Removed unused parameters

plugins/freeEnergy/serialization/src/FreeEnergyGBVISoftcoreProxy.cpp

@@ -50,11 +50,13 @@ void GBVISoftcoreForceProxy::serialize(const void* object, SerializationNode& no
     node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
     node.setDoubleProperty("quinticLwrLmtFctr", force.getQuinticLowerLimitFactor());
     node.setDoubleProperty("quinticUpprBrLmt", force.getQuinticUpperBornRadiusLimit());
+/*
     double alpha, beta, gamma;
     force.getTanhParameters( alpha, beta, gamma );
     node.setDoubleProperty("alphaT", alpha);
     node.setDoubleProperty("betaT", beta);
     node.setDoubleProperty("gammaT", gamma);
+*/
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge, radius, gamma, bornRadiusScaleFactor;
@@ -82,11 +84,13 @@ void* GBVISoftcoreForceProxy::deserialize(const SerializationNode& node) const {
         force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
         force->setQuinticLowerLimitFactor(node.getDoubleProperty("quinticLwrLmtFctr"));
         force->setQuinticUpperBornRadiusLimit(node.getDoubleProperty("quinticUpprBrLmt"));
+/*
         double alpha, beta, gamma;
         alpha  = node.getDoubleProperty("alphaT");
         beta   = node.getDoubleProperty("betaT");
         gamma  = node.getDoubleProperty("gammaT");
         force->setTanhParameters( alpha, beta, gamma );
+*/
         const SerializationNode& particles = node.getChildNode("Particles");
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {
             const SerializationNode& particle = particles.getChildren()[i];

plugins/freeEnergy/serialization/src/FreeEnergyNonbondedSoftcoreForceProxy.cpp

@@ -45,7 +45,7 @@ void NonbondedSoftcoreForceProxy::serialize(const void* object, SerializationNod
     const NonbondedSoftcoreForce& force = *reinterpret_cast<const NonbondedSoftcoreForce*>(object);
     node.setIntProperty("method", (int) force.getNonbondedMethod());
     node.setDoubleProperty("cutoff", force.getCutoffDistance());
-    node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
+    //node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
     node.setDoubleProperty("rfDielectric", force.getReactionFieldDielectric());
     //node.setIntProperty("dispersionCorrection", force.getUseDispersionCorrection());
     SerializationNode& particles = node.createChildNode("Particles");
@@ -64,13 +64,13 @@ void NonbondedSoftcoreForceProxy::serialize(const void* object, SerializationNod
 }
 
 void* NonbondedSoftcoreForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    if (node.getIntProperty("version") != 1 )
         throw OpenMMException("Unsupported version number");
     NonbondedSoftcoreForce* force = new NonbondedSoftcoreForce();
     try {
         force->setNonbondedMethod((NonbondedSoftcoreForce::NonbondedSoftcoreMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
+        //force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
         force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
         //force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
         const SerializationNode& particles = node.getChildNode("Particles");

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyGBVISoftcoreForce.cpp

@@ -49,7 +49,7 @@ void testSerialization() {
     force.setSolventDielectric(50.0);
     force.setQuinticLowerLimitFactor(0.1);
     force.setQuinticUpperBornRadiusLimit(5.1);
-    force.setTanhParameters(5.1, 4.2, 1.3);
+    //force.setTanhParameters(5.1, 4.2, 1.3);
     
     force.addParticle(1, 0.1, 0.01, 0.1);
     force.addParticle(0.5, 0.2, 0.02, 0.2);
@@ -73,6 +73,7 @@ void testSerialization() {
     ASSERT_EQUAL(force.getQuinticLowerLimitFactor(), force2.getQuinticLowerLimitFactor());
     ASSERT_EQUAL(force.getQuinticUpperBornRadiusLimit(), force2.getQuinticUpperBornRadiusLimit());
     ASSERT_EQUAL(force.getBornRadiusScalingMethod(), force2.getBornRadiusScalingMethod());
+/*
     double alpha1, beta1, gamma1;
     double alpha2, beta2, gamma2;
     force.getTanhParameters( alpha1, beta1, gamma1 );
@@ -80,6 +81,7 @@ void testSerialization() {
     ASSERT_EQUAL(alpha1, alpha2);
     ASSERT_EQUAL(beta1, beta2);
     ASSERT_EQUAL(gamma1, gamma2);
+*/
     ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge1, radius1, scale1, bornRadiusScaleFactor1;

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyNonbondedSoftcoreForce.cpp

@@ -45,7 +45,7 @@ void testSerialization() {
     NonbondedSoftcoreForce force;
     force.setNonbondedMethod(NonbondedSoftcoreForce::CutoffPeriodic);
     force.setCutoffDistance(2.0);
-    force.setEwaldErrorTolerance(1e-3);
+    //force.setEwaldErrorTolerance(1e-3);
     force.setReactionFieldDielectric(50.0);
     //force.setUseDispersionCorrection(false);
     force.addParticle(1, 0.1, 0.01);
@@ -65,7 +65,7 @@ void testSerialization() {
     NonbondedSoftcoreForce& force2 = *copy;
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
-    ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
+    //ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
     ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
     //ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
     ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());