377,7 +378,8 @@ double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& contex
  * -------------------------------------------------------------------------- */
 
 ReferenceCalcAmoebaMultipoleForceKernel::ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, System& system) : 
-         CalcAmoebaMultipoleForceKernel(name, platform), system(system) {
+         CalcAmoebaMultipoleForceKernel(name, platform), system(system), numMultipoles(0), mutualInducedMaxIterations(60), mutualInducedTargetEpsilon(1.0e-03),
+                                                         usePme(false),alphaEwald(0.0), cutoffDistance(1.0) {  
 
 }
 
@@ -448,21 +450,44 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
 
     }
 
+    polarizationType = force.getPolarizationType();
+    if( polarizationType == AmoebaMultipoleForce::Mutual ){
         mutualInducedMaxIterations = force.getMutualInducedMaxIterations();
         mutualInducedTargetEpsilon = force.getMutualInducedTargetEpsilon();
-
-    nonbondedMethod = static_cast<int>(force.getNonbondedMethod());
-    if( nonbondedMethod != 0 && nonbondedMethod != 1 ){
-         throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n");
     }
-    polarizationType = force.getPolarizationType();
 
+    // PME
+
+    nonbondedMethod  = force.getNonbondedMethod();
+    if( nonbondedMethod == AmoebaMultipoleForce::PME ){
+        usePme     = true;
+        alphaEwald = force.getAEwald();
+        cutoffDistance = force.getCutoffDistance();
+        force.getPmeGridDimensions(pmeGridDimension);
+        if (pmeGridDimension[0] == 0 || alphaEwald == 0.0) {
+            NonbondedForce nb;
+            nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
+            nb.setCutoffDistance(force.getCutoffDistance());
+            int gridSizeX, gridSizeY, gridSizeZ;
+            NonbondedForceImpl::calcPMEParameters(system, nb, alphaEwald, gridSizeX, gridSizeY, gridSizeZ);
+            pmeGridDimension[0] = gridSizeX;
+            pmeGridDimension[1] = gridSizeY;
+            pmeGridDimension[2] = gridSizeZ;
+        }    
+    } else {
+        usePme = false;
+    }
+    return;
 }
 
-double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmoebaReferenceMultipoleForce(ContextImpl& context )
+{
 
-    vector<RealVec>& posData   = extractPositions(context);
-    vector<RealVec>& forceData = extractForces(context);
+    // amoebaReferenceMultipoleForce is set to AmoebaReferenceGeneralizedKirkwoodForce if AmoebaGeneralizedKirkwoodForce is present
+    // amoebaReferenceMultipoleForce is set to AmoebaReferencePmeMultipoleForce if 'usePme' is set
+    // amoebaReferenceMultipoleForce is set to AmoebaReferenceMultipoleForce otherwise
+
+    // check if AmoebaGeneralizedKirkwoodForce is present 
 
     ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel = NULL;
     for (unsigned int ii = 0; ii < context.getForceImpls().size() && gkKernel == NULL; ii++) {
@@ -500,29 +525,55 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo
 
         // calculate Grycuk Born radii
 
+        vector<RealVec>& posData   = extractPositions(context);
         amoebaReferenceGeneralizedKirkwoodForce->calculateGrycukBornRadii( posData );
 
         amoebaReferenceMultipoleForce = new AmoebaReferenceGeneralizedKirkwoodMultipoleForce( amoebaReferenceGeneralizedKirkwoodForce );
 
+    } else if( usePme ) {
+
+         AmoebaReferencePmeMultipoleForce* amoebaReferencePmeMultipoleForce = new AmoebaReferencePmeMultipoleForce( );
+         amoebaReferencePmeMultipoleForce->setAlphaEwald( alphaEwald );
+         amoebaReferencePmeMultipoleForce->setCutoffDistance( cutoffDistance );
+         amoebaReferencePmeMultipoleForce->setPmeGridDimensions( pmeGridDimension );
+         RealVec& box = extractBoxSize(context);
+         double minAllowedSize = 1.999999*cutoffDistance;
+         if (box[0] < minAllowedSize || box[1] < minAllowedSize || box[2] < minAllowedSize){
+            throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
+         }
+         amoebaReferencePmeMultipoleForce->setPeriodicBoxSize(box);
+         amoebaReferenceMultipoleForce = static_cast<AmoebaReferenceMultipoleForce*>(amoebaReferencePmeMultipoleForce);
+
     } else {
          amoebaReferenceMultipoleForce = new AmoebaReferenceMultipoleForce( AmoebaReferenceMultipoleForce::NoCutoff );
     }
 
+    // set polarization type
+
+    if( polarizationType == AmoebaMultipoleForce::Mutual ){
+        amoebaReferenceMultipoleForce->setPolarizationType( AmoebaReferenceMultipoleForce::Mutual );
         amoebaReferenceMultipoleForce->setMutualInducedDipoleTargetEpsilon( mutualInducedTargetEpsilon );
         amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations( mutualInducedMaxIterations );
-    AmoebaReferenceMultipoleForce::PolarizationType refPolarizationType;
-    if( polarizationType == AmoebaMultipoleForce::Mutual ){
-        refPolarizationType = AmoebaReferenceMultipoleForce::Mutual;
     } else if( polarizationType == AmoebaMultipoleForce::Direct ){
-        refPolarizationType = AmoebaReferenceMultipoleForce::Direct;
+        amoebaReferenceMultipoleForce->setPolarizationType( AmoebaReferenceMultipoleForce::Direct );
     } else {
         throw OpenMMException("Polarization type not recognzied." );
     }
 
+    return amoebaReferenceMultipoleForce;
+
+}
+
+double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+
+    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
+
+    vector<RealVec>& posData   = extractPositions(context);
+    vector<RealVec>& forceData = extractForces(context);
     RealOpenMM energy          = amoebaReferenceMultipoleForce->calculateForceAndEnergy( posData, charges, dipoles, quadrupoles, tholes,
                                                                                          dampingFactors, polarity, axisTypes, 
                                                                                          multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
-                                                                                multipoleAtomCovalentInfo, refPolarizationType, forceData);
+                                                                                         multipoleAtomCovalentInfo, forceData);
 
     delete amoebaReferenceMultipoleForce;
 
@@ -531,10 +582,48 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo
 
 void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
                                                                         std::vector< double >& outputElectrostaticPotential ){
+
+    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
+    vector<RealVec>& posData                                     = extractPositions(context);
+    vector<RealVec> grid( inputGrid.size() );
+    vector<RealOpenMM> potential( inputGrid.size() );
+    for( unsigned int ii = 0; ii < inputGrid.size(); ii++ ){
+        grid[ii] = inputGrid[ii];
+    }
+    amoebaReferenceMultipoleForce->calculateElectrostaticPotential( posData, charges, dipoles, quadrupoles, tholes,
+                                                                    dampingFactors, polarity, axisTypes, 
+                                                                    multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
+                                                                    multipoleAtomCovalentInfo, grid, potential );
+
+    outputElectrostaticPotential.resize( inputGrid.size() );
+    for( unsigned int ii = 0; ii < inputGrid.size(); ii++ ){
+        outputElectrostaticPotential[ii] = potential[ii];
+    }
+
+    delete amoebaReferenceMultipoleForce;
+
     return;
 }
 
-void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMonents){
+void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments){
+
+    // retrieve masses
+
+    System& system             = context.getSystem();
+    vector<RealOpenMM> masses;
+    for (int i = 0; i <  system.getNumParticles(); ++i) {
+        masses.push_back( static_cast<RealOpenMM>(system.getParticleMass(i)) );
+    }    
+
+    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce( context );
+    vector<RealVec>& posData                                     = extractPositions(context);
+    amoebaReferenceMultipoleForce->calculateAmoebaSystemMultipoleMoments( masses, posData, charges, dipoles, quadrupoles, tholes,
+                                                                          dampingFactors, polarity, axisTypes, 
+                                                                          multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
+                                                                          multipoleAtomCovalentInfo, outputMultipoleMoments );
+
+    delete amoebaReferenceMultipoleForce;
+
     return;
 }
 
@@ -654,7 +743,6 @@ ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string
     usePBC = 0;
     cutoff = 1.0e+10;
     neighborList = NULL;
-
 }
 
 ReferenceCalcAmoebaVdwForceKernel::~ReferenceCalcAmoebaVdwForceKernel() {

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -29,7 +29,8 @@
 
 #include "openmm/System.h"
 #include "openmm/amoebaKernels.h"
-//#include "openmm/AmoebaMultipoleForce.h"
+#include "openmm/AmoebaMultipoleForce.h"
+#include "AmoebaReferenceMultipoleForce.h"
 #include "SimTKReference/ReferenceNeighborList.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
@@ -306,6 +307,14 @@ public:
      * @param force      the AmoebaMultipoleForce this kernel will be used for
      */
     void initialize(const System& system, const AmoebaMultipoleForce& force);
+    /**
+     * Setup for AmoebaReferenceMultipoleForce instance. 
+     *
+     * @param context        the current context
+     *
+     * @return pointer to initialized instance of AmoebaReferenceMultipoleForce
+     */
+    AmoebaReferenceMultipoleForce* setupAmoebaReferenceMultipoleForce(ContextImpl& context );
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -316,9 +325,9 @@ public:
      */
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
     /** 
-     * Execute the kernel to calculate the electrostatic potential
+     * Calculate the electrostatic potential given vector of grid coordinates.
      *
-     * @param context        the context in which to execute this kernel
+     * @param context                      context
      * @param inputGrid                    input grid coordinates
      * @param outputElectrostaticPotential output potential 
      */
@@ -326,19 +335,22 @@ public:
                                    std::vector< double >& outputElectrostaticPotential );
 
     /**
-     * Get the system multipole moments
+     * Get the system multipole moments.
      *
      * @param context                context 
-     * @param outputMultipoleMonents (charge,
+     * @param outputMultipoleMonents vector of multipole moments:
+                                     (charge,
                                       dipole_x, dipole_y, dipole_z,
                                       quadrupole_xx, quadrupole_xy, quadrupole_xz,
                                       quadrupole_yx, quadrupole_yy, quadrupole_yz,
                                       quadrupole_zx, quadrupole_zy, quadrupole_zz )
      */
-    void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMonents);
+    void getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments);
 
 private:
+
     int numMultipoles;
+    AmoebaMultipoleForce::NonbondedMethod nonbondedMethod;
     AmoebaMultipoleForce::PolarizationType polarizationType;
     std::vector<RealOpenMM> charges;
     std::vector<RealOpenMM> dipoles;
@@ -352,11 +364,14 @@ private:
     std::vector<int>   multipoleAtomYs;
     std::vector< std::vector< std::vector<int> > > multipoleAtomCovalentInfo;
 
-    //int iterativeMethod;
-    int nonbondedMethod;
     int mutualInducedMaxIterations;
     RealOpenMM mutualInducedTargetEpsilon;
 
+    bool usePme;
+    RealOpenMM alphaEwald;
+    RealOpenMM cutoffDistance;
+    std::vector<int> pmeGridDimension;
+
     System& system;
 };
 
@@ -465,21 +480,21 @@ public:
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
  
     /**
-     *  Get include-cavity term flag 
+     *  Get the 'include cavity term' flag.
      *
      *  @return includeCavityTerm
      */
     int getIncludeCavityTerm( void ) const;
 
     /**
-     *  Get number of particles
+     *  Get the number of particles.
      *
      *  @return number of particles
      */
     int getNumParticles( void ) const;
 
     /**
-     *  Get directPolarization flag 
+     *  Get Direct Polarization flag.
      *
      *  @return directPolarization
      *
@@ -487,7 +502,7 @@ public:
     int getDirectPolarization( void ) const;
 
     /**
-     *  Get solute dielectric
+     *  Get the solute dielectric.
      *
      *  @return soluteDielectric
      *
@@ -495,7 +510,7 @@ public:
     RealOpenMM getSoluteDielectric( void ) const;
 
     /**
-     *  Get solvent dielectric
+     *  Get the solvent dielectric.
      *
      *  @return solventDielectric
      *
@@ -503,7 +518,7 @@ public:
     RealOpenMM getSolventDielectric( void ) const;
 
     /**
-     *  Get dielectric offset
+     *  Get the dielectric offset.
      *
      *  @return dielectricOffset
      *
@@ -511,7 +526,7 @@ public:
     RealOpenMM getDielectricOffset( void ) const;
 
     /**
-     *  Get probeRadius
+     *  Get the probe radius.
      *
      *  @return probeRadius
      *
@@ -519,7 +534,7 @@ public:
     RealOpenMM getProbeRadius( void ) const;
 
     /**
-     *  Get surfaceAreaFactor
+     *  Get the surface area factor.
      *
      *  @return surfaceAreaFactor
      *
@@ -527,7 +542,7 @@ public:
     RealOpenMM getSurfaceAreaFactor( void ) const;
 
     /**
-     *  Get atomic radii
+     *  Get the vector of particle radii.
      *
      *  @param atomicRadii vector of atomic radii
      *
@@ -535,7 +550,7 @@ public:
     void getAtomicRadii( std::vector<RealOpenMM>& atomicRadii ) const;
 
     /**
-     *  Get scale factors
+     *  Get the vector of scale factors.
      *
      *  @param scaleFactors vector of scale factors
      *
@@ -543,7 +558,7 @@ public:
     void getScaleFactors( std::vector<RealOpenMM>& scaleFactors ) const;
 
     /**
-     *  Get charges
+     *  Get the vector of charges.
      *
      *  @param charges vector of charges
      *