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Commit 46c5f78f authored by Jason Swails's avatar Jason Swails
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Merge branch 'master' of https://github.com/SimTk/openmm

parents d825e6ab c4877bec
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Showing with 113 additions and 19 deletions
serialization/src/RBTorsionForceProxy.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -44,6 +44,7 @@ RBTorsionForceProxy::RBTorsionForceProxy() : SerializationProxy("RBTorsionForce"
void RBTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const RBTorsionForce& force = *reinterpret_cast<const RBTorsionForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
SerializationNode& torsions = node.createChildNode("Torsions");
for (int i = 0; i < force.getNumTorsions(); i++) {
int particle1, particle2, particle3, particle4;
......@@ -58,6 +59,7 @@ void* RBTorsionForceProxy::deserialize(const SerializationNode& node) const {
throw OpenMMException("Unsupported version number");
RBTorsionForce* force = new RBTorsionForce();
try {
force->setForceGroup(node.getIntProperty("forceGroup", 0));
const SerializationNode& torsions = node.getChildNode("Torsions");
for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
const SerializationNode& torsion = torsions.getChildren()[i];
......
serialization/src/SerializationNode.cpp
View file @ 46c5f78f
......@@ -121,6 +121,32 @@ SerializationNode& SerializationNode::setIntProperty(const string& name, int val
return *this;
}
bool SerializationNode::getBoolProperty(const string& name) const {
map<string, string>::const_iterator iter = properties.find(name);
if (iter == properties.end())
throw OpenMMException("Unknown property '"+name+"' in node '"+getName()+"'");
bool value;
stringstream(iter->second) >> value;
return value;
}
bool SerializationNode::getBoolProperty(const string& name, bool defaultValue) const {
map<string, string>::const_iterator iter = properties.find(name);
if (iter == properties.end())
return defaultValue;
bool value;
stringstream(iter->second) >> value;
return value;
}
SerializationNode& SerializationNode::setBoolProperty(const string& name, bool value) {
stringstream s;
s << value;
properties[name] = s.str();
return *this;
}
double SerializationNode::getDoubleProperty(const string& name) const {
map<string, string>::const_iterator iter = properties.find(name);
if (iter == properties.end())
......
serialization/tests/TestSerializeAndersenThermostat.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
AndersenThermostat force(250.0, 0.2);
force.setForceGroup(3);
force.setRandomNumberSeed(3);
// Serialize and then deserialize it.
......@@ -53,6 +54,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AndersenThermostat& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
ASSERT_EQUAL(force.getDefaultCollisionFrequency(), force2.getDefaultCollisionFrequency());
ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
......
serialization/tests/TestSerializeCMAPTorsion.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CMAPTorsionForce force;
force.setForceGroup(3);
vector<double> map1(9);
for (int i = 0; i < 9; i++)
map1[i] = 0.1*i;
......@@ -64,6 +65,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CMAPTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumMaps(), force2.getNumMaps());
for (int i = 0; i < force.getNumMaps(); i++) {
int size1, size2;
......
serialization/tests/TestSerializeCMMotionRemover.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CMMotionRemover force(5);
force.setForceGroup(3);
// Serialize and then deserialize it.
......@@ -52,6 +53,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CMMotionRemover& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
}
......
serialization/tests/TestSerializeCustomAngleForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomAngleForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerAngleParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomAngleForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerAngleParameters(), force2.getNumPerAngleParameters());
for (int i = 0; i < force.getNumPerAngleParameters(); i++)
......
serialization/tests/TestSerializeCustomBondForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomBondForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerBondParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
for (int i = 0; i < force.getNumPerBondParameters(); i++)
......
serialization/tests/TestSerializeCustomCompoundBondForce.cpp
View file @ 46c5f78f
......@@ -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) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomCompoundBondForce force(3, "5*sin(distance(p1,p2))^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerBondParameter("z");
......@@ -76,6 +77,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomCompoundBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumParticlesPerBond(), force2.getNumParticlesPerBond());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
......
serialization/tests/TestSerializeCustomExternalForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomExternalForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerParticleParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomExternalForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
for (int i = 0; i < force.getNumPerParticleParameters(); i++)
......
serialization/tests/TestSerializeCustomGBForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomGBForce force;
force.setForceGroup(3);
force.setNonbondedMethod(CustomGBForce::CutoffPeriodic);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
......@@ -74,6 +75,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomGBForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
......
serialization/tests/TestSerializeCustomHbondForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomHbondForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.setNonbondedMethod(CustomHbondForce::CutoffPeriodic);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
......@@ -77,6 +78,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomHbondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
......
serialization/tests/TestSerializeCustomNonbondedForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,7 +42,11 @@ void testSerialization() {
// Create a Force.
CustomNonbondedForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
force.setUseSwitchingFunction(true);
force.setUseLongRangeCorrection(true);
force.setSwitchingDistance(2.0);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
......@@ -60,6 +64,11 @@ void testSerialization() {
for (int i = 0; i < 10; i++)
values[i] = sin((double) i);
force.addFunction("f", values, 0.5, 1.5);
std::set<int> set1, set2;
set1.insert(0);
set2.insert(1);
set2.insert(2);
force.addInteractionGroup(set1, set2);
// Serialize and then deserialize it.
......@@ -70,9 +79,13 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomNonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getUseLongRangeCorrection(), force2.getUseLongRangeCorrection());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
for (int i = 0; i < force.getNumPerParticleParameters(); i++)
ASSERT_EQUAL(force.getPerParticleParameterName(i), force2.getPerParticleParameterName(i));
......@@ -111,6 +124,11 @@ void testSerialization() {
for (int j = 0; j < (int) val1.size(); j++)
ASSERT_EQUAL(val1[j], val2[j]);
}
ASSERT_EQUAL(force.getNumInteractionGroups(), force2.getNumInteractionGroups());
std::set<int> set1c, set2c;
force2.getInteractionGroupParameters(0, set1c, set2c);
ASSERT_EQUAL_CONTAINERS(set1, set1c);
ASSERT_EQUAL_CONTAINERS(set2, set2c);
}
int main() {
......
serialization/tests/TestSerializeCustomTorsionForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomTorsionForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerTorsionParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerTorsionParameters(), force2.getNumPerTorsionParameters());
for (int i = 0; i < force.getNumPerTorsionParameters(); i++)
......
serialization/tests/TestSerializeGBSAOBCForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
GBSAOBCForce force;
force.setForceGroup(3);
force.setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
force.setCutoffDistance(2.0);
force.setSoluteDielectric(5.1);
......@@ -59,6 +60,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
GBSAOBCForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
......
serialization/tests/TestSerializeGBVIForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
GBVIForce force;
force.setForceGroup(3);
force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
force.setQuinticLowerLimitFactor(0.123);
......@@ -64,6 +65,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
GBVIForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
......
serialization/tests/TestSerializeHarmonicAngleForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
HarmonicAngleForce force;
force.setForceGroup(3);
force.addAngle(0, 1, 2, 1.0, 2.0);
force.addAngle(0, 2, 3, 2.0, 2.1);
force.addAngle(2, 3, 4, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
HarmonicAngleForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
for (int i = 0; i < force.getNumAngles(); i++) {
int a1, a2, a3, b1, b2, b3;
......
serialization/tests/TestSerializeHarmonicBondForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
HarmonicBondForce force;
force.setForceGroup(3);
force.addBond(0, 1, 1.0, 2.0);
force.addBond(0, 2, 2.0, 2.1);
force.addBond(2, 3, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
HarmonicBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
for (int i = 0; i < force.getNumBonds(); i++) {
int a1, a2, b1, b2;
......
serialization/tests/TestSerializeMonteCarloBarostat.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
MonteCarloBarostat force(25.5, 250.0, 14);
force.setForceGroup(3);
force.setRandomNumberSeed(3);
// Serialize and then deserialize it.
......@@ -53,6 +54,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
MonteCarloBarostat& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
......
serialization/tests/TestSerializeNonbondedForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,11 +42,17 @@ void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setForceGroup(3);
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setSwitchingDistance(1.5);
force.setUseSwitchingFunction(true);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
......@@ -62,12 +68,22 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
double alpha2;
int nx2, ny2, nz2;
force2.getPMEParameters(alpha2, nx2, ny2, nz2);
ASSERT_EQUAL(alpha, alpha2);
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
......
serialization/tests/TestSerializePeriodicTorsionForce.cpp
View file @ 46c5f78f
......@@ -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: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
PeriodicTorsionForce force;
force.setForceGroup(3);
force.addTorsion(0, 1, 2, 3, 2, 1.0, 2.0);
force.addTorsion(0, 2, 3, 4, 2, 2.0, 2.1);
force.addTorsion(2, 3, 4, 7, 1, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
PeriodicTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int a1, a2, a3, a4, b1, b2, b3, b4, perioda, periodb;
......
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