Merge pull request #1337 from peastman/extrapolated

AMOEBA extrapolated polarization

plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp

@@ -68,7 +68,7 @@ void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentM
 }
 
 void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
 
     node.setIntProperty("nonbondedMethod",                  force.getNonbondedMethod());
@@ -87,6 +87,14 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
     force.getPmeGridDimensions(gridDimensions);
     SerializationNode& gridDimensionsNode  = node.createChildNode("MultipoleParticleGridDimension");
     gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]); 
+    
+    SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
+    vector<double> coeff = force.getExtrapolationCoefficients();
+    for (int i = 0; i < coeff.size(); i++) {
+        stringstream key;
+        key << "c" << i;
+        coefficients.setDoubleProperty(key.str(), coeff[i]);
+    }
 
     std::vector<std::string> covalentTypes;
     getCovalentTypes(covalentTypes);
@@ -124,16 +132,16 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") > 2)
+    int version = node.getIntProperty("version");
+    if (version < 0 || version > 3)
         throw OpenMMException("Unsupported version number");
     AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
 
     try {
 
         force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
-        if (node.getIntProperty("version") == 2) {
+        if (version >= 2)
             force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
-        }
         //force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
         //force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
         force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
@@ -151,6 +159,18 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
         gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
         force->setPmeGridDimensions(gridDimensions);
     
+        if (version >= 3) {
+            const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
+            vector<double> coeff;
+            for (int i = 0; ; i++) {
+                stringstream key;
+                key << "c" << i;
+                if (coefficients.getProperties().find(key.str()) == coefficients.getProperties().end())
+                    break;
+                coeff.push_back(coefficients.getDoubleProperty(key.str()));
+            }
+            force->setExtrapolationCoefficients(coeff);
+        }
         std::vector<std::string> covalentTypes;
         getCovalentTypes(covalentTypes);
 

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp

@@ -74,6 +74,12 @@ void testSerialization() {
     force1.setMutualInducedTargetEpsilon(1.0e-05); 
     //force1.setElectricConstant(138.93); 
     force1.setEwaldErrorTolerance(1.0e-05); 
+    
+    vector<double> coeff;
+    coeff.push_back(0.0);
+    coeff.push_back(-0.1);
+    coeff.push_back(1.1);
+    force1.setExtrapolationCoefficients(coeff);
 
     std::vector<std::string> covalentTypes;
     getCovalentTypes(covalentTypes);
@@ -125,6 +131,8 @@ void testSerialization() {
         ASSERT_EQUAL(gridDimension1[jj], gridDimension2[jj]);
     }
     
+    ASSERT_EQUAL_CONTAINERS(force1.getExtrapolationCoefficients(), force2.getExtrapolationCoefficients());
+    
     ASSERT_EQUAL(force1.getNumMultipoles(),  force2.getNumMultipoles());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumMultipoles()); ii++) {
 

wrappers/python/simtk/openmm/app/forcefield.py

@@ -3760,6 +3760,8 @@ class AmoebaMultipoleGenerator:
                 polarizationType = args['polarization']
                 if (polarizationType.lower() == 'direct'):
                     force.setPolarizationType(mm.AmoebaMultipoleForce.Direct)
+                elif (polarizationType.lower() == 'extrapolated'):
+                    force.setPolarizationType(mm.AmoebaMultipoleForce.Extrapolated)
                 else:
                     force.setPolarizationType(mm.AmoebaMultipoleForce.Mutual)
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -247,6 +247,7 @@ UNITS = {
 ("AmoebaMultipoleForce",                 "getPmeBSplineOrder")                            :  ( None,()),
 ("AmoebaMultipoleForce",                 "getMutualInducedMaxIterations")                 :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getMutualInducedTargetEpsilon")                 :  ( None, ()),
+("AmoebaMultipoleForce",                 "getExtrapolationCoefficients")                            :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getEwaldErrorTolerance")                        :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getPmeGridDimensions")                          :  ( None,()),