Added name property to Forces (#3049)

openmmapi/include/openmm/Force.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "internal/windowsExport.h"
+#include <string>
 
 namespace OpenMM {
 
@@ -78,6 +79,16 @@ public:
      * @param group    the group index.  Legal values are between 0 and 31 (inclusive).
      */
     void setForceGroup(int group);
+    /**
+     * Get the name of this Force.  This is an arbitrary, user modifiable identifier.
+     * By default it equals the class name, but you can change it to anything useful.
+     */
+    const std::string& getName() const;
+    /**
+     * Set the name of this Force.  This is an arbitrary, user modifiable identifier.
+     * By default it equals the class name, but you can change it to anything useful.
+     */
+    void setName(const std::string& name);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions. This method should be overridden for all Force subclasses, or
@@ -108,6 +119,7 @@ protected:
     ContextImpl& getContextImpl(Context& context);
 private:
     int forceGroup;
+    std::string name;
 };
 
 } // namespace OpenMM

openmmapi/src/Force.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) 2012 Stanford University and the Authors.           *
+ * Portions copyright (c) 2012-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,6 +34,7 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/ForceImpl.h"
+#include "openmm/serialization/SerializationProxy.h"
 #include <vector>
 
 using namespace OpenMM;
@@ -49,6 +50,28 @@ void Force::setForceGroup(int group) {
     forceGroup = group;
 }
 
+const string& Force::getName() const {
+    if (name.size() == 0) {
+        // The name hasn't been set yet, so initialize it to the class name.  We first
+        // try to use a SerializationProxy to get the name.  If none is registered,
+        // we use the mangled name generated by the compiler.  (We can't do this in the
+        // constructor, because typeid() doesn't work properly in constructors.)
+
+        Force& thisRef = *const_cast<Force*>(this);
+        try {
+            thisRef.name = SerializationProxy::getProxy(typeid(*this)).getTypeName();
+        }
+        catch (...) {
+            thisRef.name = typeid(*this).name();
+        }
+    }
+    return name;
+}
+
+void Force::setName(const string& name) {
+    this->name = name;
+}
+
 bool Force::usesPeriodicBoundaryConditions() const {
     throw OpenMMException("usesPeriodicBoundaryConditions is not implemented");
 }

plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp

@@ -46,6 +46,7 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
     const AmoebaGeneralizedKirkwoodForce& force = *reinterpret_cast<const AmoebaGeneralizedKirkwoodForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric());
     node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric",  force.getSoluteDielectric());
     //node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset",  force.getDielectricOffset());
@@ -68,8 +69,8 @@ void* AmoebaGeneralizedKirkwoodForceProxy::deserialize(const SerializationNode&
         throw OpenMMException("Unsupported version number");
     AmoebaGeneralizedKirkwoodForce* force = new AmoebaGeneralizedKirkwoodForce();
     try {
-        if (version > 1)
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setSolventDielectric(  node.getDoubleProperty("GeneralizedKirkwoodSolventDielectric"));
         force->setSoluteDielectric(   node.getDoubleProperty("GeneralizedKirkwoodSoluteDielectric"));
         //force->setDielectricOffset(   node.getDoubleProperty("GeneralizedKirkwoodDielectricOffset"));

plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp

@@ -72,6 +72,7 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
     const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setIntProperty("nonbondedMethod",                  force.getNonbondedMethod());
     node.setIntProperty("polarizationType",                 force.getPolarizationType());
     node.setIntProperty("mutualInducedMaxIterations",       force.getMutualInducedMaxIterations());
@@ -137,8 +138,8 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
     AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
 
     try {
-        if (version > 3)
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
         if (version >= 2)
             force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp

@@ -66,6 +66,7 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
     node.setIntProperty("version", 3);
     const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
 
     // grid[xIdx][yIdx][6 values]
@@ -123,8 +124,8 @@ void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node)
 
     AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
     try {
-        if (version > 1)
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         if (version > 2)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& grids                    = node.getChildNode("TorsionTorsionGrids");

plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp

@@ -47,6 +47,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
     bool useTypes = force.getUseParticleTypes();
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
     node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
     node.setDoubleProperty("VdwCutoff", force.getCutoffDistance());
@@ -101,8 +102,8 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     AmoebaVdwForce* force = new AmoebaVdwForce();
     try {
-        if (version > 1)
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
         force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
         force->setCutoffDistance(node.getDoubleProperty("VdwCutoff"));

plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp

@@ -45,6 +45,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
     node.setIntProperty("version", 2);
     const AmoebaWcaDispersionForce& force = *reinterpret_cast<const AmoebaWcaDispersionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setDoubleProperty("Epso",    force.getEpso());
     node.setDoubleProperty("Epsh",    force.getEpsh());
     node.setDoubleProperty("Rmino",   force.getRmino());
@@ -70,8 +71,8 @@ void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node)
     AmoebaWcaDispersionForce* force = new AmoebaWcaDispersionForce();
 
     try {
-        if (version > 1)
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setEpso(   node.getDoubleProperty("Epso"));
         force->setEpsh(   node.getDoubleProperty("Epsh"));
         force->setRmino(  node.getDoubleProperty("Rmino"));

plugins/amoeba/serialization/src/HippoNonbondedForceProxy.cpp

@@ -46,6 +46,7 @@ void HippoNonbondedForceProxy::serialize(const void* object, SerializationNode&
     const HippoNonbondedForce& force = *reinterpret_cast<const HippoNonbondedForce*>(object);
 
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
     node.setDoubleProperty("cutoffDistance", force.getCutoffDistance());
     node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
@@ -122,6 +123,7 @@ void* HippoNonbondedForceProxy::deserialize(const SerializationNode& node) const
     HippoNonbondedForce* force = new HippoNonbondedForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setNonbondedMethod(static_cast<HippoNonbondedForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
         force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
         force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));

plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaGeneralizedKirkwoodForce force1;
     force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.setSolventDielectric(  80.0);
     force1.setSoluteDielectric(   1.0);
     //force1.setDielectricOffset(   0.09);
@@ -66,6 +67,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaGeneralizedKirkwoodForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getSolventDielectric(),    force2.getSolventDielectric());
     ASSERT_EQUAL(force1.getSoluteDielectric(),     force2.getSoluteDielectric());
     //ASSERT_EQUAL(force1.getDielectricOffset(),     force2.getDielectricOffset());

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp

@@ -60,6 +60,7 @@ void testSerialization() {
 
     AmoebaMultipoleForce force1;
     force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
     force1.setCutoffDistance(0.9);
     force1.setAEwald(0.544);
@@ -111,6 +112,7 @@ void testSerialization() {
     AmoebaMultipoleForce& force2 = *copy;
 
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getCutoffDistance(),                force2.getCutoffDistance());
     ASSERT_EQUAL(force1.getNonbondedMethod(),               force2.getNonbondedMethod());
     ASSERT_EQUAL(force1.getAEwald(),                        force2.getAEwald());

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -82,6 +82,7 @@ void testSerialization() {
     AmoebaTorsionTorsionForce force1;
 
     force1.setForceGroup(3);
+    force1.setName("custom name");
     for (unsigned int ii = 0; ii < 5; ii++) {
         std::vector< std::vector< std::vector<double> > > gridVector;
         loadTorsionTorsionGrid(gridVector);
@@ -102,6 +103,7 @@ void testSerialization() {
 
     AmoebaTorsionTorsionForce & force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force1.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsions()); ii++) {

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaVdwForce force1;
     force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.setSigmaCombiningRule("GEOMETRIC");
     force1.setEpsilonCombiningRule("GEOMETRIC");
     force1.setCutoff(0.9);
@@ -74,6 +75,7 @@ void testSerialization() {
     AmoebaVdwForce& force2 = *copy;
 
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getSigmaCombiningRule(),    force2.getSigmaCombiningRule());
     ASSERT_EQUAL(force1.getEpsilonCombiningRule(),  force2.getEpsilonCombiningRule());
     ASSERT_EQUAL(force1.getCutoff(),                force2.getCutoff());

plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp

@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaWcaDispersionForce force1;
     force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.setEpso(   1.0);
     force1.setEpsh(   1.1);
     force1.setRmino(  1.2);
@@ -70,6 +71,7 @@ void testSerialization() {
     AmoebaWcaDispersionForce& force2 = *copy;
 
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getEpso(),    force2.getEpso());
     ASSERT_EQUAL(force1.getEpsh(),    force2.getEpsh());
     ASSERT_EQUAL(force1.getRmino(),   force2.getRmino());

plugins/amoeba/serialization/tests/TestSerializeHippoNonbondedForce.cpp

@@ -48,6 +48,7 @@ void testSerialization() {
 
     HippoNonbondedForce force1;
     force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.setNonbondedMethod(HippoNonbondedForce::PME);
     force1.setCutoffDistance(0.7);
     force1.setSwitchingDistance(0.6);
@@ -79,6 +80,7 @@ void testSerialization() {
 
     HippoNonbondedForce& force2 = *copy;
     ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force1.getCutoffDistance(), force2.getCutoffDistance());
     ASSERT_EQUAL(force1.getSwitchingDistance(), force2.getSwitchingDistance());

plugins/drude/serialization/src/DrudeForceProxy.cpp

@@ -44,6 +44,8 @@ DrudeForceProxy::DrudeForceProxy() : SerializationProxy("DrudeForce") {
 void DrudeForceProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const DrudeForce& force = *reinterpret_cast<const DrudeForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
         int p, p1, p2, p3, p4;
@@ -66,6 +68,8 @@ void* DrudeForceProxy::deserialize(const SerializationNode& node) const {
         throw OpenMMException("Unsupported version number");
     DrudeForce* force = new DrudeForce();
     try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         const SerializationNode& particles = node.getChildNode("Particles");
         for (auto& particle : particles.getChildren())
             force->addParticle(particle.getIntProperty("p"), particle.getIntProperty("p1"), particle.getIntProperty("p2"), particle.getIntProperty("p3"), particle.getIntProperty("p4"),

plugins/drude/serialization/tests/TestSerializeDrudeForce.cpp

@@ -45,6 +45,8 @@ void testSerialization() {
     // Create a Force.
 
     DrudeForce force1;
+    force1.setForceGroup(3);
+    force1.setName("custom name");
     force1.addParticle(0, 1, 2, 3, 4, 0.5, 1.0, 1.5, 2.0);
     force1.addParticle(2, 3, 7, 8, 9, 0.1, 1e-4, 1.0, 0.9);
     force1.addParticle(5, 6, -1, -1, -1, 0.2, 0.1, 1.0, 1.0);
@@ -59,6 +61,8 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     DrudeForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force1.getName(), force2.getName());
     ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
     for (int i = 0; i < (int) force1.getNumParticles(); i++) {
         int a1, a2, a3, a4, a5, b1, b2, b3, b4, b5;

serialization/src/AndersenThermostatProxy.cpp

@@ -48,6 +48,7 @@ void AndersenThermostatProxy::serialize(const void* object, SerializationNode& n
     node.setDoubleProperty("frequency", force.getDefaultCollisionFrequency());
     node.setIntProperty("randomSeed", force.getRandomNumberSeed());
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
 }
 
 void* AndersenThermostatProxy::deserialize(const SerializationNode& node) const {
@@ -57,6 +58,7 @@ void* AndersenThermostatProxy::deserialize(const SerializationNode& node) const
     try {
         AndersenThermostat* force = new AndersenThermostat(node.getDoubleProperty("temperature"), node.getDoubleProperty("frequency"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
         return force;
     }

serialization/src/CMAPTorsionForceProxy.cpp

@@ -45,6 +45,7 @@ void CMAPTorsionForceProxy::serialize(const void* object, SerializationNode& nod
     node.setIntProperty("version", 2);
     const CMAPTorsionForce& force = *reinterpret_cast<const CMAPTorsionForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     SerializationNode& maps = node.createChildNode("Maps");
     for (int i = 0; i < force.getNumMaps(); i++) {
@@ -70,6 +71,7 @@ void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const {
     CMAPTorsionForce* force = new CMAPTorsionForce();
     try {
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& maps = node.getChildNode("Maps");

serialization/src/CMMotionRemoverProxy.cpp

@@ -45,6 +45,7 @@ void CMMotionRemoverProxy::serialize(const void* object, SerializationNode& node
     node.setIntProperty("version", 1);
     const CMMotionRemover& force = *reinterpret_cast<const CMMotionRemover*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setIntProperty("frequency", force.getFrequency());
 }
 
@@ -55,6 +56,7 @@ void* CMMotionRemoverProxy::deserialize(const SerializationNode& node) const {
     try {
         CMMotionRemover* force = new CMMotionRemover(node.getIntProperty("frequency"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         return force;
     }
     catch (...) {

serialization/src/CustomAngleForceProxy.cpp

@@ -45,6 +45,7 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
     node.setIntProperty("version", 3);
     const CustomAngleForce& force = *reinterpret_cast<const CustomAngleForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("name", force.getName());
     node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
     node.setStringProperty("energy", force.getEnergyFunction());
     SerializationNode& perAngleParams = node.createChildNode("PerAngleParameters");
@@ -82,6 +83,7 @@ void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
     try {
         CustomAngleForce* force = new CustomAngleForce(node.getStringProperty("energy"));
         force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setName(node.getStringProperty("name", force->getName()));
         if (version > 1)
             force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
         const SerializationNode& perAngleParams = node.getChildNode("PerAngleParameters");