Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods...

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods exposed in the OpenMM API; implemented the getDefaultParameters() on the AmoebaVdwForceImpl to return 1.0 for AmoebaVdwAlpha; Use AmoebaVdwForce::Lambda() to refer to this parameter rather than the String AmoebaVdwAlpha

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

@@ -258,12 +258,12 @@ public:
     /**
      * Set the softcore power on lambda (default = 5).
      */
-    void setSoftcorePower(double n);
+    void setSoftcorePower(int n);
 
     /**
      * Get the softcore power on lambda.
      */
-    double getSoftcorePower() const;
+    int getSoftcorePower() const;
 
     /**
      * Set the softcore alpha value (default = 0.7).

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

@@ -60,7 +60,9 @@ public:
     }
     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::map<std::string, double> parameters;
+       parameters[AmoebaVdwForce::Lambda()] = 1.0;
+       return parameters;
     }
     std::vector<std::string> getKernelNames();
     /**

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -140,11 +140,11 @@ void AmoebaVdwForce::setAlchemicalMethod(AlchemicalMethod method) {
     alchemicalMethod = method;
 }
 
-void AmoebaVdwForce::setSoftcorePower(double power) {
+void AmoebaVdwForce::setSoftcorePower(int power) {
     n = power;
 }
 
-double AmoebaVdwForce::getSoftcorePower() const {
+int AmoebaVdwForce::getSoftcorePower() const {
     return n;
 }
 

plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp

@@ -260,3 +260,5 @@ std::vector<std::string> AmoebaVdwForceImpl::getKernelNames() {
 void AmoebaVdwForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcAmoebaVdwForceKernel>().copyParametersToContext(context, owner);
 }
+
+

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

@@ -1059,7 +1059,7 @@ double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool inc
     vector<Vec3>& forceData = extractForces(context);
     AmoebaReferenceVdwForce vdwForce(sigmaCombiningRule, epsilonCombiningRule);
     double energy;
-    double lambda = context.getParameter("AmoebaVdwLambda");
+    double lambda = context.getParameter(AmoebaVdwForce::Lambda());
     if (useCutoff) {
         vdwForce.setCutoff(cutoff);
         computeNeighborListVoxelHash(*neighborList, numParticles, posData, allExclusions, extractBoxVectors(context), usePBC, cutoff, 0.0);

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -309,15 +309,14 @@ UNITS = {
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionParameters")                   :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionGrid")                         :  ( None, ()),
 
-# LPW 2012-10 : Is this a duplicate entry?
-#("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
 ("AmoebaVdwForce",                        "getSigmaCombiningRule")                         :  ( None, ()),
 ("AmoebaVdwForce",                        "getEpsilonCombiningRule")                       :  ( None, ()),
 ("AmoebaVdwForce",                        "getParticleExclusions")                         :  ( None, ()),
+("AmoebaVdwForce",                        "getAlchemicalMethod")                           :  ( None, ()),
+("AmoebaVdwForce",                        "getSoftcorePower")                              :  ( None, ()),
+("AmoebaVdwForce",                        "getSoftcoreAlpha")                              :  ( None, ()),
 ("AmoebaVdwForce",                        "getCutoff")                                     :  ( 'unit.nanometer', ()),
-# LPW 2012-10 Modified because it no longer returns ivIndex and classIndex.
-# ("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
-("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
+("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, 'unit.nanometer', 'unit.kilojoule_per_mole', None, None)),
 
 ("AmoebaWcaDispersionForce",              "getParticleParameters")                         :  ( None, ('unit.nanometer', 'unit.kilojoule_per_mole')),
 ("AmoebaWcaDispersionForce",              "getAwater")                                     :  ( '1/(unit.nanometer*unit.nanometer*unit.nanometer)',()),