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Commit 76f7acf7 authored by Nate Stanley's avatar Nate Stanley
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Merge branch 'master' into update_ug

parents 4fd6934b c3847685
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Showing with 124 additions and 47 deletions
plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,9 +42,10 @@ AmoebaGeneralizedKirkwoodForceProxy::AmoebaGeneralizedKirkwoodForceProxy() : Ser
}
void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaGeneralizedKirkwoodForce& force = *reinterpret_cast<const AmoebaGeneralizedKirkwoodForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric());
node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric", force.getSoluteDielectric());
//node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset", force.getDielectricOffset());
......@@ -62,11 +63,13 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
}
void* AmoebaGeneralizedKirkwoodForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaGeneralizedKirkwoodForce* force = new AmoebaGeneralizedKirkwoodForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setSolventDielectric( node.getDoubleProperty("GeneralizedKirkwoodSolventDielectric"));
force->setSoluteDielectric( node.getDoubleProperty("GeneralizedKirkwoodSoluteDielectric"));
//force->setDielectricOffset( node.getDoubleProperty("GeneralizedKirkwoodDielectricOffset"));
......
plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -43,9 +43,10 @@ AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProx
void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaInPlaneAngleForce& force = *reinterpret_cast<const AmoebaInPlaneAngleForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setDoubleProperty("cubic", force.getAmoebaGlobalInPlaneAngleCubic());
node.setDoubleProperty("quartic", force.getAmoebaGlobalInPlaneAngleQuartic());
node.setDoubleProperty("pentic", force.getAmoebaGlobalInPlaneAnglePentic());
......@@ -61,11 +62,13 @@ void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNo
}
void* AmoebaInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaInPlaneAngleForce* force = new AmoebaInPlaneAngleForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setAmoebaGlobalInPlaneAngleCubic( node.getDoubleProperty("cubic"));
force->setAmoebaGlobalInPlaneAngleQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalInPlaneAnglePentic(node.getDoubleProperty("pentic"));
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -68,9 +68,10 @@ 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", 4);
const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
node.setIntProperty("polarizationType", force.getPolarizationType());
//node.setIntProperty("pmeBSplineOrder", force.getPmeBSplineOrder());
......@@ -87,6 +88,14 @@ 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 +133,17 @@ 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 > 4)
throw OpenMMException("Unsupported version number");
AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
try {
if (version > 3)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
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 +161,18 @@ 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/src/AmoebaOutOfPlaneBendForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,8 +42,9 @@ AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : Serialization
}
void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaOutOfPlaneBendForce& force = *reinterpret_cast<const AmoebaOutOfPlaneBendForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setDoubleProperty("cubic", force.getAmoebaGlobalOutOfPlaneBendCubic());
node.setDoubleProperty("quartic", force.getAmoebaGlobalOutOfPlaneBendQuartic());
node.setDoubleProperty("pentic", force.getAmoebaGlobalOutOfPlaneBendPentic());
......@@ -59,11 +60,13 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
}
void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("cubic"));
force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("pentic"));
......
plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,8 +42,9 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
}
void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
SerializationNode& bonds = node.createChildNode("PiTorsion");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5, particle6;
......@@ -54,10 +55,13 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
}
void* AmoebaPiTorsionForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaPiTorsionForce* force = new AmoebaPiTorsionForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
const SerializationNode& bonds = node.getChildNode("PiTorsion");
for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii];
......
plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,8 +42,9 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
}
void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
node.setIntProperty("version", 3);
const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
SerializationNode& bonds = node.createChildNode("StretchBendAngles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
int particle1, particle2, particle3;
......@@ -56,10 +57,12 @@ void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNod
void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version != 1 && version != 2)
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
try {
if (version > 2)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
const SerializationNode& bonds = node.getChildNode("StretchBendAngles");
for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii];
......
plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -63,8 +63,9 @@ static void loadGrid(const SerializationNode& grid, std::vector< std::vector< st
}
void AmoebaTorsionTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
// grid[xIdx][yIdx][6 values]
......@@ -116,12 +117,14 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
const SerializationNode& grids = node.getChildNode("TorsionTorsionGrids");
const std::vector<SerializationNode>& gridList = grids.getChildren();
for (unsigned int ii = 0; ii < gridList.size(); ii++) {
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,9 +42,10 @@ AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce"
}
void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
node.setDoubleProperty("VdwCutoff", force.getCutoff());
......@@ -72,11 +73,13 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
}
void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaVdwForce* force = new AmoebaVdwForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
force->setCutoff(node.getDoubleProperty("VdwCutoff"));
......
plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,8 +42,9 @@ AmoebaWcaDispersionForceProxy::AmoebaWcaDispersionForceProxy() : SerializationPr
}
void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const AmoebaWcaDispersionForce& force = *reinterpret_cast<const AmoebaWcaDispersionForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setDoubleProperty("Epso", force.getEpso());
node.setDoubleProperty("Epsh", force.getEpsh());
node.setDoubleProperty("Rmino", force.getRmino());
......@@ -63,12 +64,14 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
}
void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
AmoebaWcaDispersionForce* force = new AmoebaWcaDispersionForce();
try {
if (version > 1)
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setEpso( node.getDoubleProperty("Epso"));
force->setEpsh( node.getDoubleProperty("Epsh"));
force->setRmino( node.getDoubleProperty("Rmino"));
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaAngleForce force1;
force1.setForceGroup(3);
force1.setAmoebaGlobalAngleCubic(12.3);
force1.setAmoebaGlobalAngleQuartic(98.7);
force1.setAmoebaGlobalAnglePentic(91.7);
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaAngleForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getAmoebaGlobalAngleCubic(), force2.getAmoebaGlobalAngleCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalAngleQuartic(), force2.getAmoebaGlobalAngleQuartic());
ASSERT_EQUAL(force1.getAmoebaGlobalAnglePentic(), force2.getAmoebaGlobalAnglePentic());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaBondForce force1;
force1.setForceGroup(3);
force1.setAmoebaGlobalBondCubic(12.3);
force1.setAmoebaGlobalBondQuartic(98.7);
force1.addBond(0, 1, 1.0, 2.0);
......@@ -60,6 +61,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaBondForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getAmoebaGlobalBondCubic(), force2.getAmoebaGlobalBondCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalBondQuartic(), force2.getAmoebaGlobalBondQuartic());
ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaGeneralizedKirkwoodForce force1;
force1.setForceGroup(3);
force1.setSolventDielectric( 80.0);
force1.setSoluteDielectric( 1.0);
//force1.setDielectricOffset( 0.09);
......@@ -64,6 +65,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaGeneralizedKirkwoodForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getSolventDielectric(), force2.getSolventDielectric());
ASSERT_EQUAL(force1.getSoluteDielectric(), force2.getSoluteDielectric());
//ASSERT_EQUAL(force1.getDielectricOffset(), force2.getDielectricOffset());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,6 +46,7 @@ void testSerialization() {
AmoebaInPlaneAngleForce force1;
force1.setForceGroup(3);
force1.setAmoebaGlobalInPlaneAngleCubic(12.3);
force1.setAmoebaGlobalInPlaneAngleQuartic(98.7);
force1.setAmoebaGlobalInPlaneAnglePentic(91.7);
......@@ -65,6 +66,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaInPlaneAngleForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleCubic(), force2.getAmoebaGlobalInPlaneAngleCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleQuartic(), force2.getAmoebaGlobalInPlaneAngleQuartic());
ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAnglePentic(), force2.getAmoebaGlobalInPlaneAnglePentic());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -59,6 +59,7 @@ void testSerialization() {
// Create a Force.
AmoebaMultipoleForce force1;
force1.setForceGroup(3);
force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
force1.setCutoffDistance(0.9);
force1.setAEwald(0.544);
......@@ -74,6 +75,12 @@ 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);
......@@ -105,6 +112,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaMultipoleForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force1.getAEwald(), force2.getAEwald());
......@@ -125,6 +133,8 @@ 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++) {
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,6 +46,7 @@ void testSerialization() {
AmoebaOutOfPlaneBendForce force1;
force1.setForceGroup(3);
force1.setAmoebaGlobalOutOfPlaneBendCubic(12.3);
force1.setAmoebaGlobalOutOfPlaneBendQuartic(98.7);
force1.setAmoebaGlobalOutOfPlaneBendPentic(91.7);
......@@ -65,6 +66,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaOutOfPlaneBendForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendCubic(), force2.getAmoebaGlobalOutOfPlaneBendCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendQuartic(), force2.getAmoebaGlobalOutOfPlaneBendQuartic());
ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendPentic(), force2.getAmoebaGlobalOutOfPlaneBendPentic());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaPiTorsionForce force1;
force1.setForceGroup(3);
force1.addPiTorsion(0, 1, 3, 4, 5, 6, 2.0);
force1.addPiTorsion(0, 2, 3, 5, 12, 13, 2.1);
force1.addPiTorsion(2, 3, 5, 6, 81, 91, 2.2);
......@@ -58,6 +59,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaPiTorsionForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getNumPiTorsions(), force2.getNumPiTorsions());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumPiTorsions()); ii++) {
int a1, a2, a3, a4, a5, a6, b1, b2, b3, b4, b5, b6;
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaStretchBendForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaStretchBendForce force1;
force1.setForceGroup(3);
force1.addStretchBend(0, 1, 3, 1.0, 1.2, 150.1, 83.2, 100.);
force1.addStretchBend(2, 4, 4, 1.1, 2.2, 180.1, 89.2, 100.);
force1.addStretchBend(5, 0, 1, 3.1, 8.2, 140.1, 98.2, 100.);
......@@ -57,6 +58,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaStretchBendForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getNumStretchBends(), force2.getNumStretchBends());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumStretchBends()); ii++) {
int p11, p12, p13;
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -81,6 +81,7 @@ void testSerialization() {
AmoebaTorsionTorsionForce force1;
force1.setForceGroup(3);
for (unsigned int ii = 0; ii < 5; ii++) {
std::vector< std::vector< std::vector<double> > > gridVector;
loadTorsionTorsionGrid(gridVector);
......@@ -99,6 +100,7 @@ void testSerialization() {
// Compare the two force1s to see if they are identical.
AmoebaTorsionTorsionForce & force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
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
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaVdwForce force1;
force1.setForceGroup(3);
force1.setSigmaCombiningRule("GEOMETRIC");
force1.setEpsilonCombiningRule("GEOMETRIC");
force1.setCutoff(0.9);
......@@ -70,6 +71,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
AmoebaVdwForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getSigmaCombiningRule(), force2.getSigmaCombiningRule());
ASSERT_EQUAL(force1.getEpsilonCombiningRule(), force2.getEpsilonCombiningRule());
ASSERT_EQUAL(force1.getCutoff(), force2.getCutoff());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp
View file @ 76f7acf7
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,6 +45,7 @@ void testSerialization() {
// Create a Force.
AmoebaWcaDispersionForce force1;
force1.setForceGroup(3);
force1.setEpso( 1.0);
force1.setEpsh( 1.1);
force1.setRmino( 1.2);
......@@ -68,6 +69,7 @@ void testSerialization() {
AmoebaWcaDispersionForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getEpso(), force2.getEpso());
ASSERT_EQUAL(force1.getEpsh(), force2.getEpsh());
ASSERT_EQUAL(force1.getRmino(), force2.getRmino());
......
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