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Commit 780bbf8f authored by peastman's avatar peastman
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Merge pull request #412 from peastman/master 

Cleanup to the recent serialization code changes
parents 436d542d 7a6f4b2f
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Showing with 47 additions and 46 deletions
serialization/src/CustomNonbondedForceProxy.cpp
View file @ 780bbf8f
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -102,7 +102,7 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
try {
CustomNonbondedForce* force = new CustomNonbondedForce(node.getStringProperty("energy"));
force->setNonbondedMethod((CustomNonbondedForce::NonbondedMethod) node.getIntProperty("method"));
force->setCutoffDistance(node.getDoubleProperty("cutoff", 1.0));
force->setCutoffDistance(node.getDoubleProperty("cutoff"));
force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
......@@ -149,8 +149,12 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
// Catch exceptions if InteractionGroups node is missing, in order to give backwards compatibility.
try{
bool hasInteractionGroups = false; // Older files will be missing this block.
for (int i = 0; i < (int) node.getChildren().size(); i++) {
if (node.getChildren()[i].getName() == "InteractionGroups")
hasInteractionGroups = true;
}
if (hasInteractionGroups) {
const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
......@@ -166,8 +170,6 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
set2.insert(set2node.getChildren()[j].getIntProperty("index"));
force->addInteractionGroup(set1, set2);
}
} catch (...) {
// do nothing to allow backwards-compatibility
}
return force;
}
......
serialization/src/NonbondedForceProxy.cpp
View file @ 780bbf8f
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -80,20 +80,18 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
NonbondedForce* force = new NonbondedForce();
try {
force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
force->setCutoffDistance(node.getDoubleProperty("cutoff",1.0));
force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction",false));
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance",-1.0));
force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance",5e-4));
force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric",78.3));
force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection",true));
double alpha;
int nx, ny, nz;
alpha = node.getDoubleProperty("alpha",0.0);
nx = node.getIntProperty("nx",0);
ny = node.getIntProperty("ny",0);
nz = node.getIntProperty("nz",0);
force->setCutoffDistance(node.getDoubleProperty("cutoff"));
force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
double alpha = node.getDoubleProperty("alpha", 0.0);
int nx = node.getIntProperty("nx", 0);
int ny = node.getIntProperty("ny", 0);
int nz = node.getIntProperty("nz", 0);
force->setPMEParameters(alpha, nx, ny, nz);
force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup",-1));
force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
......
serialization/tests/TestSerializeCustomNonbondedForce.cpp
View file @ 780bbf8f
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -66,6 +66,7 @@ void testSerialization() {
std::set<int> set1, set2;
set1.insert(0);
set2.insert(1);
set2.insert(2);
force.addInteractionGroup(set1, set2);
// Serialize and then deserialize it.
......
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