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Unverified Commit d7307530 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Serialization records integration force groups (#4734)

parent ecbe32b0
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Showing with 86 additions and 13 deletions
openmmapi/include/openmm/CompoundIntegrator.h
View file @ d7307530
......@@ -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) 2015-2020 Stanford University and the Authors. *
* Portions copyright (c) 2015-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -158,6 +158,23 @@ public:
* @param steps the number of time steps to take
*/
void step(int steps);
/**
* Get which force groups to use for integration. By default, all force groups
* are included. This is interpreted as a set of bit flags: the forces from group i
* will be included if (groups&(1<<i)) != 0.
*
* This method returns the integration force groups for the current Integator.
*/
int getIntegrationForceGroups() const;
/**
* Set which force groups to use for integration. By default, all force groups
* are included. This is interpreted as a set of bit flags: the forces from group i
* will be included if (groups&(1<<i)) != 0.
*
* Calling this method sets the integration force groups for all Integrators
* containined in this CompoundIntegrator.
*/
void setIntegrationForceGroups(int groups);
protected:
/**
* This will be called by the Context when it is created. It informs the Integrator
......
openmmapi/src/CompoundIntegrator.cpp
View file @ d7307530
......@@ -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) 2015-2020 Stanford University and the Authors. *
* Portions copyright (c) 2015-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -99,6 +99,15 @@ void CompoundIntegrator::step(int steps) {
integrators[currentIntegrator]->step(steps);
}
int CompoundIntegrator::getIntegrationForceGroups() const {
return integrators[currentIntegrator]->getIntegrationForceGroups();
}
void CompoundIntegrator::setIntegrationForceGroups(int groups) {
for (int i = 0; i < integrators.size(); i++)
integrators[i]->setIntegrationForceGroups(groups);
}
void CompoundIntegrator::initialize(ContextImpl& context) {
if (integrators.size() == 0)
throw OpenMMException("CompoundIntegrator must contain at least one Integrator");
......
plugins/drude/serialization/src/DrudeLangevinIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -50,6 +50,7 @@ void DrudeLangevinIntegratorProxy::serialize(const void* object, SerializationNo
node.setDoubleProperty("drudeTemperature", integrator.getDrudeTemperature());
node.setDoubleProperty("drudeFriction", integrator.getDrudeFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* DrudeLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -60,5 +61,6 @@ void* DrudeLangevinIntegratorProxy::deserialize(const SerializationNode& node) c
node.getDoubleProperty("drudeFriction"), node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
\ No newline at end of file
plugins/drude/serialization/src/DrudeNoseHooverIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Andrew C. Simmonett, Andreas Krämer *
* Contributors: *
* *
......@@ -57,6 +57,7 @@ void DrudeNoseHooverIntegratorProxy::serialize(const void* object, Serialization
node.setIntProperty("chainLength", integrator.getThermostat().getChainLength());
node.setIntProperty("numMTS", integrator.getThermostat().getNumMultiTimeSteps());
node.setIntProperty("numYS", integrator.getThermostat().getNumYoshidaSuzukiTimeSteps());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* DrudeNoseHooverIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -75,6 +76,7 @@ void* DrudeNoseHooverIntegratorProxy::deserialize(const SerializationNode& node)
);
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setMaximumPairDistance(node.getDoubleProperty("maximumPairDistance"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
plugins/drude/serialization/tests/TestSerializeDrudeLangevinIntegrator.cpp
View file @ d7307530
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,6 +46,7 @@ void testSerialization() {
DrudeLangevinIntegrator integ1(301.1, 0.95, 10.5, 1.2, 0.001);
integ1.setRandomNumberSeed(18);
integ1.setIntegrationForceGroups(3);
// Serialize and then deserialize it.
......@@ -61,6 +62,7 @@ void testSerialization() {
ASSERT_EQUAL(integ1.getDrudeTemperature(), integ2.getDrudeTemperature());
ASSERT_EQUAL(integ1.getDrudeFriction(), integ2.getDrudeFriction());
ASSERT_EQUAL(integ1.getRandomNumberSeed(), integ2.getRandomNumberSeed());
ASSERT_EQUAL(integ1.getIntegrationForceGroups(), integ2.getIntegrationForceGroups());
}
int main() {
......
plugins/drude/serialization/tests/TestSerializeDrudeNoseHooverIntegrator.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Andrew C. Simmonett and Andreas Kraemer
* Contributors: *
* *
......@@ -51,6 +51,7 @@ void assertIntegratorsEqual(const DrudeNoseHooverIntegrator& integrator1, const
ASSERT_EQUAL(integrator1.getConstraintTolerance(), integrator2.getConstraintTolerance());
ASSERT_EQUAL(integrator1.getMaximumPairDistance(), integrator2.getMaximumPairDistance());
ASSERT_EQUAL(integrator1.getNumThermostats(), integrator2.getNumThermostats());
ASSERT_EQUAL(integrator1.getIntegrationForceGroups(), integrator2.getIntegrationForceGroups());
for (int i = 0; i < integrator1.getNumThermostats(); i++) {
const auto &thermostat1 = integrator1.getThermostat(i);
const auto &thermostat2 = integrator2.getThermostat(i);
......@@ -84,6 +85,7 @@ void testSerialization() {
system.addForce(new DrudeForce());
for (int i=0; i<10; i++) system.addParticle(1.0);
DrudeNoseHooverIntegrator integrator(331, 0.21, 1.1, 0.1, 0.004, 5, 5, 5);
integrator.setIntegrationForceGroups(3);
// Serialize and then deserialize it.
stringstream buffer2;
......
serialization/src/BrownianIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -47,6 +47,7 @@ void BrownianIntegratorProxy::serialize(const void* object, SerializationNode& n
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("friction", integrator.getFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* BrownianIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -57,5 +58,6 @@ void* BrownianIntegratorProxy::deserialize(const SerializationNode& node) const
node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
\ No newline at end of file
serialization/src/CustomIntegratorProxy.cpp
View file @ d7307530
......@@ -65,6 +65,7 @@ void CustomIntegratorProxy::serialize(const void* object, SerializationNode& nod
functions.createChildNode("Function", &integrator.getTabulatedFunction(i)).setStringProperty("name", integrator.getTabulatedFunctionName(i));
node.setStringProperty("kineticEnergyExpression", integrator.getKineticEnergyExpression());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
}
......@@ -124,6 +125,7 @@ void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
}
integrator->setKineticEnergyExpression(node.getStringProperty("kineticEnergyExpression"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
return integrator;
}
serialization/src/LangevinIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -47,6 +47,7 @@ void LangevinIntegratorProxy::serialize(const void* object, SerializationNode& n
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("friction", integrator.getFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* LangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -57,5 +58,6 @@ void* LangevinIntegratorProxy::deserialize(const SerializationNode& node) const
node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
\ No newline at end of file
serialization/src/LangevinMiddleIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2019 Stanford University and the Authors. *
* Portions copyright (c) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -47,6 +47,7 @@ void LangevinMiddleIntegratorProxy::serialize(const void* object, SerializationN
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("friction", integrator.getFriction());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* LangevinMiddleIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -56,5 +57,6 @@ void* LangevinMiddleIntegratorProxy::deserialize(const SerializationNode& node)
node.getDoubleProperty("friction"), node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
\ No newline at end of file
serialization/src/NoseHooverIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Andrew C. Simmonett, Andreas Krämer *
* Contributors: *
* *
......@@ -47,6 +47,7 @@ void NoseHooverIntegratorProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("maximumPairDistance", integrator.getMaximumPairDistance());
node.setBoolProperty("hasSubsystemThermostats", integrator.hasSubsystemThermostats());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
if (integrator.hasSubsystemThermostats()) {
// Serialize all thermostats separately
for (int i = 0; i < integrator.getNumThermostats(); i++){
......@@ -123,6 +124,7 @@ void* NoseHooverIntegratorProxy::deserialize(const SerializationNode& node) cons
}
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setMaximumPairDistance(node.getDoubleProperty("maximumPairDistance"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
serialization/src/VariableLangevinIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2019 Stanford University and the Authors. *
* Portions copyright (c) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -48,6 +48,7 @@ void VariableLangevinIntegratorProxy::serialize(const void* object, Serializatio
node.setDoubleProperty("errorTol", integrator.getErrorTolerance());
node.setDoubleProperty("maxStepSize", integrator.getMaximumStepSize());
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* VariableLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -60,6 +61,7 @@ void* VariableLangevinIntegratorProxy::deserialize(const SerializationNode& node
integrator->setStepSize(node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
if (version > 1)
integrator->setMaximumStepSize(node.getDoubleProperty("maxStepSize"));
return integrator;
......
serialization/src/VariableVerletIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2019 Stanford University and the Authors. *
* Portions copyright (c) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void VariableVerletIntegratorProxy::serialize(const void* object, SerializationN
node.setDoubleProperty("maxStepSize", integrator.getMaximumStepSize());
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* VariableVerletIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -54,6 +55,7 @@ void* VariableVerletIntegratorProxy::deserialize(const SerializationNode& node)
VariableVerletIntegrator *integrator = new VariableVerletIntegrator(node.getDoubleProperty("errorTol"));
integrator->setStepSize(node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
if (version > 1)
integrator->setMaximumStepSize(node.getDoubleProperty("maxStepSize"));
return integrator;
......
serialization/src/VerletIntegratorProxy.cpp
View file @ d7307530
......@@ -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) 2010-2024 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao *
* Contributors: *
* *
......@@ -44,6 +44,7 @@ void VerletIntegratorProxy::serialize(const void* object, SerializationNode& nod
const VerletIntegrator& integrator = *reinterpret_cast<const VerletIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
}
void* VerletIntegratorProxy::deserialize(const SerializationNode& node) const {
......@@ -51,5 +52,6 @@ void* VerletIntegratorProxy::deserialize(const SerializationNode& node) const {
throw OpenMMException("Unsupported version number");
VerletIntegrator *integrator = new VerletIntegrator(node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
return integrator;
}
\ No newline at end of file
serialization/tests/TestSerializeIntegrator.cpp
View file @ d7307530
......@@ -52,17 +52,21 @@ using namespace std;
void testSerializeVerletIntegrator() {
VerletIntegrator *intg = new VerletIntegrator(0.00342);
intg->setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "VerletIntegrator", ss);
VerletIntegrator *intg2 = dynamic_cast<VerletIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg->getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg;
delete intg2;
}
void testSerializeLangevinIntegrator() {
LangevinIntegrator *intg = new LangevinIntegrator(372.4, 1.234, 0.0018);
intg->setRandomNumberSeed(10);
intg->setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "LangevinIntegrator", ss);
LangevinIntegrator *intg2 = dynamic_cast<LangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
......@@ -71,12 +75,15 @@ void testSerializeLangevinIntegrator() {
ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg->getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg;
delete intg2;
}
void testSerializeLangevinMiddleIntegrator() {
LangevinMiddleIntegrator *intg = new LangevinMiddleIntegrator(372.4, 1.234, 0.0018);
intg->setRandomNumberSeed(10);
intg->setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "LangevinMiddleIntegrator", ss);
LangevinMiddleIntegrator *intg2 = dynamic_cast<LangevinMiddleIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
......@@ -85,12 +92,15 @@ void testSerializeLangevinMiddleIntegrator() {
ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg->getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg;
delete intg2;
}
void testSerializeBrownianIntegrator() {
BrownianIntegrator *intg = new BrownianIntegrator(243.1, 3.234, 0.0021);
intg->setRandomNumberSeed(10);
intg->setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "BrownianIntegrator", ss);
BrownianIntegrator *intg2 = dynamic_cast<BrownianIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
......@@ -99,6 +109,7 @@ void testSerializeBrownianIntegrator() {
ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg->getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg;
delete intg2;
}
......@@ -106,6 +117,7 @@ void testSerializeBrownianIntegrator() {
void testSerializeVariableVerletIntegrator() {
VariableVerletIntegrator intg(0.04234);
intg.setMaximumStepSize(0.32);
intg.setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(&intg, "VariableVerletIntegrator", ss);
VariableVerletIntegrator *intg2 = dynamic_cast<VariableVerletIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
......@@ -113,12 +125,15 @@ void testSerializeVariableVerletIntegrator() {
ASSERT_EQUAL(intg.getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg.getErrorTolerance(), intg2->getErrorTolerance());
ASSERT_EQUAL(intg.getMaximumStepSize(), intg2->getMaximumStepSize());
ASSERT_EQUAL(intg.getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg2;
}
void testSerializeVariableLangevinIntegrator() {
VariableLangevinIntegrator intg(243.1, 3.234, 0.0021);
intg.setMaximumStepSize(0.32);
intg.setRandomNumberSeed(10);
intg.setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(&intg, "VariableLangevinIntegrator", ss);
VariableLangevinIntegrator *intg2 = dynamic_cast<VariableLangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
......@@ -129,11 +144,14 @@ void testSerializeVariableLangevinIntegrator() {
ASSERT_EQUAL(intg.getTemperature(), intg2->getTemperature());
ASSERT_EQUAL(intg.getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg.getMaximumStepSize(), intg2->getMaximumStepSize());
ASSERT_EQUAL(intg.getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
delete intg2;
}
void testSerializeCustomIntegrator() {
CustomIntegrator *intg = new CustomIntegrator(0.002234);
intg->setRandomNumberSeed(10);
intg->setIntegrationForceGroups(3);
intg->addPerDofVariable("temp",0);
vector<Vec3> initialValues(123);
for(int i = 0; i < 123; i++)
......@@ -209,6 +227,7 @@ void testSerializeCustomIntegrator() {
}
ASSERT_EQUAL(intg->getKineticEnergyExpression(), intg2->getKineticEnergyExpression());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg->getIntegrationForceGroups(), intg2->getIntegrationForceGroups());
ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
ASSERT_EQUAL(intg->getNumTabulatedFunctions(), intg2->getNumTabulatedFunctions());
......@@ -233,10 +252,12 @@ void testSerializeCompoundIntegrator() {
integ.addIntegrator(new LangevinIntegrator(372.4, 1.234, 0.0018));
integ.addIntegrator(new VerletIntegrator(0.002));
integ.setCurrentIntegrator(1);
integ.setIntegrationForceGroups(3);
stringstream ss;
XmlSerializer::serialize<Integrator>(&integ, "CompoundIntegrator", ss);
CompoundIntegrator *integ2 = dynamic_cast<CompoundIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(integ.getCurrentIntegrator(), integ2->getCurrentIntegrator());
ASSERT_EQUAL(integ.getIntegrationForceGroups(), integ2->getIntegrationForceGroups());
LangevinIntegrator& langevin1 = dynamic_cast<LangevinIntegrator&>(integ.getIntegrator(0));
LangevinIntegrator& langevin2 = dynamic_cast<LangevinIntegrator&>(integ2->getIntegrator(0));
ASSERT_EQUAL(langevin1.getConstraintTolerance(), langevin2.getConstraintTolerance());
......
serialization/tests/TestSerializeNoseHooverIntegrator.cpp
View file @ d7307530
......@@ -45,6 +45,7 @@ void assertIntegratorsEqual(const NoseHooverIntegrator& integrator1, const NoseH
ASSERT_EQUAL(integrator1.getConstraintTolerance(), integrator2.getConstraintTolerance());
ASSERT_EQUAL(integrator1.getMaximumPairDistance(), integrator2.getMaximumPairDistance());
ASSERT_EQUAL(integrator1.getNumThermostats(), integrator2.getNumThermostats());
ASSERT_EQUAL(integrator1.getIntegrationForceGroups(), integrator2.getIntegrationForceGroups());
for (int i = 0; i < integrator1.getNumThermostats(); i++) {
const auto &thermostat1 = integrator1.getThermostat(i);
const auto &thermostat2 = integrator2.getThermostat(i);
......@@ -82,6 +83,7 @@ void testSerialization() {
integrator_sub.addSubsystemThermostat(
{0,1,2,3,4,7}, {{0,7}}, 301.1, 1.1, 1.2, 1.3, 9, 2, 5
);
integrator_sub.setIntegrationForceGroups(3);
// Serialize and then deserialize it.
......
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