Merge pull request #2115 from peastman/offsetxml

Serialization of parameter offsets

serialization/src/NonbondedForceProxy.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,7 +42,7 @@ NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce"
 }
 
 void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
@@ -65,6 +65,22 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
     node.setIntProperty("ljny", ny);
     node.setIntProperty("ljnz", nz);
     node.setIntProperty("recipForceGroup", force.getReciprocalSpaceForceGroup());
+    SerializationNode& particleOffsets = node.createChildNode("ParticleOffsets");
+    for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
+        int particle;
+        double chargeScale, sigmaScale, epsilonScale;
+        string parameter;
+        force.getParticleParameterOffset(i, parameter, particle, chargeScale, sigmaScale, epsilonScale);
+        particleOffsets.createChildNode("Offset").setStringProperty("parameter", parameter).setIntProperty("particle", particle).setDoubleProperty("q", chargeScale).setDoubleProperty("sig", sigmaScale).setDoubleProperty("eps", epsilonScale);
+    }
+    SerializationNode& exceptionOffsets = node.createChildNode("ExceptionOffsets");
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        int exception;
+        double chargeProdScale, sigmaScale, epsilonScale;
+        string parameter;
+        force.getExceptionParameterOffset(i, parameter, exception, chargeProdScale, sigmaScale, epsilonScale);
+        exceptionOffsets.createChildNode("Offset").setStringProperty("parameter", parameter).setIntProperty("exception", exception).setDoubleProperty("q", chargeProdScale).setDoubleProperty("sig", sigmaScale).setDoubleProperty("eps", epsilonScale);
+    }
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge, sigma, epsilon;
@@ -82,7 +98,7 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
 
 void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version < 1 || version > 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     NonbondedForce* force = new NonbondedForce();
     try {
@@ -107,6 +123,14 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
             force->setLJPMEParameters(alpha, nx, ny, nz);
         }
         force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
+        if (version >= 3) {
+            const SerializationNode& particleOffsets = node.getChildNode("ParticleOffsets");
+            for (auto& offset : particleOffsets.getChildren())
+                force->addParticleParameterOffset(offset.getStringProperty("parameter"), offset.getIntProperty("particle"), offset.getDoubleProperty("q"), offset.getDoubleProperty("sig"), offset.getDoubleProperty("eps"));
+            const SerializationNode& exceptionOffsets = node.getChildNode("ExceptionOffsets");
+            for (auto& offset : exceptionOffsets.getChildren())
+                force->addExceptionParameterOffset(offset.getStringProperty("parameter"), offset.getIntProperty("exception"), offset.getDoubleProperty("q"), offset.getDoubleProperty("sig"), offset.getDoubleProperty("eps"));
+        }
         const SerializationNode& particles = node.getChildNode("Particles");
         for (auto& particle : particles.getChildren())
             force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"));

serialization/tests/TestSerializeNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -61,6 +61,8 @@ void testSerialization() {
     force.addParticle(-0.5, 0.3, 0.03);
     force.addException(0, 1, 2, 0.5, 0.1);
     force.addException(1, 2, 0.2, 0.4, 0.2);
+    force.addParticleParameterOffset("scale1", 2, 1.5, 2.0, 2.5);
+    force.addExceptionParameterOffset("scale2", 1, -0.1, -0.2, -0.3);
 
     // Serialize and then deserialize it.
 
@@ -80,6 +82,9 @@ void testSerialization() {
     ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
     ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
     ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
+    ASSERT_EQUAL(force.getNumParticleParameterOffsets(), force2.getNumParticleParameterOffsets());
+    ASSERT_EQUAL(force.getNumExceptionParameterOffsets(), force2.getNumExceptionParameterOffsets());
     double alpha2;
     int nx2, ny2, nz2;
     force2.getPMEParameters(alpha2, nx2, ny2, nz2);
@@ -94,6 +99,32 @@ void testSerialization() {
     ASSERT_EQUAL(dnx, dnx2);
     ASSERT_EQUAL(dny, dny2);
     ASSERT_EQUAL(dnz, dnz2);    
+    for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
+        int index1, index2;
+        string param1, param2;
+        double charge1, sigma1, epsilon1;
+        double charge2, sigma2, epsilon2;
+        force.getParticleParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
+        force2.getParticleParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
+        ASSERT_EQUAL(index1, index1);
+        ASSERT_EQUAL(param1, param2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+    }
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        int index1, index2;
+        string param1, param2;
+        double charge1, sigma1, epsilon1;
+        double charge2, sigma2, epsilon2;
+        force.getExceptionParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
+        force2.getExceptionParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
+        ASSERT_EQUAL(index1, index1);
+        ASSERT_EQUAL(param1, param2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+    }
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge1, sigma1, epsilon1;
         double charge2, sigma2, epsilon2;