Proof of concept API changes to support softcore AMOEBA vdW interactions

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

@@ -70,6 +70,21 @@ public:
         CutoffPeriodic = 1,
     };
 
+    /**
+     * This is an enumeration of the different alchemical methods used when applying softcore interactions.
+     */
+    enum AlchemicalMethod {
+        /**
+         * Maintain full strength vdW interactions between two alchemical particles. This is the default.
+         */
+        Decouple = 0,
+        /**
+         * Interactions between two alchemical particles are turned off at lambda=0.
+         */
+        Annihilate = 1,
+    };
+
+
     /**
      * Create an Amoeba VdwForce.
      */
@@ -91,8 +106,9 @@ public:
      * @param epsilon         vdw epsilon
      * @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
+     * @param isAlchemical    if true, this vdW particle is undergoing an alchemical change.
      */
-    void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
+    void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical);
 
     /**
      * Get the force field parameters for a vdw particle.
@@ -103,8 +119,11 @@ public:
      * @param[out] epsilon         vdw epsilon
      * @param[out] reductionFactor the fraction of the distance along the line from the parent particle to this particle
      *                             at which the interaction site should be placed
+     * @param[out] isAlchemical    if true, this vdW particle is undergoing an alchemical change.
      */
-    void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
+     */
+    void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, 
+                               double& reductionFactor, bool& isAlchemical) const;
 
 
     /**
@@ -115,9 +134,10 @@ public:
      * @param epsilon         vdw epsilon
      * @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
+     * @param isAlchemical    if true, this vdW particle is undergoing an alchemical change.
      * @return index of added particle
      */
-    int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
+    int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical);
 
     /**
      * Set sigma combining rule
@@ -223,6 +243,47 @@ public:
      * Set the method used for handling long range nonbonded interactions.
      */
     void setNonbondedMethod(NonbondedMethod method);
+
+    /**
+     * Set the vdw Lambda value.
+     */
+    void setLambda(double lambda);
+
+    /**
+     * Get the vdw Lambda value.
+     */
+    double getLambda() const;
+
+    /**
+     * Set the softcore power on lambda.
+     */
+    void setN(double n);
+
+    /**
+     * Get the softcore power on lambda.
+     */
+    double getN() const;
+
+    /**
+     * Set the softcore alpha value.
+     */
+    void setAlpha(double alpha);
+
+    /**
+     * Get the softcore alpha value.
+     */
+    double getAlpha() const;
+
+    /**
+     * Get the method used for alchemical interactions.
+     */
+    AlchemicalMethod getAlchemicalMethod() const;
+
+    /**
+     * Set the method used for handling long range nonbonded interactions.
+     */
+    void setAlchemicalMethod(AlchemicalMethod method);
+
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
@@ -250,6 +311,9 @@ private:
     NonbondedMethod nonbondedMethod;
     double cutoff;
     bool useDispersionCorrection;
+    double amoebaVdwLambda;
+    int n;
+    double alpha;
 
     std::string sigmaCombiningRule;
     std::string epsilonCombiningRule;
@@ -267,14 +331,16 @@ class AmoebaVdwForce::VdwInfo {
 public:
     int parentIndex;
     double reductionFactor, sigma, epsilon, cutoff;
+    bool isAlchemical;
     VdwInfo() {
         parentIndex = -1;
         reductionFactor      = 0.0;
         sigma                = 1.0;
         epsilon              = 0.0;
+        isAlchemical         = false;
     }
-    VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
-        parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon)  {
+    VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical) :
+        parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon), isAlchemical(isAlchemical)  {
     }
 };