Removed SASAForce -- not currently used

Added checks for nonbonded methods
Removed unused functionality from GK force
Moved non-accessor methods from Force classes to ForceImpl classes

plugins/amoeba/openmmapi/include/AmoebaGeneralizedKirkwoodForce.h

@@ -39,7 +39,7 @@
 namespace OpenMM {
 
 /**
- * This class implements an implicit solvation force using the GBSA-OBC model.
+ * This class implements an implicit solvation force using the generalized Kirkwood/OBC model.
  * <p>
  * To use this class, create a AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the
  * System to define its parameters.  The number of particles for which you define GBSA parameters must
@@ -51,26 +51,6 @@ namespace OpenMM {
 class OPENMM_EXPORT AmoebaGeneralizedKirkwoodForce : public Force {
 public:
 
-    /**
-     * This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
-     */
-    enum NonbondedMethod {
-        /**
-         * No cutoff is applied to nonbonded interactions.  The full set of N^2 interactions is computed exactly.
-         * This necessarily means that periodic boundary conditions cannot be used.  This is the default.
-         */
-        NoCutoff = 0,
-        /**
-         * Interactions beyond the cutoff distance are ignored.
-         */
-        CutoffNonPeriodic = 1,
-        /**
-         * Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
-         * each other particle.  Interactions beyond the cutoff distance are ignored.
-         */
-        CutoffPeriodic = 2,
-    };
-
     /*
      * Create a AmoebaGeneralizedKirkwoodForce.
      */
@@ -84,7 +64,7 @@ public:
     }
 
     /**
-     * Add the GBSA parameters for a particle.  This should be called once for each particle
+     * Add the  parameters for a particle.  This should be called once for each particle
      * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
      *
      * @param charge         the charge of the particle, measured in units of the proton charge
@@ -141,27 +121,6 @@ public:
     void setSoluteDielectric(double dielectric) {
         soluteDielectric = dielectric;
     }
-    /**
-     * Get the method used for handling long range nonbonded interactions.
-     */
-    NonbondedMethod getNonbondedMethod() const;
-
-    /**
-     * Set the method used for handling long range nonbonded interactions.
-     */
-    void setNonbondedMethod(NonbondedMethod method);
-
-    /**
-     * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
-     * is NoCutoff, this value will have no effect.
-     */
-    double getCutoffDistance() const;
-
-    /**
-     * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
-     * is NoCutoff, this value will have no effect.
-     */
-    void setCutoffDistance(double distance);
 
     /**
      * Get the dielectric offset (nm) used in OBC
@@ -207,9 +166,8 @@ protected:
     ForceImpl* createImpl();
 private:
     class ParticleInfo;
-    NonbondedMethod nonbondedMethod;
     int includeCavityTerm;
-    double cutoffDistance, solventDielectric, soluteDielectric, dielectricOffset,
+    double solventDielectric, soluteDielectric, dielectricOffset,
            probeRadius, surfaceAreaFactor;
     std::vector<ParticleInfo> particles;
 };
@@ -227,4 +185,4 @@ public:
 
 } // namespace OpenMM
 
-#endif /*AMOEBA_OPENMM_GBSA_OBC_FORCE_FIELD_H_*/
+#endif /*AMOEBA_OPENMM_GK_FORCE_FIELD_H_*/

plugins/amoeba/openmmapi/include/AmoebaHarmonicAngleForce.h

@@ -39,8 +39,8 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a HarmonicAngleForce object then call addAngle() once for each angle.  After
+ * This class implements an interaction between triplets of particles that varies harmonically with the angle
+ * between them.  To use it, create a AmoebaHarmonicAngleForce object then call addAngle() once for each angle.  After
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
@@ -120,8 +120,8 @@ public:
      * @param particle1     the index of the first particle connected by the angle
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the angle measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
      * @return the index of the angle that was added
      */
     int addAngle(int particle1, int particle2, int particle3, double length, 
@@ -134,8 +134,8 @@ public:
      * @param particle1     the index of the first particle connected by the angle
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the equilibrium angle, measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length,
                             double& quadraticK ) const;
@@ -147,8 +147,8 @@ public:
      * @param particle1     the index of the first particle connected by the angle
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the equilibrium angle, measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, double length, double quadraticK );
 

plugins/amoeba/openmmapi/include/AmoebaHarmonicBondForce.h

@@ -43,7 +43,7 @@ namespace OpenMM {
 
 /**
  * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a HarmonicBondForce object then call addBond() once for each bond.  After
+ * between them.  To use it, create a AmoebaHarmonicBondForce object then call addBond() once for each bond.  After
  * a bond has been added, you can modify its force field parameters by calling setBondParameters().
  */
 

plugins/amoeba/openmmapi/include/AmoebaHarmonicInPlaneAngleForce.h

@@ -39,7 +39,8 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
+ * This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy
+ * between four particles; the energy varies harmonically with the angle
  * between them.  To use it, create a AmoebaHarmonicInPlaneAngle object then call addAngle() once for each angle.  After
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
@@ -73,9 +74,9 @@ public:
     double getAmoebaGlobalHarmonicInPlaneAngleCubic( void ) const;
 
     /**
-     * Set the global cubic term
+     * Set the global quartic term
      * 
-     * @param quarticK       the quartic harmonic force constant for the angle
+     * @param quarticK the quartic harmonic force constant for the angle
      */
     void setAmoebaGlobalHarmonicInPlaneAngleQuartic( double quarticK );
 
@@ -121,8 +122,8 @@ public:
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
      * @param particle4     the index of the fourth particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the equilibrium angle, measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle measured in kJ/mol/radian^2
      * @return the index of the angle that was added
      */
     int addAngle(int particle1, int particle2, int particle3, int particle4, double length, 
@@ -136,8 +137,8 @@ public:
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
      * @param particle4     the index of the fourth particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the equilibrium angle, measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle measured in kJ/mol/radian^2
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& length,
                             double& quadraticK ) const;
@@ -150,8 +151,8 @@ public:
      * @param particle2     the index of the second particle connected by the angle
      * @param particle3     the index of the third particle connected by the angle
      * @param particle4     the index of the fourth particle connected by the angle
-     * @param length        the equilibrium length of the angle, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the angle
+     * @param length        the equilibrium angle, measured in radians
+     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK );
 

plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h

@@ -52,21 +52,23 @@ public:
  
     enum MultipoleAxisTypes { ZThenX, Bisector };
 
-    enum MutualInducedIterationMethod { SOR, ConjugateGradient };
+    // Algorithm used to converge mutual induced dipoles:
+    //     SOR: successive-over-relaxation
+
+    //enum MutualInducedIterationMethod { SOR, ConjugateGradient };
+    enum MutualInducedIterationMethod { SOR };
 
     enum CovalentType { 
                           Covalent12, Covalent13, Covalent14, Covalent15, 
                           PolarizationCovalent11, PolarizationCovalent12, PolarizationCovalent13, PolarizationCovalent14, CovalentEnd };
 
-    static const int CovalentDegrees[8];
-
     /**
      * Create a Amoeba MultipoleForce.
      */
     AmoebaMultipoleForce();
 
     /**
-     * Get the number of pi torsion terms in the potential function
+     * Get the number of particles in the potential function
      */
     int getNumMultipoles() const {
         return multipoles.size();
@@ -148,22 +150,6 @@ public:
      */
     void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists ) const;
 
-    /**
-     * Get the CovalentMap for an atom
-     * 
-     * @param index                the index of the atom for which to set parameters
-     * @param minCovalentIndex     minimum covalent index
-     * @param maxCovalentIndex     maximum covalent index
-     */
-    void getCovalentRange(int index, const std::vector<CovalentType>& lists, int* minCovalentIndex, int* maxCovalentIndex ) const;
-
-    /**
-     * Get the covalent degree for the  CovalentEnd lists
-     * 
-     * @param covalentDegree     covalent degrees for the CovalentEnd lists
-     */
-    void getCovalentDegree( std::vector<int>& covalentDegree ) const;
-
     /**
      * Get the iteration method to be used for calculating the mutual induced dipoles
      * 
@@ -222,7 +208,7 @@ public:
     
     /**
      * Get the electric constant
-     * 
+      
      * @return the electric constant
      */
     double getElectricConstant( void ) const;
@@ -284,15 +270,6 @@ public:
         charge(charge), axisType(axisType), multipoleAtomId1(multipoleAtomId1), multipoleAtomId2(multipoleAtomId2),
         thole(thole), dampingFactor(dampingFactor), polarity(polarity) {
 
-       // only 'Z-then-X' or 'Bisector' currently handled
-
-       if( axisType != ZThenX && axisType != Bisector ){
-           std::stringstream buffer;
-           buffer << "AmoebaMultipoleForce: axis type=" << axisType;
-           buffer << " not currently handled - only axisTypes[ " << ZThenX << ", " << Bisector << "] (ZThenX, Bisector) currently handled .";
-           throw OpenMMException(buffer.str());
-       }
-
        covalentInfo.resize( CovalentEnd );
 
        molecularDipole.resize( 3 );

plugins/amoeba/openmmapi/include/AmoebaOpenMM.h

@@ -42,7 +42,6 @@
 #include "AmoebaTorsionTorsionForce.h"
 #include "AmoebaMultipoleForce.h"
 #include "AmoebaGeneralizedKirkwoodForce.h"
-#include "AmoebaSASAForce.h"
 #include "AmoebaVdwForce.h"
 #include "AmoebaWcaDispersionForce.h"
 

plugins/amoeba/openmmapi/include/AmoebaPiTorsionForce.h

@@ -33,7 +33,6 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-//#include "openmm/Vec3.h"
 #include <vector>
 #include "openmm/internal/windowsExport.h"
 

plugins/amoeba/openmmapi/include/AmoebaSASAForce.h

-#ifndef AMOEBA_OPENMM_SASA_FORCE_FIELD_H_
-#define AMOEBA_OPENMM_SASA_FORCE_FIELD_H_
-
-/* -------------------------------------------------------------------------- *
- *                                   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) 2008-2009 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.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/Force.h"
-#include <vector>
-#include "openmm/internal/windowsExport.h"
-
-namespace OpenMM {
-
-/**
- * This class implements an SASA force
- * by performing an analytical computation of the weighted
- * solvent accessible surface area of each atom and the first
- * derivatives of the area with respect to Cartesian coordinates
- * 
- * Literature references:
- * 
- * T. J. Richmond, "Solvent Accessible Surface Area and
- * Excluded Volume in Proteins", Journal of Molecular Biology,
- * 178, 63-89 (1984)
- * 
- * L. Wesson and D. Eisenberg, "Atomic Solvation Parameters
- * Applied to Molecular Dynamics of Proteins in Solution",
- * Protein Science, 1, 227-235 (1992)
- *
- * <p>
- * To use this class, create a AmoebaSASAForce object, then call addParticle() once for each particle in the
- * System to define its parameters.  The number of particles for which you define SASA parameters must
- * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
- * try to create a Context.  After a particle has been added, you can modify its force field parameters
- * by calling setParticleParameters().
- */
-
-class OPENMM_EXPORT AmoebaSASAForce : public Force {
-public:
-    /*
-     * Create a AmoebaSASAForce.
-     */
-    AmoebaSASAForce();
-
-    /**
-     * Get the number of particles in the system.
-     */
-    int getNumParticles() const {
-        return particles.size();
-    }
-
-    /**
-     * Add the SASA parameters for a particle.  This should be called once for each particle
-     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
-     *
-     * @param radius         the radius of the particle, measured in nm
-     * @param weight         the sasa weight (Tinker asolv())
-     * @return the index of the particle that was added
-     */
-    int addParticle(double radius, double weight);
-
-    /**
-     * Get the force field parameters for a particle.
-     * 
-     * @param index          the index of the particle for which to get parameters
-     * @param radius         the radius of the particle, measured in nm
-     * @param weight         the sasa weight(Tinker asolv())
-     */
-    void getParticleParameters(int index, double& radius, double& weight) const;
-
-    /**
-     * Set the force field parameters for a particle.
-     * 
-     * @param index          the index of the particle for which to set parameters
-     * @param radius         the radius of the particle, measured in nm
-     * @param weight         the sasa weight(Tinker asolv())
-     */
-    void setParticleParameters(int index, double radius, double weight);
-
-    /**
-     * Get the probe radius
-     */
-    double getProbeRadius() const;
-
-    /**
-     * Set the probe radius
-     */
-    void setProbeRadius(double distance);
-
-protected:
-    ForceImpl* createImpl();
-private:
-    class ParticleInfo;
-    double probeRadius;
-    std::vector<ParticleInfo> particles;
-};
-
-class AmoebaSASAForce::ParticleInfo {
-public:
-    double radius, weight;
-    ParticleInfo() {
-        radius = weight = 0.0;
-    }
-    ParticleInfo(double radius, double weight) :
-        radius(radius), weight(weight) {
-    }
-};
-
-} // namespace OpenMM
-
-#endif /*AMOEBA_OPENMM_GBSA_OBC_FORCE_FIELD_H_*/

plugins/amoeba/openmmapi/include/AmoebaTorsionForce.h

@@ -145,6 +145,7 @@ private:
             }
         }
     }
+
 public:
     int particle1, particle2, particle3, particle4;
     std::vector< std::vector<double> > torsionParameters;

plugins/amoeba/openmmapi/include/AmoebaVdwForce.h

@@ -174,7 +174,7 @@ public:
     VdwInfo() {
         ivIndex = classIndex = -1;
         reductionFactor      = 0.0;
-        sigma               = 1.0;
+        sigma                = 1.0;
         epsilon              = 0.0;
     }
     VdwInfo(int ivIndex, int classIndex, double sigma, double epsilon, double  reductionFactor ) :

plugins/amoeba/openmmapi/include/AmoebaWcaDispersionForce.h

@@ -85,42 +85,27 @@ public:
      */
     int addParticle( double radius, double epsilon );
 
-    /**
-     * Get the maximum dispersion energy for a particle
-     * 
-     * @param particleIndex       the particle index
-     * @param maxDispersionEnergy maximum dispersion energy
-     */
-    void getMaximumDispersionEnergy(int particleIndex, double& maxDispersionEnergy ) const;
-
-    /**
-     * Get the total maximum dispersion energy
-     * 
-     * @return total maximum dispersion energy for the system
-     */
-    double getTotalMaximumDispersionEnergy( void ) const;
-
     /* 
      * Constants
      */
 
-    double getEpso( void ) const;
-    double getEpsh( void ) const;
-    double getRmino( void ) const;
-    double getRminh( void ) const;
-    double getAwater( void ) const;
-    double getShctd( void ) const;
-    double getDispoff( void ) const;
-    double getSlevy( void ) const;
-
-    void setEpso( double inputValue );
-    void setEpsh( double inputValue );
-    void setRmino( double inputValue );
-    void setRminh( double inputValue );
-    void setAwater( double inputValue );
-    void setShctd( double inputValue );
-    void setDispoff( double inputValue );
-    void setSlevy( double inputValue );
+    double getEpso(     void ) const;
+    double getEpsh(     void ) const;
+    double getRmino(    void ) const;
+    double getRminh(    void ) const;
+    double getAwater(   void ) const;
+    double getShctd(    void ) const;
+    double getDispoff(  void ) const;
+    double getSlevy(    void ) const;
+
+    void setEpso(     double inputValue );
+    void setEpsh(     double inputValue );
+    void setRmino(    double inputValue );
+    void setRminh(    double inputValue );
+    void setAwater(   double inputValue );
+    void setShctd(    double inputValue );
+    void setDispoff(  double inputValue );
+    void setSlevy(    double inputValue );
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/amoebaKernels.h

@@ -324,34 +324,6 @@ public:
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
 };
 
-/**
- * This kernel is invoked by AmoebaSASAForce to calculate the solvent-accessible surface area forces acting on the system and the energy of the system.
- */
-class CalcAmoebaSASAForceKernel : public KernelImpl {
-public:
-    static std::string Name() {
-        return "CalcAmoebaSASAForce";
-    }
-    CalcAmoebaSASAForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
-    }
-
-    /**
-     * Initialize the kernel.
-     * 
-     * @param system     the System this kernel will be applied to
-     * @param force      the GBSAOBCForce this kernel will be used for
-     */
-    virtual void initialize(const System& system, const AmoebaSASAForce& force) = 0;
-    /**
-     * Execute the kernel to calculate the forces and/or energy.
-     *
-     * @param context        the context in which to execute this kernel
-     * @param includeForces  true if forces should be calculated
-     * @param includeEnergy  true if the energy should be calculated
-     * @return the potential energy due to the force
-     */
-    virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
-};
 
 /**
  * This kernel is invoked by AmoebaVdwForce to calculate the vdw forces acting on the system and the vdw energy of the system.

plugins/amoeba/openmmapi/include/internal/AmoebaMultipoleForceImpl.h

@@ -60,9 +60,34 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+
+    /**
+     * Get the CovalentMap for an atom
+     * 
+     * @param force                AmoebaMultipoleForce force reference
+     * @param index                the index of the atom for which to set parameters
+     * @param minCovalentIndex     minimum covalent index
+     * @param maxCovalentIndex     maximum covalent index
+     */
+    static void getCovalentRange( const AmoebaMultipoleForce& force, int index,
+                                  const std::vector< AmoebaMultipoleForce::CovalentType>& lists,
+                                  int* minCovalentIndex, int* maxCovalentIndex );
+
+    /**
+     * Get the covalent degree for the  CovalentEnd lists
+     * 
+     * @param force                AmoebaMultipoleForce force reference
+     * @param covalentDegree      covalent degrees for the CovalentEnd lists
+     */
+    static void getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree );
+
 private:
     AmoebaMultipoleForce& owner;
     Kernel kernel;
+
+    static int CovalentDegrees[AmoebaMultipoleForce::CovalentEnd];
+    static bool initializedCovalentDegrees;
+    static const int* getCovalentDegrees( void );
 };
 
 } // namespace OpenMM

plugins/amoeba/openmmapi/include/internal/AmoebaSASAForceImpl.h

-#ifndef OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_
-#define OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_
-
-/* -------------------------------------------------------------------------- *
- *                                   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.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/internal/ForceImpl.h"
-#include "AmoebaSASAForce.h"
-#include "openmm/Kernel.h"
-#include <string>
-
-namespace OpenMM {
-
-/**
- * This is the internal implementation of AmoebaSASAForce.
- */
-
-class AmoebaSASAForceImpl : public ForceImpl {
-public:
-    AmoebaSASAForceImpl(AmoebaSASAForce& owner);
-    void initialize(ContextImpl& context);
-    AmoebaSASAForce& getOwner() {
-        return owner;
-    }
-    void updateContextState(ContextImpl& context) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy);
-    std::map<std::string, double> getDefaultParameters() {
-        return std::map<std::string, double>(); // This force field doesn't define any parameters.
-    }
-    std::vector<std::string> getKernelNames();
-private:
-    AmoebaSASAForce& owner;
-    Kernel kernel;
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_*/

plugins/amoeba/openmmapi/include/internal/AmoebaWcaDispersionForceImpl.h

@@ -61,6 +61,25 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+
+    /** 
+     * Get the maximum dispersion energy for a particle
+     * 
+     * @param force               AmoebaWcaDispersionForce reference
+     * @param particleIndex       the particle index
+     * @param maxDispersionEnergy maximum dispersion energy
+     */
+    static void getMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force, int particleIndex, double& maxDispersionEnergy );
+
+    /** 
+     * Get the total maximum dispersion energy
+     * 
+     * @param force               AmoebaWcaDispersionForce reference
+     *
+     * @return total maximum dispersion energy for the system
+     */
+    static double getTotalMaximumDispersionEnergy( const AmoebaWcaDispersionForce& force);
+
 private:
     AmoebaWcaDispersionForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp

@@ -36,8 +36,7 @@
 
 using namespace OpenMM;
 
-AmoebaGeneralizedKirkwoodForce::AmoebaGeneralizedKirkwoodForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0),
-                                                                   dielectricOffset(0.009), includeCavityTerm(1), probeRadius(0.14) {
+AmoebaGeneralizedKirkwoodForce::AmoebaGeneralizedKirkwoodForce() : solventDielectric(78.3), soluteDielectric(1.0), dielectricOffset(0.009), includeCavityTerm(1), probeRadius(0.14) {
 
      surfaceAreaFactor = -6.0* 3.1415926535*0.0216*1000.0*0.4184;
 }
@@ -59,22 +58,6 @@ void AmoebaGeneralizedKirkwoodForce::setParticleParameters(int index, double cha
     particles[index].scalingFactor = scalingFactor;
 }
 
-AmoebaGeneralizedKirkwoodForce::NonbondedMethod AmoebaGeneralizedKirkwoodForce::getNonbondedMethod() const {
-    return nonbondedMethod;
-}
-
-void AmoebaGeneralizedKirkwoodForce::setNonbondedMethod(NonbondedMethod method) {
-    nonbondedMethod = method;
-}
-
-double AmoebaGeneralizedKirkwoodForce::getCutoffDistance() const {
-    return cutoffDistance;
-}
-
-void AmoebaGeneralizedKirkwoodForce::setCutoffDistance(double distance) {
-    cutoffDistance = distance;
-}
-
 double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
     return dielectricOffset;
 }

plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForceImpl.cpp

@@ -40,6 +40,12 @@ AmoebaGeneralizedKirkwoodForceImpl::AmoebaGeneralizedKirkwoodForceImpl(AmoebaGen
 }
 
 void AmoebaGeneralizedKirkwoodForceImpl::initialize(ContextImpl& context) {
+
+    System& system = context.getSystem();
+    if (owner.getNumParticles() != system.getNumParticles())
+        throw OpenMMException("AmoebaGeneralizedKirkwoodForce must have exactly as many particles as the System it belongs to.");
+
+
     kernel = context.getPlatform().createKernel(CalcAmoebaGeneralizedKirkwoodForceKernel::Name(), context);
     if (owner.getNumParticles() != context.getSystem().getNumParticles())
         throw OpenMMException("AmoebaGeneralizedKirkwoodForce must have exactly as many particles as the System it belongs to.");

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -36,9 +36,6 @@
 
 using namespace OpenMM;
 
-const int AmoebaMultipoleForce::CovalentDegrees[8] = { 1, 2, 3, 4, 0, 1, 2, 3 };
-
-
 AmoebaMultipoleForce::AmoebaMultipoleForce() {
 
     mutualInducedIterationMethod  = SOR;
@@ -187,31 +184,6 @@ void AmoebaMultipoleForce::getCovalentMaps(int index, std::vector< std::vector<i
     }
 }
 
-void AmoebaMultipoleForce::getCovalentRange( int index, const std::vector<CovalentType>& lists, int* minCovalentIndex, int* maxCovalentIndex ) const {
-
-    *minCovalentIndex =  999999999;
-    *maxCovalentIndex = -999999999;
-    for( unsigned int kk = 0; kk < lists.size(); kk++ ){
-        CovalentType jj = lists[kk];
-        std::vector<int> covalentList = multipoles[index].covalentInfo[jj];
-        for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
-            if( *minCovalentIndex > covalentList[ii] ){
-               *minCovalentIndex = covalentList[ii];
-            }
-            if( *maxCovalentIndex < covalentList[ii] ){
-               *maxCovalentIndex = covalentList[ii];
-            }
-        }
-    }
-}
-
-void AmoebaMultipoleForce::getCovalentDegree( std::vector<int>& covalentDegree ) const {
-    covalentDegree.resize( CovalentEnd );
-    for( unsigned int kk = 0; kk < CovalentEnd; kk++ ){
-        covalentDegree[kk] = CovalentDegrees[kk];
-    }
-}
-
 ForceImpl* AmoebaMultipoleForce::createImpl() {
     return new AmoebaMultipoleForceImpl(*this);
 }

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -37,6 +37,9 @@ using namespace OpenMM;
 
 using std::vector;
 
+bool AmoebaMultipoleForceImpl::initializedCovalentDegrees = false;
+int AmoebaMultipoleForceImpl::CovalentDegrees[]           = { 1,2,3,4,0,1,2,3};
+
 AmoebaMultipoleForceImpl::AmoebaMultipoleForceImpl(AmoebaMultipoleForce& owner) : owner(owner) {
 }
 
@@ -44,6 +47,30 @@ AmoebaMultipoleForceImpl::~AmoebaMultipoleForceImpl() {
 }
 
 void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
+
+    System& system = context.getSystem();
+    if (owner.getNumMultipoles() != system.getNumParticles())
+        throw OpenMMException("AmoebaMultipoleForce must have exactly as many particles as the System it belongs to.");
+
+    for( int ii = 0; ii < system.getNumParticles(); ii++ ){
+
+        int index, axisType, multipoleAtomId1, multipoleAtomId2;
+        double charge, thole, dampingFactor, polarity ;
+        std::vector<double> molecularDipole;
+        std::vector<double> molecularQuadrupole;
+
+        owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomId1, multipoleAtomId2,
+                                      thole, dampingFactor, polarity );
+
+       // only 'Z-then-X' or 'Bisector' currently handled
+
+        if( axisType != AmoebaMultipoleForce::ZThenX && axisType != AmoebaMultipoleForce::Bisector ){
+             std::stringstream buffer;
+             buffer << "AmoebaMultipoleForce: axis type=" << axisType;
+             buffer << " not currently handled - only axisTypes[ " << AmoebaMultipoleForce::ZThenX << ", " << AmoebaMultipoleForce::Bisector << "] (ZThenX, Bisector) currently handled .";
+             throw OpenMMException(buffer.str());
+        }
+    }
     kernel = context.getPlatform().createKernel(CalcAmoebaMultipoleForceKernel::Name(), context);
     dynamic_cast<CalcAmoebaMultipoleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
@@ -58,3 +85,47 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
     return names;
 }
 
+const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
+    if( !initializedCovalentDegrees ){
+        initializedCovalentDegrees                                      = true;
+        CovalentDegrees[AmoebaMultipoleForce::Covalent12]               = 1;
+        CovalentDegrees[AmoebaMultipoleForce::Covalent13]               = 2;
+        CovalentDegrees[AmoebaMultipoleForce::Covalent14]               = 3;
+        CovalentDegrees[AmoebaMultipoleForce::Covalent15]               = 4;
+        CovalentDegrees[AmoebaMultipoleForce::PolarizationCovalent11]   = 0;
+        CovalentDegrees[AmoebaMultipoleForce::PolarizationCovalent12]   = 1;
+        CovalentDegrees[AmoebaMultipoleForce::PolarizationCovalent13]   = 2;
+        CovalentDegrees[AmoebaMultipoleForce::PolarizationCovalent14]   = 3;
+    }
+    return CovalentDegrees;
+}
+
+void AmoebaMultipoleForceImpl::getCovalentRange( const AmoebaMultipoleForce& force, int atomIndex, const std::vector<AmoebaMultipoleForce::CovalentType>& lists,
+                                                 int* minCovalentIndex, int* maxCovalentIndex ){
+
+    *minCovalentIndex =  999999999;
+    *maxCovalentIndex = -999999999;
+    for( unsigned int kk = 0; kk < lists.size(); kk++ ){
+        AmoebaMultipoleForce::CovalentType jj = lists[kk];
+        std::vector<int> covalentList;
+        force.getCovalentMap( atomIndex, jj, covalentList );
+        for( unsigned int ii = 0; ii < covalentList.size(); ii++ ){
+            if( *minCovalentIndex > covalentList[ii] ){
+               *minCovalentIndex = covalentList[ii];
+            }
+            if( *maxCovalentIndex < covalentList[ii] ){
+               *maxCovalentIndex = covalentList[ii];
+            }
+        }
+    }   
+    return;
+}
+
+void AmoebaMultipoleForceImpl::getCovalentDegree( const AmoebaMultipoleForce& force, std::vector<int>& covalentDegree ){
+    covalentDegree.resize( AmoebaMultipoleForce::CovalentEnd );
+    const int* CovalentDegrees = AmoebaMultipoleForceImpl::getCovalentDegrees();
+    for( unsigned int kk = 0; kk < AmoebaMultipoleForce::CovalentEnd; kk++ ){
+        covalentDegree[kk] = CovalentDegrees[kk];
+    }   
+    return;
+}

plugins/amoeba/openmmapi/src/AmoebaSASAForce.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) 2008-2009 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.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/Force.h"
-#include "openmm/OpenMMException.h"
-#include "AmoebaSASAForce.h"
-#include "internal/AmoebaSASAForceImpl.h"
-
-using namespace OpenMM;
-
-AmoebaSASAForce::AmoebaSASAForce() : probeRadius(0.14) {
-}
-
-int AmoebaSASAForce::addParticle( double radius, double weight) {
-    particles.push_back(ParticleInfo(radius, weight));
-    return particles.size()-1;
-}
-
-void AmoebaSASAForce::getParticleParameters(int index, double& radius, double& weight) const {
-    radius = particles[index].radius;
-    weight = particles[index].weight;
-}
-
-void AmoebaSASAForce::setParticleParameters(int index, double radius, double weight) {
-    particles[index].radius = radius;
-    particles[index].weight = weight;
-}
-
-double AmoebaSASAForce::getProbeRadius() const {
-    return probeRadius;
-}
-
-void AmoebaSASAForce::setProbeRadius(double distance) {
-    probeRadius = distance;
-}
-
-ForceImpl* AmoebaSASAForce::createImpl() {
-    return new AmoebaSASAForceImpl(*this);
-}