Major cleanup of the AMOEBA API

plugins/amoeba/openmmapi/include/OpenMMAmoeba.h

@@ -33,10 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AmoebaHarmonicBondForce.h"
-#include "openmm/AmoebaUreyBradleyForce.h"
 #include "openmm/AmoebaHarmonicAngleForce.h"
 #include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
-#include "openmm/AmoebaTorsionForce.h"
 #include "openmm/AmoebaPiTorsionForce.h"
 #include "openmm/AmoebaStretchBendForce.h"
 #include "openmm/AmoebaOutOfPlaneBendForce.h"

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

@@ -9,8 +9,8 @@
  * 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                                                     *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,10 +39,10 @@
 namespace OpenMM {
 
 /**
- * This class implements an implicit solvation force using the generalized Kirkwood/OBC model.
+ * This class implements an implicit solvation force using the generalized Kirkwood/Grycuk 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
+ * To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define parameters must
  * be 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().
@@ -53,7 +53,7 @@ class OPENMM_EXPORT AmoebaGeneralizedKirkwoodForce : public Force {
 public:
 
     /*
-     * Create a AmoebaGeneralizedKirkwoodForce.
+     * Create an AmoebaGeneralizedKirkwoodForce.
      */
     AmoebaGeneralizedKirkwoodForce();
 
@@ -69,8 +69,8 @@ public:
      * 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
-     * @param radius         the GBSA radius of the particle, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the particle
+     * @param radius         the atomic radius of the particle, measured in nm
+     * @param scalingFactor  the scaling factor for the particle
      * @return the index of the particle that was added
      */
     int addParticle(double charge, double radius, double scalingFactor);
@@ -80,8 +80,8 @@ public:
      * 
      * @param index          the index of the particle for which to get parameters
      * @param charge         the charge of the particle, measured in units of the proton charge
-     * @param radius         the GBSA radius of the particle, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the particle
+     * @param radius         the atomic radius of the particle, measured in nm
+     * @param scalingFactor  the scaling factor for the particle
      */
     void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
 
@@ -90,8 +90,8 @@ public:
      * 
      * @param index          the index of the particle for which to set parameters
      * @param charge         the charge of the particle, measured in units of the proton charge
-     * @param radius         the GBSA radius of the particle, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the particle
+     * @param radius         the atomic radius of the particle, measured in nm
+     * @param scalingFactor  the scaling factor for the particle
      */
     void setParticleParameters(int index, double charge, double radius, double scalingFactor);
 
@@ -124,22 +124,12 @@ public:
     }
 
     /**
-     * Get the dielectric offset (nm) used in OBC
-     */
-    //double getDielectricOffset() const;
-
-    /**
-     * Set the dielectric offset (nm) used in OBC
-     */
-    //void setDielectricOffset(double dielectricOffset);
-
-    /**
-     * Get the flag signalling whether the cavity term should be included
+     * Get the flag signaling whether the cavity term should be included
      */
     int getIncludeCavityTerm( ) const;
 
     /**
-     * Set the flag signalling whether the cavity term should be included
+     * Set the flag signaling whether the cavity term should be included
      */
     void setIncludeCavityTerm(int includeCavityTerm);
 

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,9 +39,13 @@
 namespace OpenMM {
 
 /**
- * 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().
+ * This class implements an interaction between triplets of particles that varies with the angle
+ * between them.  The interaction is defined by a 6th order polynomial.  Only the quadratic term
+ * is set per-angle.  The coefficients of the higher order terms each have a single value that
+ * is set globally.
+ * 
+ * To use it, create an AmoebaHarmonicAngleForce object then call addAngle() once for each angle.  After
+ * an angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
 class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
@@ -49,7 +53,7 @@ class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
 public:
 
     /**
-     * Create a Amoeba HarmonicAngleForce.
+     * Create an AmoebaHarmonicAngleForce.
      */
     AmoebaHarmonicAngleForce();
 
@@ -63,7 +67,7 @@ public:
     /**
      * Set the global cubic term
      * 
-     * @param cubicK        the cubic harmonic force constant for the angle
+     * @param cubicK        the cubic force constant for the angle
      */
     void setAmoebaGlobalHarmonicAngleCubic( double cubicK );
 
@@ -75,9 +79,9 @@ public:
     double getAmoebaGlobalHarmonicAngleCubic( 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 force constant for the angle
      */
     void setAmoebaGlobalHarmonicAngleQuartic( double quarticK );
 
@@ -91,7 +95,7 @@ public:
     /**
      * Set the global pentic term
      * 
-     * @param penticK the pentic harmonic force constant for the angle
+     * @param penticK the pentic force constant for the angle
      */
     void setAmoebaGlobalHarmonicAnglePentic( double penticK );
 
@@ -105,50 +109,50 @@ public:
     /**
      * Set the global sextic term
      * 
-     * @param sexticK       the sextic harmonic force constant for the angle
+     * @param sexticK       the sextic force constant for the angle
      */
     void setAmoebaGlobalHarmonicAngleSextic( double sexticK );
 
     /**
      * Get the global sextic term
      * 
-     * @return global  sextic term
+     * @return global sextic term
      */
     double getAmoebaGlobalHarmonicAngleSextic( void ) const;
 
     /**
-     * Add a angle term to the force field.
+     * Add an angle term to the force field.
      *
      * @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 angle measured in degrees
-     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
+     * @param quadratic k   the quadratic 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, double quadraticK );
 
     /**
-     * Get the force field parameters for a angle term.
+     * Get the force field parameters for an angle term.
      * 
      * @param index         the index of the angle for which to get parameters
      * @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 angle, measured in degress
-     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
+     * @param quadratic k   the quadratic 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;
 
     /**
-     * Set the force field parameters for a angle term.
+     * Set the force field parameters for an angle term.
      * 
      * @param index         the index of the angle for which to set parameters
      * @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 angle, measured in degrees
-     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
+     * @param quadratic k   the quadratic 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 );
 
@@ -156,21 +160,8 @@ protected:
     ForceImpl* createImpl();
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
-
     class AngleInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<AngleInfo> angles;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaHarmonicAngleForce::AngleInfo {

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -41,8 +41,12 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a AmoebaHarmonicBondForce object then call addBond() once for each bond.  After
+ * This class implements an interaction between pairs of particles that varies with the distance
+ * between them.  The interaction is defined by a 4th order polynomial.  Only the quadratic term
+ * is set per-bond.  The coefficients of the higher order terms each have a single value that
+ * is set globally.
+ * 
+ * To use it, create an 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().
  */
 
@@ -51,11 +55,11 @@ class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
 public:
 
     /**
-     * Create a Amoeba HarmonicBondForce.
+     * Create an AmoebaHarmonicBondForce.
      */
     AmoebaHarmonicBondForce();
     /**
-     * Get the number of harmonic bond stretch terms in the potential function
+     * Get the number of bond stretch terms in the potential function
      */
     int getNumBonds() const {
         return bonds.size();
@@ -64,7 +68,7 @@ public:
     /**
      * Set the global cubic term
      * 
-     * @param cubicK        the cubic harmonic force constant for the bond
+     * @param cubicK        the cubic force constant for the bond
      */
     void setAmoebaGlobalHarmonicBondCubic( double cubicK );
 
@@ -76,9 +80,9 @@ public:
     double getAmoebaGlobalHarmonicBondCubic( void ) const;
 
     /**
-     * Set the global cubic term
+     * Set the global quartic term
      * 
-     * @param quarticK       the quartic harmonic force constant for the bond
+     * @param quarticK       the quartic force constant for the bond
      */
     void setAmoebaGlobalHarmonicBondQuartic( double quarticK );
 
@@ -95,7 +99,7 @@ public:
      * @param particle1     the index of the first particle connected by the bond
      * @param particle2     the index of the second particle connected by the bond
      * @param length        the equilibrium length of the bond, measured in nm
-     * @param k             the quadratic harmonic force constant for the bond
+     * @param k             the quadratic force constant for the bond
      * @return the index of the bond that was added
      */
 
@@ -108,7 +112,7 @@ public:
      * @param particle1     the index of the first particle connected by the bond
      * @param particle2     the index of the second particle connected by the bond
      * @param length        the equilibrium length of the bond, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant for the bond
+     * @param quadratic k   the quadratic force constant for the bond
      */
 
     void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
@@ -120,7 +124,7 @@ public:
      * @param particle1 the index of the first particle connected by the bond
      * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
-     * @param k         the quadratic harmonic force constant for the bond
+     * @param k         the quadratic force constant for the bond
      */
     void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
 
@@ -128,21 +132,8 @@ protected:
     double _globalQuarticK, _globalCubicK;
     ForceImpl* createImpl();
 private:
-
     class BondInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<BondInfo> bonds;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaHarmonicBondForce::BondInfo {

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -40,9 +40,12 @@ namespace OpenMM {
 
 /**
  * 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().
+ * between four particles.  The interaction is defined by a 6th order polynomial in the angle between them.  Only the
+ * quadratic term is set per-angle.  The coefficients of the higher order terms each have a single value that
+ * is set globally.
+ * 
+ * To use it, create an AmoebaHarmonicInPlaneAngle object then call addAngle() once for each angle.  After
+ * an angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
 class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
@@ -50,12 +53,12 @@ class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
 public:
 
     /**
-     * Create a Amoeba HarmonicAngleForce.
+     * Create an AmoebaHarmonicAngleForce.
      */
     AmoebaHarmonicInPlaneAngleForce();
 
     /**
-     * Get the number of harmonic angle stretch terms in the potential function
+     * Get the number of in-plane angle terms in the potential function
      */
     int getNumAngles() const {
         return angles.size();
@@ -64,7 +67,7 @@ public:
     /**
      * Set the global cubic term
      * 
-     * @param cubicK        the cubic harmonic force constant for the angle
+     * @param cubicK        the cubic force constant for the angle
      */
     void setAmoebaGlobalHarmonicInPlaneAngleCubic( double cubicK );
 
@@ -78,7 +81,7 @@ public:
     /**
      * Set the global quartic term
      * 
-     * @param quarticK the quartic harmonic force constant for the angle
+     * @param quarticK the quartic force constant for the angle
      */
     void setAmoebaGlobalHarmonicInPlaneAngleQuartic( double quarticK );
 
@@ -92,7 +95,7 @@ public:
     /**
      * Set the global pentic term
      * 
-     * @param penticK the pentic harmonic force constant for the angle
+     * @param penticK the pentic force constant for the angle
      */
     void setAmoebaGlobalHarmonicInPlaneAnglePentic( double penticK );
 
@@ -106,7 +109,7 @@ public:
     /**
      * Set the global sextic term
      * 
-     * @param sexticK       the sextic harmonic force constant for the angle
+     * @param sexticK       the sextic force constant for the angle
      */
     void setAmoebaGlobalHarmonicInPlaneAngleSextic( double sexticK );
 
@@ -118,21 +121,21 @@ public:
     double getAmoebaGlobalHarmonicInPlaneAngleSextic( void ) const;
 
     /**
-     * Add a angle term to the force field.
+     * Add an angle term to the force field.
      *
      * @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 particle4     the index of the fourth particle connected by 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
+     * @param quadratic k   the quadratic 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, 
                  double quadraticK );
 
     /**
-     * Get the force field parameters for a angle term.
+     * Get the force field parameters for an angle term.
      * 
      * @param index         the index of the angle for which to get parameters
      * @param particle1     the index of the first particle connected by the angle
@@ -140,13 +143,13 @@ public:
      * @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 angle, measured in radians
-     * @param quadratic k   the quadratic harmonic force constant for the angle measured in kJ/mol/radian^2
+     * @param quadratic k   the quadratic 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;
 
     /**
-     * Set the force field parameters for a angle term.
+     * Set the force field parameters for an angle term.
      * 
      * @param index         the index of the angle for which to set parameters
      * @param particle1     the index of the first particle connected by the angle
@@ -154,7 +157,7 @@ public:
      * @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 angle, measured in radians
-     * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
+     * @param quadratic k   the quadratic 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 );
 
@@ -162,21 +165,8 @@ protected:
     ForceImpl* createImpl();
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
-
     class AngleInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<AngleInfo> angles;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaHarmonicInPlaneAngleForce::AngleInfo {

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -43,18 +43,19 @@
 namespace OpenMM {
 
 /**
- * This class implements the Amoeba multipole interaction
- * To use it, create a MultipoleForce object then call addMultipole() once for each atom.  After
- * a entry has been added, you can modify its force field parameters by calling setMultipoleParameters().
+ * This class implements the Amoeba multipole interaction.
+ *
+ * To use it, create an AmoebaMultipoleForce object then call addMultipole() once for each atom.  After
+ * an entry has been added, you can modify its force field parameters by calling setMultipoleParameters().
  */
 
 class OPENMM_EXPORT AmoebaMultipoleForce : public Force {
 
 public:
- 
-    enum AmoebaNonbondedMethod {
 
-        /** 
+    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.
          */
@@ -64,36 +65,30 @@ public:
          * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
          * with all periodic copies of every other particle.
          */
-        PME = 1 
-    };  
+        PME = 1
+    };
 
-    enum AmoebaPolarizationType {
+    enum PolarizationType {
 
-        /** 
+        /**
          * Mutual polarization
          */
         Mutual = 0,
 
         /**
-         * Direct polarization 
+         * Direct polarization
          */
-        Direct = 1 
-    };  
+        Direct = 1
+    };
 
     enum MultipoleAxisTypes { ZThenX = 0, Bisector = 1, ZBisect = 2, ThreeFold = 3, ZOnly = 4, NoAxisType = 5, LastAxisTypeIndex = 6 };
 
-    // Algorithm used to converge mutual induced dipoles:
-    //     SOR: successive-over-relaxation
-
-    //enum MutualInducedIterationMethod { SOR, ConjugateGradient };
-    enum MutualInducedIterationMethod { SOR = 0 };
-
-    enum CovalentType { 
-                          Covalent12 = 0, Covalent13 = 1, Covalent14 = 2, Covalent15 = 3, 
+    enum CovalentType {
+                          Covalent12 = 0, Covalent13 = 1, Covalent14 = 2, Covalent15 = 3,
                           PolarizationCovalent11 = 4, PolarizationCovalent12 = 5, PolarizationCovalent13 = 6, PolarizationCovalent14 = 7, CovalentEnd = 8 };
 
     /**
-     * Create a Amoeba MultipoleForce.
+     * Create an AmoebaMultipoleForce.
      */
     AmoebaMultipoleForce();
 
@@ -107,22 +102,22 @@ public:
     /**
      * Get the method used for handling long-range nonbonded interactions.
      */
-    AmoebaNonbondedMethod getNonbondedMethod( void ) const;
+    NonbondedMethod getNonbondedMethod() const;
 
     /**
      * Set the method used for handling long-range nonbonded interactions.
      */
-    void setNonbondedMethod(AmoebaNonbondedMethod method);
+    void setNonbondedMethod(NonbondedMethod method);
 
     /**
      * Get polarization type
      */
-    AmoebaPolarizationType getPolarizationType( void ) const;
+    PolarizationType getPolarizationType() const;
 
     /**
      * Set the polarization type
      */
-    void setPolarizationType(AmoebaPolarizationType type );
+    void setPolarizationType(PolarizationType type);
 
     /**
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
@@ -130,7 +125,7 @@ public:
      *
      * @return the cutoff distance, measured in nm
      */
-    double getCutoffDistance( void ) const;
+    double getCutoffDistance(void) const;
 
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
@@ -140,55 +135,52 @@ public:
      */
     void setCutoffDistance(double distance);
 
-   /**		   
-     * Get the aEwald parameter		 
-     *		 
-     * @return the Ewald parameter		 
-     */		 
-    double getAEwald() const;			 
-		 
-    /**		 
-     * Set the aEwald parameter		 
-     *		 
-     * @param Ewald parameter			 
-     */		 
-    void setAEwald(double aewald);		 
-		 
-   /**		   
-     * Get the B-spline order parameter		 
-     *		 
-     * @return the B-spline order parameter
-     */		 
-    int getPmeBSplineOrder( ) const;
-        
-   /**		   
-     * Set the B-spline order parameter		 
-     *		 
-     * @param the B-spline order parameter
-     */		 
-    //void setPmeBSplineOrder(int inputBSplineOrder);
-     
-   /**		   
-     * Get the PME grid dimensions		 
-     *		 
+    /**
+     * Get the Ewald alpha parameter.  If this is 0 (the default), a value is chosen automatically
+     * based on the Ewald error tolerance.
+     *
+     * @return the Ewald alpha parameter
+     */
+    double getAEwald() const;
+
+    /**
+     * Set the Ewald alpha parameter.  If this is 0 (the default), a value is chosen automatically
+     * based on the Ewald error tolerance.
+     *
+     * @param Ewald alpha parameter
+     */
+    void setAEwald(double aewald);
+
+    /**
+     * Get the B-spline order to use for PME charge spreading
+     *
+     * @return the B-spline order
+     */
+    int getPmeBSplineOrder() const;
+
+    /**
+     * Get the PME grid dimensions.  If Ewald alpha is 0 (the default), this is ignored and grid dimensions
+     * are chosen automatically based on the Ewald error tolerance.
+     *
      * @return the PME grid dimensions
-     */		 
-    void getPmeGridDimensions( std::vector<int>& gridDimension ) const;
-         
-   /**		   
-     * Set the PME grid dimensions		 
-     *		 
+     */
+    void getPmeGridDimensions(std::vector<int>& gridDimension) const;
+
+   /**
+     * Set the PME grid dimensions.  If Ewald alpha is 0 (the default), this is ignored and grid dimensions
+     * are chosen automatically based on the Ewald error tolerance.
+     *
      * @param the PME grid dimensions
-     */		 
-    void setPmeGridDimensions( const std::vector<int>& gridDimension );
-    
+     */
+    void setPmeGridDimensions(const std::vector<int>& gridDimension);
+
     /**
-     * Add multipole-related info for a particle 
+     * Add multipole-related info for a particle
      *
      * @param charge               the particle's charge
      * @param molecularDipole      the particle's molecular dipole (vector of size 3)
      * @param molecularQuadrupole  the particle's molecular quadrupole (vector of size 9)
-     * @param axisType             the particle's axis type ( ZThenX, Bisector )
+     * @param axisType             the particle's axis type
      * @param multipoleAtomZ       index of first atom used in constructing lab<->molecular frames
      * @param multipoleAtomX       index of second atom used in constructing lab<->molecular frames
      * @param multipoleAtomY       index of second atom used in constructing lab<->molecular frames
@@ -198,17 +190,17 @@ public:
      *
      * @return the index of the particle that was added
      */
-    int addParticle( double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
-                     int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity );
- 
+    int addParticle(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
+                     int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity);
+
     /**
      * Get the multipole parameters for a particle.
-     * 
+     *
      * @param index                the index of the atom for which to get parameters
      * @param charge               the particle's charge
      * @param molecularDipole      the particle's molecular dipole (vector of size 3)
      * @param molecularQuadrupole  the particle's molecular quadrupole (vector of size 9)
-     * @param axisType             the particle's axis type ( ZThenX, Bisector )
+     * @param axisType             the particle's axis type
      * @param multipoleAtomZ       index of first atom used in constructing lab<->molecular frames
      * @param multipoleAtomX       index of second atom used in constructing lab<->molecular frames
      * @param multipoleAtomY       index of second atom used in constructing lab<->molecular frames
@@ -217,16 +209,16 @@ public:
      * @param polarity             polarity parameter
      */
     void getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
-                                int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity ) const;
+                                int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity) const;
 
     /**
      * Set the multipole parameters for a particle.
-     * 
+     *
      * @param index                the index of the atom for which to set parameters
      * @param charge               the particle's charge
      * @param molecularDipole      the particle's molecular dipole (vector of size 3)
      * @param molecularQuadrupole  the particle's molecular quadrupole (vector of size 9)
-     * @param axisType             the particle's axis type ( ZThenX, Bisector )
+     * @param axisType             the particle's axis type
      * @param multipoleAtomZ       index of first atom used in constructing lab<->molecular frames
      * @param multipoleAtomX       index of second atom used in constructing lab<->molecular frames
      * @param multipoleAtomY       index of second atom used in constructing lab<->molecular frames
@@ -237,84 +229,74 @@ public:
 
     /**
      * Set the CovalentMap for an atom
-     * 
+     *
      * @param index                the index of the atom for which to set parameters
      * @param typeId               CovalentTypes type
      * @param covalentAtoms        vector of covalent atoms associated w/ the specfied CovalentType
      */
-    void setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms );
+    void setCovalentMap(int index, CovalentType typeId, const std::vector<int>& covalentAtoms);
 
     /**
      * Get the CovalentMap for an atom
-     * 
+     *
      * @param index                the index of the atom for which to set parameters
      * @param typeId               CovalentTypes type
      * @param covalentAtoms        output vector of covalent atoms associated w/ the specfied CovalentType
      */
-    void getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms ) const;
+    void getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms) const;
 
     /**
      * Get the CovalentMap for an atom
-     * 
+     *
      * @param index                the index of the atom for which to set parameters
      * @param covalentLists        output vector of covalent lists of atoms
      */
-    void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists ) const;
+    void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists) const;
 
-    /**
-     * Get the iteration method to be used for calculating the mutual induced dipoles
-     * 
-     * @return iteration method to be used for calculating the mutual induced dipole
-     */
-    //MutualInducedIterationMethod getMutualInducedIterationMethod( void ) const;
-    
-    /**
-     * Set the iteration method to be used for calculating the mutual induced dipoles
-     * 
-     * @param iteration method to be used for calculating the mutual induced dipole
-     */
-    //void setMutualInducedIterationMethod( MutualInducedIterationMethod inputMutualInducedIterationMethod ); 
-    
     /**
      * Get the max number of iterations to be used in calculating the mutual induced dipoles
-     * 
+     *
      * @return max number of iterations
      */
-    int getMutualInducedMaxIterations( void ) const;
-    
+    int getMutualInducedMaxIterations(void) const;
+
     /**
      * Set the max number of iterations to be used in calculating the mutual induced dipoles
-     * 
+     *
      * @param max number of iterations
      */
-    void setMutualInducedMaxIterations( int inputMutualInducedMaxIterations ); 
-    
+    void setMutualInducedMaxIterations(int inputMutualInducedMaxIterations);
+
     /**
      * Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
-     * 
+     *
      * @return target epsilon
      */
-    double getMutualInducedTargetEpsilon( void ) const;
-    
+    double getMutualInducedTargetEpsilon(void) const;
+
     /**
      * Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
-     * 
+     *
      * @param target epsilon
      */
-    void setMutualInducedTargetEpsilon( double inputMutualInducedTargetEpsilon ); 
-    
+    void setMutualInducedTargetEpsilon(double inputMutualInducedTargetEpsilon);
+
     /**
      * Get the error tolerance for Ewald summation.  This corresponds to the fractional error in the forces
-     * which is acceptable.  This value is used to select the reciprocal space cutoff and separation
+     * which is acceptable.  This value is used to select the grid dimensions and separation (alpha)
      * parameter so that the average error level will be less than the tolerance.  There is not a
      * rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
+     * 
+     * This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
      */
     double getEwaldErrorTolerance() const;
     /**
      * Get the error tolerance for Ewald summation.  This corresponds to the fractional error in the forces
-     * which is acceptable.  This value is used to select the reciprocal space cutoff and separation
+     * which is acceptable.  This value is used to select the grid dimensions and separation (alpha)
      * parameter so that the average error level will be less than the tolerance.  There is not a
      * rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
+     * 
+     * This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.
      */
     void setEwaldErrorTolerance(double tol);
 
@@ -323,44 +305,46 @@ public:
      *
      * @param inputGrid    input grid points over which the potential is to be evaluated
      * @param context      context
-     * @param outputElectrostaticPotential output potential 
+     * @param outputElectrostaticPotential output potential
      */
 
-    void getElectrostaticPotential( const std::vector< Vec3 >& inputGrid,
-                                    Context& context, std::vector< double >& outputElectrostaticPotential );
+    void getElectrostaticPotential(const std::vector< Vec3 >& inputGrid,
+                                    Context& context, std::vector< double >& outputElectrostaticPotential);
 
 
     /**
-     * Get the system multipole moments
+     * Get the system multipole moments.
+     * 
+     * This method is most useful for non-periodic systems.  When called for a periodic system, only the
+     * <i>lowest nonvanishing moment</i> has a well defined value.  This means that if the system has a net
+     * nonzero charge, the dipole and quadrupole moments are not well defined and should be ignored.  If the
+     * net charge is zero, the dipole moment is well defined (and really represents a dipole density), but
+     * the quadrupole moment is still undefined and should be ignored.
      *
-     * @param origin       origin
      * @param context      context
      * @param outputMultipoleMonents (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 )
+                                      quadrupole_zx, quadrupole_zy, quadrupole_zz)
      */
 
-    void getSystemMultipoleMoments( const Vec3& origin, Context& context, std::vector< double >& outputMultipoleMonents );
+    void getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMonents);
 
 protected:
     ForceImpl* createImpl();
 private:
-
-    AmoebaNonbondedMethod nonbondedMethod;
-    AmoebaPolarizationType polarizationType;
+    NonbondedMethod nonbondedMethod;
+    PolarizationType polarizationType;
     double cutoffDistance;
     double aewald;
     int pmeBSplineOrder;
     std::vector<int> pmeGridDimension;
-    MutualInducedIterationMethod mutualInducedIterationMethod;
     int mutualInducedMaxIterations;
     double mutualInducedTargetEpsilon;
     double scalingDistanceCutoff;
     double electricConstant;
     double ewaldErrorTol;
-
     class MultipoleInfo;
     std::vector<MultipoleInfo> multipoles;
 };
@@ -379,24 +363,24 @@ public:
         axisType = multipoleAtomZ = multipoleAtomX = multipoleAtomY = -1;
         charge   = thole          = dampingFactor  = 0.0;
 
-        molecularDipole.resize( 3 );
-        molecularQuadrupole.resize( 9 );
+        molecularDipole.resize(3);
+        molecularQuadrupole.resize(9);
 
     }
 
-    MultipoleInfo( double charge, const std::vector<double>& inputMolecularDipole, const std::vector<double>& inputMolecularQuadrupole,
+    MultipoleInfo(double charge, const std::vector<double>& inputMolecularDipole, const std::vector<double>& inputMolecularQuadrupole,
                    int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) :
         charge(charge), axisType(axisType), multipoleAtomZ(multipoleAtomZ), multipoleAtomX(multipoleAtomX), multipoleAtomY(multipoleAtomY),
         thole(thole), dampingFactor(dampingFactor), polarity(polarity) {
 
-       covalentInfo.resize( CovalentEnd );
+       covalentInfo.resize(CovalentEnd);
 
-       molecularDipole.resize( 3 );
-       molecularDipole[0]          = inputMolecularDipole[0]; 
-       molecularDipole[1]          = inputMolecularDipole[1]; 
-       molecularDipole[2]          = inputMolecularDipole[2]; 
+       molecularDipole.resize(3);
+       molecularDipole[0]          = inputMolecularDipole[0];
+       molecularDipole[1]          = inputMolecularDipole[1];
+       molecularDipole[2]          = inputMolecularDipole[2];
 
-       molecularQuadrupole.resize( 9 );
+       molecularQuadrupole.resize(9);
        molecularQuadrupole[0]      = inputMolecularQuadrupole[0];
        molecularQuadrupole[1]      = inputMolecularQuadrupole[1];
        molecularQuadrupole[2]      = inputMolecularQuadrupole[2];

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,9 +39,10 @@
 namespace OpenMM {
 
 /**
- * This class implements the Amoeba Out-of-plane bend interaction
- * To use it, create a OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend.  After
- * a outOfPlaneBend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters().
+ * This class implements the Amoeba out-of-plane bend interaction.
+ * 
+ * To use it, create an OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend.  After
+ * an out-of-plane bend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters().
  */
 
 class OPENMM_EXPORT AmoebaOutOfPlaneBendForce : public Force {
@@ -49,12 +50,12 @@ class OPENMM_EXPORT AmoebaOutOfPlaneBendForce : public Force {
 public:
 
     /**
-     * Create a Amoeba OutOfPlaneBendForce.
+     * Create an AmoebaOutOfPlaneBendForce.
      */
     AmoebaOutOfPlaneBendForce();
 
     /**
-     * Get the number of outOfPlaneBend terms in the potential function
+     * Get the number of out-of-plane bend terms in the potential function
      */
     int getNumOutOfPlaneBends() const {
         return outOfPlaneBends.size();
@@ -63,114 +64,101 @@ public:
     /** 
      * Set the global cubic term
      * 
-     * @param cubicK        the cubic harmonic force constant for the angle
+     * @param cubicK        the cubic force constant for the angle
      */
-    void setAmoebaGlobalOutOfPlaneBendCubic( double cubicK );
+    void setAmoebaGlobalOutOfPlaneBendCubic(double cubicK);
 
     /** 
      * Get the global cubic term
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalOutOfPlaneBendCubic( void ) const;
+    double getAmoebaGlobalOutOfPlaneBendCubic(void) const;
 
     /** 
      * Set the global cubic term
      * 
-     * @param quarticK       the quartic harmonic force constant for the angle
+     * @param quarticK       the quartic force constant for the angle
      */
-    void setAmoebaGlobalOutOfPlaneBendQuartic( double quarticK );
+    void setAmoebaGlobalOutOfPlaneBendQuartic(double quarticK);
 
     /** 
      * Get the global quartic term
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalOutOfPlaneBendQuartic( void ) const;
+    double getAmoebaGlobalOutOfPlaneBendQuartic(void) const;
 
     /** 
      * Set the global pentic term
      * 
-     * @param penticK the pentic harmonic force constant for the angle
+     * @param penticK the pentic force constant for the angle
      */
-    void setAmoebaGlobalOutOfPlaneBendPentic( double penticK );
+    void setAmoebaGlobalOutOfPlaneBendPentic(double penticK);
 
     /** 
      * Get the global pentic term
      * 
      * @return global penticK term
      */
-    double getAmoebaGlobalOutOfPlaneBendPentic( void ) const;
+    double getAmoebaGlobalOutOfPlaneBendPentic(void) const;
 
     /** 
      * Set the global sextic term
      * 
-     * @param sexticK       the sextic harmonic force constant for the angle
+     * @param sexticK       the sextic force constant for the angle
      */
-    void setAmoebaGlobalOutOfPlaneBendSextic( double sexticK );
+    void setAmoebaGlobalOutOfPlaneBendSextic(double sexticK);
 
     /** 
      * Get the global sextic term
      * 
      * @return global sexticK term
      */
-    double getAmoebaGlobalOutOfPlaneBendSextic( void ) const;
+    double getAmoebaGlobalOutOfPlaneBendSextic(void) const;
 
     /**
-     * Add a outOfPlaneBend term to the force field.
+     * Add an out-of-plane bend term to the force field.
      *
      * @param particle1     the index of the first particle connected by the outOfPlaneBend
      * @param particle2     the index of the second particle connected by the outOfPlaneBend
      * @param particle3     the index of the third particle connected by the outOfPlaneBend
      * @param particle4     the index of the fourth particle connected by the outOfPlaneBend
-     * @param k             the force constant for the outOfPlaneBend
-     * @return the index of the outOfPlaneBend that was added
+     * @param k             the force constant for the out-of-plane bend
+     * @return the index of the out-of-plane bend that was added
      */
-    int addOutOfPlaneBend(int particle1, int particle2, int particle3, int particle4, double k );
+    int addOutOfPlaneBend(int particle1, int particle2, int particle3, int particle4, double k);
 
     /**
-     * Get the force field parameters for a outOfPlaneBend term.
+     * Get the force field parameters for an out-of-plane bend term.
      * 
      * @param index         the index of the outOfPlaneBend for which to get parameters
      * @param particle1     the index of the first particle connected by the outOfPlaneBend
      * @param particle2     the index of the second particle connected by the outOfPlaneBend
      * @param particle3     the index of the third particle connected by the outOfPlaneBend
      * @param particle4     the index of the fourth particle connected by the outOfPlaneBend
-     * @param k             the force constant for the outOfPlaneBend
+     * @param k             the force constant for the out-of-plane bend
      */
-    void getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& k ) const;
+    void getOutOfPlaneBendParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& k) const;
 
     /**
-     * Set the force field parameters for a outOfPlaneBend term.
+     * Set the force field parameters for an out-of-plane bend term.
      * 
      * @param index         the index of the outOfPlaneBend for which to set parameters
      * @param particle1     the index of the first particle connected by the outOfPlaneBend
      * @param particle2     the index of the second particle connected by the outOfPlaneBend
      * @param particle3     the index of the third particle connected by the outOfPlaneBend
      * @param particle4     the index of the fourth particle connected by the outOfPlaneBend
-     * @param k             the force constant for the outOfPlaneBend
+     * @param k             the force constant for the out-of-plane bend
      */
-    void setOutOfPlaneBendParameters(int index, int particle1, int particle2, int particle3, int particle4, double k );
+    void setOutOfPlaneBendParameters(int index, int particle1, int particle2, int particle3, int particle4, double k);
 
 protected:
     ForceImpl* createImpl();
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;
 private:
-
     class OutOfPlaneBendInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<OutOfPlaneBendInfo> outOfPlaneBends;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaOutOfPlaneBendForce::OutOfPlaneBendInfo {
@@ -182,7 +170,7 @@ public:
         k   = 0.0;
     }
     OutOfPlaneBendInfo(int particle1, int particle2, int particle3, int particle4,
-                           double k ) :
+                           double k) :
                     particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4), k(k) {
      
     }

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,8 +39,9 @@
 namespace OpenMM {
 
 /**
- * This class implements the Amoeba pi-torsion interaction
- * To use it, create a PiTorsionForce object then call addPiTorsion() once for each torsion.  After
+ * This class implements the Amoeba pi-torsion interaction.
+ * 
+ * To use it, create an AmoebaPiTorsionForce object then call addPiTorsion() once for each torsion.  After
  * a torsion has been added, you can modify its force field parameters by calling setPiTorsionParameters().
  */
 
@@ -49,7 +50,7 @@ class OPENMM_EXPORT AmoebaPiTorsionForce : public Force {
 public:
 
     /**
-     * Create a Amoeba PiTorsionForce.
+     * Create an AmoebaPiTorsionForce.
      */
     AmoebaPiTorsionForce();
 
@@ -72,7 +73,7 @@ public:
      * @param k             the force constant for the torsion
      * @return the index of the torsion that was added
      */
-    int addPiTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k );
+    int addPiTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k);
 
     /**
      * Get the force field parameters for a torsion term.
@@ -86,7 +87,7 @@ public:
      * @param particle6     the index of the sixth particle connected by the torsion
      * @param k             the force constant for the torsion
      */
-    void getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k ) const;
+    void getPiTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& particle6, double& k) const;
 
     /**
      * Set the force field parameters for a pi torsion term.
@@ -100,26 +101,13 @@ public:
      * @param particle6     the index of the sixth particle connected by the torsion
      * @param k             the force constant for the torsion
      */
-    void setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k );
+    void setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k);
 
 protected:
     ForceImpl* createImpl();
 private:
-
     class PiTorsionInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<PiTorsionInfo> piTorsions;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaPiTorsionForce::PiTorsionInfo {
@@ -130,7 +118,7 @@ public:
         particle1 = particle2  = particle3 = particle4 = particle5 = particle6 = -1;
         k = 0.0;
     }
-    PiTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k ) :
+    PiTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k) :
         particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4), particle5(particle5), particle6(particle6), k(k) {
     }
 };

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,9 +39,10 @@
 namespace OpenMM {
 
 /**
- * This class implements the Amoeba stretch bend interaction
- * To use it, create a StretchBendForce object then call addStretchBend() once for each stretchBend.  After
- * a stretchBend has been added, you can modify its force field parameters by calling setStretchBendParameters().
+ * This class implements the Amoeba stretch-bend interaction.
+ * 
+ * To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend.  After
+ * a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters().
  */
 
 class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
@@ -49,58 +50,58 @@ class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
 public:
 
     /**
-     * Create a Amoeba StretchBendForce.
+     * Create an AmoebaStretchBendForce.
      */
     AmoebaStretchBendForce();
 
     /**
-     * Get the number of stretchBend terms in the potential function
+     * Get the number of stretch-bend terms in the potential function
      */
     int getNumStretchBends() const {
         return stretchBends.size();
     }
 
     /**
-     * Add a stretchBend term to the force field.
+     * Add a stretch-bend term to the force field.
      *
-     * @param particle1     the index of the first particle connected by the stretchBend
-     * @param particle2     the index of the second particle connected by the stretchBend
-     * @param particle3     the index of the third particle connected by the stretchBend
-     * @param lengthAB      the equilibrium length of the stretchBend in bond ab [particle1, particle2], measured in nm
-     * @param lengthCB      the equilibrium length of the stretchBend in bond cb [particle3, particle2], measured in nm
+     * @param particle1     the index of the first particle connected by the stretch-bend
+     * @param particle2     the index of the second particle connected by the stretch-bend
+     * @param particle3     the index of the third particle connected by the stretch-bend
+     * @param lengthAB      the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
+     * @param lengthCB      the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
      * @param angle         the equilibrium angle in radians
-     * @param k             the force constant for the stretchBend
-     * @return the index of the stretchBend that was added
+     * @param k             the force constant for the stretch-bend
+     * @return the index of the stretch-bend that was added
      */
     int addStretchBend(int particle1, int particle2, int particle3, double lengthAB,  double lengthCB, double angle,
                        double k );
 
     /**
-     * Get the force field parameters for a stretchBend term.
+     * Get the force field parameters for a stretch-bend term.
      * 
-     * @param index         the index of the stretchBend for which to get parameters
-     * @param particle1     the index of the first particle connected by the stretchBend
-     * @param particle2     the index of the second particle connected by the stretchBend
-     * @param particle3     the index of the third particle connected by the stretchBend
-     * @param lengthAB      the equilibrium length of the stretchBend in bond ab [particle1, particle2], measured in nm
-     * @param lengthCB      the equilibrium length of the stretchBend in bond cb [particle3, particle2], measured in nm
+     * @param index         the index of the stretch-bend for which to get parameters
+     * @param particle1     the index of the first particle connected by the stretch-bend
+     * @param particle2     the index of the second particle connected by the stretch-bend
+     * @param particle3     the index of the third particle connected by the stretch-bend
+     * @param lengthAB      the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
+     * @param lengthCB      the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
      * @param angle         the equilibrium angle in radians
-     * @param k             the force constant for the stretchBend
+     * @param k             the force constant for the stretch-bend
      */
     void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3,
                                   double& lengthAB, double& lengthCB, double& angle, double& k ) const;
 
     /**
-     * Set the force field parameters for a stretchBend term.
+     * Set the force field parameters for a stretch-bend term.
      * 
-     * @param index         the index of the stretchBend for which to set parameters
-     * @param particle1     the index of the first particle connected by the stretchBend
-     * @param particle2     the index of the second particle connected by the stretchBend
-     * @param particle3     the index of the third particle connected by the stretchBend
-     * @param lengthAB      the equilibrium length of the stretchBend in bond ab [particle1, particle2], measured in nm
-     * @param lengthCB      the equilibrium length of the stretchBend in bond cb [particle3, particle2], measured in nm
+     * @param index         the index of the stretch-bend for which to set parameters
+     * @param particle1     the index of the first particle connected by the stretch-bend
+     * @param particle2     the index of the second particle connected by the stretch-bend
+     * @param particle3     the index of the third particle connected by the stretch-bend
+     * @param lengthAB      the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
+     * @param lengthCB      the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
      * @param angle         the equilibrium angle in radians
-     * @param k             the force constant for the stretchBend
+     * @param k             the force constant for the stretch-bend
      */
     void setStretchBendParameters(int index, int particle1, int particle2, int particle3, 
                                   double lengthAB,  double lengthCB, double angle, double k );
@@ -108,21 +109,8 @@ public:
 protected:
     ForceImpl* createImpl();
 private:
-
     class StretchBendInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<StretchBendInfo> stretchBends;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaStretchBendForce::StretchBendInfo {

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

-#ifndef OPENMM_AMOEBA_TORSION_FORCE_H_
-#define OPENMM_AMOEBA_TORSION_FORCE_H_
-
-/* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
- * -------------------------------------------------------------------------- *
- * 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:                                                                   *
- * 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 "openmm/internal/windowsExport.h"
-#include <vector>
-#include <sstream>
-
-namespace OpenMM {
-
-/**
- * This class implements an torsion interaction among four particles.
- * To use it, create a TorsionForce object then call addTorsion() once for each angle.  After
- * a angle has been added, you can modify its force field parameters by calling setTorsionParameters().
- */
-
-class OPENMM_EXPORT AmoebaTorsionForce : public Force {
-
-public:
-
-    static const unsigned int ParametersPerTorsion  = 2;
-
-    /**
-     * Create a Amoeba TorsionForce.
-     */
-    AmoebaTorsionForce();
-
-    /**
-     * Get the number of torsion terms in the potential function
-     */
-    int getNumTorsions() const {
-        return torsions.size();
-    }
-
-    /**
-     * Add a torsion term to the force field.
-     *
-     * @param particle1     the index of the first particle connected by the torsion
-     * @param particle2     the index of the second particle connected by the torsion
-     * @param particle3     the index of the third particle connected by the torsion
-     * @param particle4     the index of the fourth particle connected by the torsion
-     * @param torsion1      the vector of torsion params for first index (amplitude, phase, fold)
-     * @param torsion2      the vector of torsion params for second index (amplitude, phase, fold)
-     * @param torsion3      the vector of torsion params for third index (amplitude, phase, fold)
-     * @return the index of the torsion that was added
-     */
-    int addTorsion(int particle1, int particle2, int particle3, int particle4,
-                   const std::vector<double>& torsion1, const std::vector<double>& torsion2, const std::vector<double>& torsion3 );
-
-    /**
-     * Get the force field parameters for a torsion term.
-     * 
-     * @param index         the index of the torsion for which to get parameters
-     * @param particle1     the index of the first particle connected by the torsion
-     * @param particle2     the index of the second particle connected by the torsion
-     * @param particle3     the index of the third particle connected by the torsion
-     * @param particle4     the index of the fourth particle connected by the torsion
-     * @param torsion1      the vector of torsion params for first index (amplitude, phase, fold)
-     * @param torsion2      the vector of torsion params for second index (amplitude, phase, fold)
-     * @param torsion3      the vector of torsion params for third index (amplitude, phase, fold)
-     */
-    void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, 
-                              std::vector<double>& torsion1, std::vector<double>& torsion2, std::vector<double>& torsion3 ) const;
-
-    /**
-     * Set the force field parameters for a torsion term.
-     * 
-     * @param index         the index of the torsion for which to set parameters
-     * @param particle1     the index of the first particle connected by the torsion
-     * @param particle2     the index of the second particle connected by the torsion
-     * @param particle3     the index of the third particle connected by the torsion
-     * @param particle4     the index of the fourth particle connected by the torsion
-     * @param torsion1      the vector of torsion params for first index (amplitude, phase, fold)
-     * @param torsion2      the vector of torsion params for second index (amplitude, phase, fold)
-     * @param torsion3      the vector of torsion params for third index (amplitude, phase, fold)
-     */
-    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, 
-                              const std::vector<double>& torsion1, const std::vector<double>& torsion2, const std::vector<double>& torsion3 );
-
-protected:
-    ForceImpl* createImpl();
-private:
-
-    class TorsionInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
-    std::vector<TorsionInfo> torsions;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
-};
-
-class AmoebaTorsionForce::TorsionInfo {
-private:
-
-    // max number of torsion sets of parameters; in current amoebapro.prm max is 3
-    // but code goes up to 6
-
-    static const unsigned int maxTorsions           = 3;
-
-    void _initialize() {
-
-        torsionParameters.resize( maxTorsions );     
-        for( unsigned int ii = 0; ii < torsionParameters.size(); ii++ ){
-            torsionParameters[ii].resize( AmoebaTorsionForce::ParametersPerTorsion );
-            for( unsigned int jj = 0; jj < AmoebaTorsionForce::ParametersPerTorsion; jj++ ){
-                torsionParameters[ii][jj] = 0.0;
-            }
-        }
-    }
-
-public:
-    int particle1, particle2, particle3, particle4;
-    std::vector< std::vector<double> > torsionParameters;
-    TorsionInfo() {
-        particle1 = particle2  = particle3 = particle4 = -1;
-        _initialize();
-    }
-    TorsionInfo(int particle1, int particle2, int particle3, int particle4, const std::vector<double>& torsion1, const std::vector<double>& torsion2, const std::vector<double>& torsion3 ) :
-        particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4)  {
-
-        if( torsion1.size() != AmoebaTorsionForce::ParametersPerTorsion ){
-           std::stringstream buffer;
-           buffer << "TorsionInfo::TorsionInfo: torsion1 size(=" << torsion1.size() << ") is not " << AmoebaTorsionForce::ParametersPerTorsion;
-           throw OpenMMException( buffer.str() );
-        }
-
-        if( torsion2.size() != AmoebaTorsionForce::ParametersPerTorsion ){
-           std::stringstream buffer;
-           buffer << "TorsionInfo::TorsionInfo: torsion2 size(=" << torsion2.size() << ") is not " << AmoebaTorsionForce::ParametersPerTorsion;
-           throw OpenMMException( buffer.str() );
-        }
-
-        if( torsion3.size() != AmoebaTorsionForce::ParametersPerTorsion ){
-           std::stringstream buffer;
-           buffer << "TorsionInfo::TorsionInfo: torsion3 size(=" << torsion3.size() << ") is not " << AmoebaTorsionForce::ParametersPerTorsion;
-           throw OpenMMException( buffer.str() );
-        }
-
-       _initialize();   
-       for( unsigned int ii = 0; ii < AmoebaTorsionForce::ParametersPerTorsion; ii++ ){
-           torsionParameters[0][ii] = torsion1[ii];
-           torsionParameters[1][ii] = torsion2[ii];
-           torsionParameters[2][ii] = torsion3[ii];
-       }
-    }
-    int copyTorsionParameter(int index, const std::vector<double>& torsionParameter ) {
-
-        if( torsionParameter.size() != AmoebaTorsionForce::ParametersPerTorsion ){
-           std::stringstream buffer;
-           buffer << "TorsionInfo::copyTorsionParameter: input torsionParameter size(=" << torsionParameter.size() << ") is not " << AmoebaTorsionForce::ParametersPerTorsion;
-           throw OpenMMException( buffer.str() );
-        }
-
-        if( index >= 0 && index < maxTorsions ){
-            for( unsigned int ii = 0; ii < AmoebaTorsionForce::ParametersPerTorsion; ii++ ){
-                torsionParameters[index][ii] = torsionParameter[ii];
-            }
-        } else {
-           std::stringstream buffer;
-           buffer << "TorsionInfo::copyTorsionParameter: input torsionParameter index(=" << index << ") is not in range [0," << maxTorsions << ")!";
-           throw OpenMMException( buffer.str() );
-        }
-        return 0;
-    }
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_AMOEBA_TORSION_FORCE_H_*/

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -44,119 +44,105 @@ typedef std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid;
 typedef std::vector< std::vector< std::vector<float> > > TorsionTorsionGridFloat;
 
 /**
- * This class implements the Amoeba torsion-torsion interaction
- * To use it, create a TorsionTorsionForce object then call addTorsionTorsion() once for each torsionTorsion.  After
- * a torsionTorsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
+ * This class implements the Amoeba torsion-torsion interaction.
+ *
+ * To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion.  After
+ * a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
  */
 
 class OPENMM_EXPORT AmoebaTorsionTorsionForce : public Force {
 
 public:
     /**
-     * Create a Amoeba TorsionTorsionForce.
+     * Create an AmoebaTorsionTorsionForce.
      */
-    AmoebaTorsionTorsionForce( void );
+    AmoebaTorsionTorsionForce(void);
 
     /**
-     * Get the number of torsionTorsion terms in the potential function
+     * Get the number of torsion-torsion terms in the potential function
      */
-    int getNumTorsionTorsions( void ) const {
+    int getNumTorsionTorsions(void) const {
         return torsionTorsions.size();
     }
 
     /**
-     * Get the number of torsionTorsion grids
+     * Get the number of torsion-torsion grids
      */
-    int getNumTorsionTorsionGrids( void ) const {
+    int getNumTorsionTorsionGrids(void) const {
         return torsionTorsionGrids.size();
     }
 
     /**
-     * Add a torsionTorsion term to the force field.
+     * Add a torsion-torsion term to the force field.
      *
-     * @param particle1                 the index of the first particle connected by the torsionTorsion
-     * @param particle2                 the index of the second particle connected by the torsionTorsion
-     * @param particle3                 the index of the third particle connected by the torsionTorsion
-     * @param particle4                 the index of the fourth particle connected by the torsionTorsion
-     * @param particle5                 the index of the fifth particle connected by the torsionTorsion
+     * @param particle1                 the index of the first particle connected by the torsion-torsion
+     * @param particle2                 the index of the second particle connected by the torsion-torsion
+     * @param particle3                 the index of the third particle connected by the torsion-torsion
+     * @param particle4                 the index of the fourth particle connected by the torsion-torsion
+     * @param particle5                 the index of the fifth particle connected by the torsion-torsion
      * @param chiralCheckAtomIndex      the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
      * @param gridIndex                 the index to the grid to be used
-     * @return                          the index of the torsionTorsion that was added
+     * @return                          the index of the torsion-torsion that was added
      */
-    int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex );
+    int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex);
 
     /**
-     * Get the force field parameters for a torsionTorsion term.
-     * 
-     * @param index                     the index of the torsionTorsion for which to get parameters
-     * @param particle1                 the index of the first particle connected by the torsionTorsion
-     * @param particle2                 the index of the second particle connected by the torsionTorsion
-     * @param particle3                 the index of the third particle connected by the torsionTorsion
-     * @param particle4                 the index of the fourth particle connected by the torsionTorsion
-     * @param particle5                 the index of the fifth particle connected by the torsionTorsion
+     * Get the force field parameters for a torsion-torsion term.
+     *
+     * @param index                     the index of the torsion-torsion for which to get parameters
+     * @param particle1                 the index of the first particle connected by the torsion-torsion
+     * @param particle2                 the index of the second particle connected by the torsion-torsion
+     * @param particle3                 the index of the third particle connected by the torsion-torsion
+     * @param particle4                 the index of the fourth particle connected by the torsion-torsion
+     * @param particle5                 the index of the fifth particle connected by the torsion-torsion
      * @param chiralCheckAtomIndex      the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
      * @param gridIndex                 the grid index
      */
-    void getTorsionTorsionParameters( int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex ) const;
+    void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const;
 
     /**
-     * Set the force field parameters for a torsionTorsion term.
-     * 
-     * @param index                     the index of the torsionTorsion for which to set parameters
-     * @param particle1                 the index of the first particle connected by the torsionTorsion
-     * @param particle2                 the index of the second particle connected by the torsionTorsion
-     * @param particle3                 the index of the third particle connected by the torsionTorsion
-     * @param particle4                 the index of the fourth particle connected by the torsionTorsion
-     * @param particle5                 the index of the fifth particle connected by the torsionTorsion
+     * Set the force field parameters for a torsion-torsion term.
+     *
+     * @param index                     the index of the torsion-torsion for which to set parameters
+     * @param particle1                 the index of the first particle connected by the torsion-torsion
+     * @param particle2                 the index of the second particle connected by the torsion-torsion
+     * @param particle3                 the index of the third particle connected by the torsion-torsion
+     * @param particle4                 the index of the fourth particle connected by the torsion-torsion
+     * @param particle5                 the index of the fifth particle connected by the torsion-torsion
      * @param chiralCheckAtomIndex      the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
      * @param gridIndex                 the grid index
      */
-    void setTorsionTorsionParameters( int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex );
+    void setTorsionTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex);
 
     /**
      * Get the torsion-torsion grid at the specified index
-     * 
+     *
      * @param gridIndex     the grid index
      * @return grid         return grid reference
      */
-    //const TorsionTorsionGrid& getTorsionTorsionGrid( int index ) const;
-    const std::vector< std::vector< std::vector<double> > >& getTorsionTorsionGrid( int index ) const;
+    const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const;
 
     /**
      * Set the torsion-torsion grid at the specified index
-     * 
-     * @param index         the index of the torsionTorsion for which to get parameters
+     *
+     * @param index         the index of the torsion-torsion for which to get parameters
      * @param grid          grid
-     *                         grid[x][y][0] = x value 
-     *                         grid[x][y][1] = y value 
-     *                         grid[x][y][2] = function value 
-     *                         grid[x][y][3] = dfdx value 
-     *                         grid[x][y][4] = dfdy value 
-     *                         grid[x][y][5] = dfd(xy) value 
+     *                         grid[x][y][0] = x value
+     *                         grid[x][y][1] = y value
+     *                         grid[x][y][2] = function value
+     *                         grid[x][y][3] = dfdx value
+     *                         grid[x][y][4] = dfdy value
+     *                         grid[x][y][5] = dfd(xy) value
      */
-    //void setTorsionTorsionGrid(int index, TorsionTorsionGrid& grid );
-    void setTorsionTorsionGrid(int index, const std::vector< std::vector< std::vector<double> > >& grid );
+    void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
 
 protected:
     ForceImpl* createImpl();
 private:
-
     class TorsionTorsionInfo;
     class TorsionTorsionGridInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<TorsionTorsionInfo> torsionTorsions;
     std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
@@ -170,10 +156,10 @@ public:
         particle1 = particle2  = particle3 = particle4 = particle5 = chiralCheckAtomIndex = -1;
         gridIndex = 0;
     }
-    TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex ) :
+    TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) :
                        particle1(particle1), particle2(particle2), particle3(particle3),
                        particle4(particle4), particle5(particle5), gridIndex(gridIndex), chiralCheckAtomIndex(chiralCheckAtomIndex) {
-     
+
     }
 };
 
@@ -181,37 +167,28 @@ class AmoebaTorsionTorsionForce::TorsionTorsionGridInfo {
 
 public:
 
-    TorsionTorsionGridInfo( ) {
+    TorsionTorsionGridInfo() {
         _size[0]        = _size[1]        = 0;
         _startValues[0] = _startValues[1] = 0.0;
         _spacing[0]     = _spacing[1]     = 1.0;
     }
 
-    TorsionTorsionGridInfo( const TorsionTorsionGrid& grid ) {
+    TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
 
-        _grid.resize( grid.size() );
-        for( unsigned int kk = 0; kk < grid.size(); kk++ ){
-            _grid[kk].resize( grid[kk].size() );
-            for( unsigned int jj = 0; jj < grid[kk].size(); jj++ ){
-                _grid[kk][jj].resize( grid[kk][jj].size() );
-                for( unsigned int ii = 0; ii < grid[kk][jj].size(); ii++ ){
+        _grid.resize(grid.size());
+        for(unsigned int kk = 0; kk < grid.size(); kk++){
+            _grid[kk].resize(grid[kk].size());
+            for(unsigned int jj = 0; jj < grid[kk].size(); jj++){
+                _grid[kk][jj].resize(grid[kk][jj].size());
+                for(unsigned int ii = 0; ii < grid[kk][jj].size(); ii++){
                     _grid[kk][jj][ii] = grid[kk][jj][ii];
                 }
             }
-        }   
-/*
-        for( unsigned int kk = 0; kk < grid.size(); kk++ ){
-            for( unsigned int jj = 0; jj < grid[kk].size(); jj++ ){
-                fprintf( stderr, "xGrid %4d %4d %12.3f %12.3f  %15.7e  %15.7e\n", kk, jj,  grid[kk][jj][0], grid[kk][jj][1], grid[kk][jj][2], grid[kk][jj][2]/4.184 );
-            }
         }
-*/
 
         _startValues[0] =  _grid[0][0][0];
         _startValues[1] =  _grid[0][0][1];
 
-        //_spacing[0]     =  fabs( _grid[1][0][0] - _grid[0][0][0] );
-        //_spacing[1]     =  fabs( _grid[0][1][1] - _grid[0][0][1] );
         _spacing[0]     = static_cast<double>(_grid.size()-1)/360.0;
         _spacing[1]     = static_cast<double>(grid.size()-1)/360.0;
 
@@ -220,16 +197,16 @@ public:
 
     }
 
-    const TorsionTorsionGrid& getTorsionTorsionGrid( void ) const {
+    const TorsionTorsionGrid& getTorsionTorsionGrid(void) const {
         return _grid;
     }
-    int getDimensionSize( int index ) const {
+    int getDimensionSize(int index) const {
         return _size[index];
     }
-    double getStartValue( int index ) const {
+    double getStartValue(int index) const {
         return _startValues[index];
     }
-    double getSpacing( int index ) const {
+    double getSpacing(int index) const {
         return _spacing[index];
     }
 

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

-#ifndef OPENMM_AMOEBA_UREY_BRADLEY_FORCE_H_
-#define OPENMM_AMOEBA_UREY_BRADLEY_FORCE_H_
-
-/* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
- * -------------------------------------------------------------------------- *
- * 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:                                                                   *
- * 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/Vec3.h"
-#include "openmm/internal/windowsExport.h"
-
-#include <map>
-#include <vector>
-
-namespace OpenMM {
-
-/**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a AmoebaUreyBradleyForce object then call addUreyBradley() once for each bond.  After
- * a bond has been added, you can modify its force field parameters by calling setUreyBradleyParameters().
- */
-
-class OPENMM_EXPORT AmoebaUreyBradleyForce : public Force {
-
-public:
-
-    /**
-     * Create a Amoeba UreyBradleyForce.
-     */
-    AmoebaUreyBradleyForce();
-    /**
-     * Get the number of UB terms in the potential function
-     */
-    int getNumInteractions() const {
-        return bonds.size();
-    }
-
-    /**
-     * Set the global cubic term
-     * 
-     * @param cubicK      the cubic force constant
-     */
-    void setAmoebaGlobalUreyBradleyCubic( double cubicK );
-
-    /**
-     * Get the global cubic term
-     * 
-     * @return global cubicK term
-     */
-    double getAmoebaGlobalUreyBradleyCubic( void ) const;
-
-    /**
-     * Set the global cubic term
-     * 
-     * @param quarticK  the quartic force constant
-     */
-    void setAmoebaGlobalUreyBradleyQuartic( double quarticK );
-
-    /**
-     * Get the global quartic term
-     * 
-     * @return global  quartic term
-     */
-    double getAmoebaGlobalUreyBradleyQuartic( void ) const;
-
-    /**
-     * Add a UB term to the force field.
-     *
-     * @param particle1     the index of the first particle 
-     * @param particle2     the index of the second particle
-     * @param length        the equilibrium length, measured in nm
-     * @param k             the quadratic harmonic force constant 
-     * @return the index of the bond that was added
-     */
-
-    int addUreyBradley(int particle1, int particle2, double length, double quadraticK );
-
-    /**
-     * Get the force field parameters for a bond term.
-     * 
-     * @param index         the index of the ixn for which to get parameters
-     * @param particle1     the index of the first particle
-     * @param particle2     the index of the second particle
-     * @param length        the equilibrium distance, measured in nm
-     * @param quadratic k   the quadratic harmonic force constant
-     */
-
-    void getUreyBradleyParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
-
-    /**
-     * Set the force field parameters for a UB term.
-     * 
-     * @param index     the index of the ixn for which to set parameters
-     * @param particle1 the index of the first particle
-     * @param particle2 the index of the second particle
-     * @param length    the equilibrium distance, measured in nm
-     * @param k         the quadratic harmonic force constant for the bond
-     */
-    void setUreyBradleyParameters(int index, int particle1, int particle2, double length, double quadraticK );
-
-protected:
-    double _globalQuarticK, _globalCubicK;
-    ForceImpl* createImpl();
-private:
-
-    class UreyBradleyInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
-    std::vector<UreyBradleyInfo> bonds;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
-};
-
-class AmoebaUreyBradleyForce::UreyBradleyInfo {
-public:
-    int particle1, particle2;
-    double length, quadraticK;
-    UreyBradleyInfo() {
-        particle1 = particle2    = -1;
-        length    = quadraticK   = 0.0;
-    }
-    UreyBradleyInfo(int particle1, int particle2, double length, double  quadraticK ) :
-        particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
-    }
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_AMOEBA_UREY_BRADLEY_FORCE_H_*/

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,17 +39,38 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a VdwForce object then call addAngle() once for each angle.  After
- * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
+ * This class implements a buffered 14-7 potential used to model van der Waals forces.
+ * 
+ * To use it, create an AmoebaVdwForce object then call addParticle() once for each particle.  After
+ * a particle has been added, you can modify its force field parameters by calling setParticleParameters().
+ * 
+ * A unique feature of this class is that the interaction site for a particle does not need to be
+ * exactly at the particle's location.  Instead, it can be placed a fraction of the distance from that
+ * particle to another one.  This is typically done for hydrogens to place the interaction site slightly
+ * closer to the parent atom.  The fraction is known as the "reduction factor", since it reduces the distance
+ * from the parent atom to the interaction site.
  */
 
 class OPENMM_EXPORT AmoebaVdwForce : 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,
+        /**
+         * 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 = 1,
+    };
 
     /**
-     * Create a Amoeba VdwForce.
+     * Create an Amoeba VdwForce.
      */
     AmoebaVdwForce();
 
@@ -64,73 +85,69 @@ public:
      * Set the force field parameters for a vdw particle.
      * 
      * @param particleIndex   the particle index
-     * @param ivIndex         the iv index
-     * @param classIndex      the class index into the sig-eps table
+     * @param parentIndex     the index of the parent particle
      * @param sigma           vdw sigma
      * @param epsilon         vdw epsilon
-     * @param reductionFactor the reduction factor 
+     * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
+     *                        at which the interaction site should be placed
      */
-    void setParticleParameters(int particleIndex, int ivIndex, int classIndex,
-                               double sigma, double epsilon, double reductionFactor );
+    void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
 
     /**
      * Get the force field parameters for a vdw particle.
      * 
      * @param particleIndex   the particle index
-     * @param ivIndex         the iv index
-     * @param classIndex      the class index into the sig-eps table
+     * @param parentIndex     the index of the parent particle
      * @param sigma           vdw sigma
      * @param epsilon         vdw epsilon
-     * @param reductionFactor the reduction factor 
+     * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
+     *                        at which the interaction site should be placed
      */
-    void getParticleParameters(int particleIndex, int& ivIndex, int& classIndex,
-                               double& sigma, double& epsilon, double& reductionFactor ) const;
+    void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
 
 
     /**
-     * Set the force field parameters for a vdw particle.
+     * Add the force field parameters for a vdw particle.
      * 
-     * @param particleIndex   the particle index
-     * @param ivIndex         the iv index
-     * @param classIndex      the class index into the sig-eps table
+     * @param parentIndex     the index of the parent particle
      * @param sigma           vdw sigma
      * @param epsilon         vdw epsilon
-     * @param reductionFactor the reduction factor
+     * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
+     *                        at which the interaction site should be placed
      * @return index of added particle
      */
-    int addParticle(int ivIndex, int classIndex, 
-                    double sigma, double epsilon, double reductionFactor );
+    int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
 
     /**
      * Set sigma combining rule
      * 
      * @param sigmaCombiningRule   sigma combining rule:  'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
      */
-    void setSigmaCombiningRule( const std::string& sigmaCombiningRule );
+    void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
 
     /**
      * Get sigma combining rule
      * 
      * @return sigmaCombiningRule   sigma combining rule:  'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
      */
-    const std::string& getSigmaCombiningRule( void ) const;
+    const std::string& getSigmaCombiningRule(void) const;
 
     /**
      * Set epsilon combining rule
      * 
      * @param epsilonCombiningRule   epsilon combining rule:   'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
      */
-    void setEpsilonCombiningRule( const std::string& epsilonCombiningRule );
+    void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
 
     /**
      * Get epsilon combining rule
      * 
      * @return epsilonCombiningRule   epsilon combining rule:  'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
      */
-    const std::string& getEpsilonCombiningRule( void ) const;
+    const std::string& getEpsilonCombiningRule(void) const;
 
     /**
-     * LPW: Get whether to add a contribution to the energy that approximately represents the effect of VdW
+     * Get whether to add a contribution to the energy that approximately represents the effect of VdW
      * interactions beyond the cutoff distance.  The energy depends on the volume of the periodic box, and is only
      * applicable when periodic boundary conditions are used.  When running simulations at constant pressure, adding
      * this contribution can improve the quality of results.
@@ -153,67 +170,44 @@ public:
      * Set exclusions for specified particle
      * 
      * @param particleIndex particle index
-     * @param exclusions output vector of exclusions
+     * @param exclusions vector of exclusions
      */
-    void setParticleExclusions( int particleIndex, const std::vector< int >& exclusions );
+    void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);
 
     /**
      * Get exclusions for specified particle
      * 
      * @param particleIndex particle index
-     * @param exclusions output vector of exclusions
+     * @param exclusions vector of exclusions
      */
-    void getParticleExclusions( int particleIndex, std::vector< int >& exclusions ) const;
+    void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
 
     /**
-     * Set cutoff
-     * 
-     * @param cutoff cutoff
+     * Set the cutoff distance.
      */
-    void setCutoff( double cutoff );
+    void setCutoff(double cutoff);
 
     /**
-     * Get cutoff
-     * 
-     * @return cutoff
+     * Get the cutoff distance.
      */
-    double getCutoff( void ) const;
+    double getCutoff(void) const;
 
     /**
-     * Set flag for using neighbor list for vdw ixn
-     * 
-     * @param neighboristFlag neighbor list flag
+     * Get the method used for handling long range nonbonded interactions.
      */
-    void setUseNeighborList( int neighborListFlag );
+    NonbondedMethod getNonbondedMethod() const;
 
     /**
-     * Get neighbor list flag for vdw ixn
-     * 
-     * @return neighbor list flag
+     * Set the method used for handling long range nonbonded interactions.
      */
-    int getUseNeighborList( void ) const;
-
-    /**
-     * Set flag for employing periodic boundary conditions
-     * 
-     * @param pbcFlag if nonozero, use periodic boundary conditions
-     */
-    void setPBC( int pbcFlag );
-
-    /**
-     * Get periodic boundary conditions flag
-     * 
-     * @return periodic boundary conditions flag (nonzero -> use PBC)
-     */
-    int getPBC( void ) const;
+    void setNonbondedMethod(NonbondedMethod method);
 
 protected:
     ForceImpl* createImpl();
 private:
 
     class VdwInfo;
-    int usePBC;
-    int useNeighborList;
+    NonbondedMethod nonbondedMethod;
     double cutoff;
     bool useDispersionCorrection;
 
@@ -221,34 +215,22 @@ private:
     std::string epsilonCombiningRule;
 
     std::vector< std::vector<int> > exclusions;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<VdwInfo> parameters;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
     std::vector< std::vector< std::vector<double> > > sigEpsTable;
 };
 
 class AmoebaVdwForce::VdwInfo {
 public:
-    int ivIndex, classIndex;
+    int parentIndex;
     double reductionFactor, sigma, epsilon, cutoff;
     VdwInfo() {
-        ivIndex = classIndex = -1;
+        parentIndex = -1;
         reductionFactor      = 0.0;
         sigma                = 1.0;
         epsilon              = 0.0;
     }
-    VdwInfo(int ivIndex, int classIndex, double sigma, double epsilon, double  reductionFactor ) :
-        ivIndex(ivIndex), classIndex(classIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor)  {
+    VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
+        parentIndex(parentIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor)  {
     }
 };
 

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

@@ -9,8 +9,8 @@
  * 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:                                                                   *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Authors: Mark Friedrichs, Peter Eastman                                    *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -39,9 +39,11 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  To use it, create a WcaDispersionForce object then call addAngle() once for each angle.  After
- * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
+ * This class implements a nonbonded interaction between pairs of particles typically used along with
+ * AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model.
+ * 
+ * To use it, create an AmoebaWcaDispersionForce object then call addParticle() once for each particle.  After
+ * a particle has been added, you can modify its force field parameters by calling setParticleParameters().
  */
 
 class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
@@ -49,7 +51,7 @@ class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
 public:
 
     /**
-     * Create a Amoeba WcaDispersionForce.
+     * Create an AmoebaWcaDispersionForce.
      */
     AmoebaWcaDispersionForce();
 
@@ -61,16 +63,16 @@ public:
     }
 
     /**
-     * Set the force field parameters for a wca dispersion particle.
+     * Set the force field parameters for a WCA dispersion particle.
      * 
      * @param particleIndex   the particle index
      * @param radius          radius
      * @param epsilon         epsilon 
      */
-    void setParticleParameters(int particleIndex, double radius, double epsilon );
+    void setParticleParameters(int particleIndex, double radius, double epsilon);
 
     /**
-     * Get the force field parameters for a wca dispersion particle.
+     * Get the force field parameters for a WCA dispersion particle.
      * 
      * @param particleIndex   the particle index
      * @param radius          radius
@@ -79,42 +81,40 @@ public:
     void getParticleParameters(int particleIndex, double& radius, double& epsilon) const;
 
     /**
-     * Set the force field parameters for a wca dispersion particle.
+     * Set the force field parameters for a WCA dispersion particle.
      * 
      * @param radius          radius
      * @param epsilon         epsilon 
      * @return index of added particle
      */
-    int addParticle( double radius, double epsilon );
+    int addParticle(double radius, double epsilon);
 
     /* 
      * 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() const;
+    double getEpsh() const;
+    double getRmino() const;
+    double getRminh() const;
+    double getAwater() const;
+    double getShctd() const;
+    double getDispoff() const;
+    double getSlevy() 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();
 private:
-
     class WcaDispersionInfo;
-
     double epso;
     double epsh;
     double rmino;
@@ -123,19 +123,7 @@ private:
     double slevy;
     double shctd;
     double dispoff;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<WcaDispersionInfo> parameters;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 class AmoebaWcaDispersionForce::WcaDispersionInfo {
@@ -145,7 +133,7 @@ public:
         radius              = 1.0;
         epsilon             = 0.0;
     }
-    WcaDispersionInfo( double radius, double epsilon ) : radius(radius), epsilon(epsilon) {
+    WcaDispersionInfo(double radius, double epsilon) : radius(radius), epsilon(epsilon) {
     }
 };
 

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

@@ -77,37 +77,6 @@ public:
 
 };
 
-class CalcAmoebaUreyBradleyForceKernel : public KernelImpl {
-
-public:
-
-    static std::string Name() {
-        return "CalcAmoebaUreyBradleyForce";
-    }
-
-    CalcAmoebaUreyBradleyForceKernel(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 AmoebaUreyBradleyForce this kernel will be used for
-     */
-    virtual void initialize(const System& system, const AmoebaUreyBradleyForce& 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 AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
  */
@@ -174,39 +143,6 @@ public:
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
 };
 
-/**
- * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
- */
-class CalcAmoebaTorsionForceKernel : public KernelImpl {
-
-public:
-
-    static std::string Name() {
-        return "CalcAmoebaTorsionForce";
-    }
-
-    CalcAmoebaTorsionForceKernel(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 TorsionForce this kernel will be used for
-     */
-    virtual void initialize(const System& system, const AmoebaTorsionForce& 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 AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
@@ -374,7 +310,7 @@ public:
     virtual void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
                                             std::vector< double >& outputElectrostaticPotential ) = 0;
 
-    virtual void getSystemMultipoleMoments( ContextImpl& context, const Vec3& origin, std::vector< double >& outputMultipoleMonents ) = 0;
+    virtual void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMonents ) = 0;
 
 };
 

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

@@ -85,7 +85,7 @@ public:
     void getElectrostaticPotential( ContextImpl& context, const std::vector< Vec3 >& inputGrid,
                                     std::vector< double >& outputElectrostaticPotential );
 
-    void getSystemMultipoleMoments( ContextImpl& context, const Vec3& origin, std::vector< double >& outputMultipoleMonents );
+    void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMonents );
  
 
 private:

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaTorsionForceImpl.h

-#ifndef OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_
-#define OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_
-
-/* -------------------------------------------------------------------------- *
- *                                OpenMMAmoeba                                *
- * -------------------------------------------------------------------------- *
- * 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:                                                                   *
- * 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 "openmm/AmoebaTorsionForce.h"
-#include "openmm/Kernel.h"
-#include <utility>
-#include <set>
-#include <map>
-#include <string>
-
-namespace OpenMM {
-
-/**
- * This is the internal implementation of AmoebaTorsionForce.
- */
-
-class AmoebaTorsionForceImpl : public ForceImpl {
-public:
-    AmoebaTorsionForceImpl(AmoebaTorsionForce& owner);
-    ~AmoebaTorsionForceImpl();
-    void initialize(ContextImpl& context);
-    AmoebaTorsionForce& getOwner() {
-        return owner;
-    }
-    void updateContextState(ContextImpl& context) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
-    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:
-    AmoebaTorsionForce& owner;
-    Kernel kernel;
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_*/

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaUreyBradleyForceImpl.h

-#ifndef OPENMM_AMOEBA_UREY_BRADLEY_FORCE_IMPL_H_
-#define OPENMM_AMOEBA_UREY_BRADLEY_FORCE_IMPL_H_
-
-/* -------------------------------------------------------------------------- *
- *                                OpenMMAmoeba                                *
- * -------------------------------------------------------------------------- *
- * 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:                                                                   *
- * 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 "openmm/AmoebaUreyBradleyForce.h"
-#include "openmm/Kernel.h"
-#include <utility>
-#include <set>
-#include <string>
-
-namespace OpenMM {
-
-/**
- * This is the internal implementation of AmoebaUreyBradleyForce.
- */
-
-class AmoebaUreyBradleyForceImpl : public ForceImpl {
-public:
-    AmoebaUreyBradleyForceImpl(AmoebaUreyBradleyForce& owner);
-    ~AmoebaUreyBradleyForceImpl();
-    void initialize(ContextImpl& context);
-    AmoebaUreyBradleyForce& getOwner() {
-        return owner;
-    }
-    void updateContextState(ContextImpl& context) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
-    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:
-    AmoebaUreyBradleyForce& owner;
-    Kernel kernel;
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_AMOEBA_UREY_BRADLEY_FORCE_IMPL_H_*/

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -39,25 +39,25 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
-AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polarizationType(Mutual), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(1e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
+AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polarizationType(Mutual), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(1e-4), mutualInducedMaxIterations(60),
                                                mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), aewald(0.0) {
     pmeGridDimension.resize(3);
     pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
 }
 
-AmoebaMultipoleForce::AmoebaNonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
+AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
     return nonbondedMethod;
 }
 
-void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::AmoebaNonbondedMethod method) {
+void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMethod method) {
     nonbondedMethod = method;
 }
 
-AmoebaMultipoleForce::AmoebaPolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
+AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
     return polarizationType;
 }
 
-void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::AmoebaPolarizationType type ) {
+void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::PolarizationType type ) {
     polarizationType = type;
 }
 
@@ -230,8 +230,8 @@ void AmoebaMultipoleForce::getElectrostaticPotential( const std::vector< Vec3 >&
     dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getElectrostaticPotential(getContextImpl(context), inputGrid, outputElectrostaticPotential);
 }
 
-void AmoebaMultipoleForce::getSystemMultipoleMoments( const Vec3& origin, Context& context, std::vector< double >& outputMultipoleMonents ){
-    dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getSystemMultipoleMoments(getContextImpl(context), origin, outputMultipoleMonents);
+void AmoebaMultipoleForce::getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMonents ){
+    dynamic_cast<AmoebaMultipoleForceImpl&>(getImplInContext(context)).getSystemMultipoleMoments(getContextImpl(context), outputMultipoleMonents);
 }
 
 ForceImpl* AmoebaMultipoleForce::createImpl() {

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -188,7 +188,7 @@ void AmoebaMultipoleForceImpl::getElectrostaticPotential( ContextImpl& context,
     kernel.getAs<CalcAmoebaMultipoleForceKernel>().getElectrostaticPotential(context, inputGrid, outputElectrostaticPotential);
 }
 
-void AmoebaMultipoleForceImpl::getSystemMultipoleMoments( ContextImpl& context, const Vec3& origin, std::vector< double >& outputMultipoleMonents ){
-    kernel.getAs<CalcAmoebaMultipoleForceKernel>().getSystemMultipoleMoments(context, origin, outputMultipoleMonents);
+void AmoebaMultipoleForceImpl::getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMonents ){
+    kernel.getAs<CalcAmoebaMultipoleForceKernel>().getSystemMultipoleMoments(context, outputMultipoleMonents);
 }