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Commit d95b90b9 authored by peastman's avatar peastman
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Cleaned up formatting in AMOEBA code

parent a568bb12
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Showing with 243 additions and 243 deletions
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ d95b90b9
......@@ -41,29 +41,29 @@ using namespace std;
AmoebaMultipoleForceProxy::AmoebaMultipoleForceProxy() : SerializationProxy("AmoebaMultipoleForce") {
}
static void getCovalentTypes( std::vector<std::string>& covalentTypes ){
static void getCovalentTypes(std::vector<std::string>& covalentTypes) {
covalentTypes.push_back( "Covalent12" );
covalentTypes.push_back( "Covalent13" );
covalentTypes.push_back( "Covalent14" );
covalentTypes.push_back( "Covalent15" );
covalentTypes.push_back("Covalent12");
covalentTypes.push_back("Covalent13");
covalentTypes.push_back("Covalent14");
covalentTypes.push_back("Covalent15");
covalentTypes.push_back( "PolarizationCovalent11" );
covalentTypes.push_back( "PolarizationCovalent12" );
covalentTypes.push_back( "PolarizationCovalent13" );
covalentTypes.push_back( "PolarizationCovalent14" );
covalentTypes.push_back("PolarizationCovalent11");
covalentTypes.push_back("PolarizationCovalent12");
covalentTypes.push_back("PolarizationCovalent13");
covalentTypes.push_back("PolarizationCovalent14");
}
static void addCovalentMap( SerializationNode& particleExclusions, int particleIndex, std::string mapName, std::vector< int > covalentMap ){
static void addCovalentMap(SerializationNode& particleExclusions, int particleIndex, std::string mapName, std::vector< int > covalentMap) {
SerializationNode& map = particleExclusions.createChildNode(mapName);
for (unsigned int ii = 0; ii < covalentMap.size(); ii++) {
map.createChildNode("Cv").setIntProperty( "v", covalentMap[ii] );
map.createChildNode("Cv").setIntProperty("v", covalentMap[ii]);
}
}
void loadCovalentMap( const SerializationNode& map, std::vector< int >& covalentMap ){
void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentMap) {
for (unsigned int ii = 0; ii < map.getChildren().size(); ii++) {
covalentMap.push_back( map.getChildren()[ii].getIntProperty( "v" ) );
covalentMap.push_back(map.getChildren()[ii].getIntProperty("v"));
}
}
......@@ -84,12 +84,12 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance());
std::vector<int> gridDimensions;
force.getPmeGridDimensions( gridDimensions );
force.getPmeGridDimensions(gridDimensions);
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension");
gridDimensionsNode.setIntProperty( "d0", gridDimensions[0] ).setIntProperty( "d1", gridDimensions[1] ).setIntProperty( "d2", gridDimensions[2] );
gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]);
std::vector<std::string> covalentTypes;
getCovalentTypes( covalentTypes );
getCovalentTypes(covalentTypes);
SerializationNode& particles = node.createChildNode("MultipoleParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
......@@ -100,25 +100,25 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole;
force.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole,
axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity );
force.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole,
axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity);
SerializationNode& particle = particles.createChildNode("Particle");
particle.setIntProperty("axisType", axisType).setIntProperty("multipoleAtomZ", multipoleAtomZ).setIntProperty("multipoleAtomX", multipoleAtomX).setIntProperty("multipoleAtomY", multipoleAtomY);
particle.setDoubleProperty("charge", charge).setDoubleProperty("thole", thole).setDoubleProperty("damp", dampingFactor).setDoubleProperty("polarity", polarity);
SerializationNode& dipole = particle.createChildNode("Dipole");
dipole.setDoubleProperty( "d0", molecularDipole[0] ).setDoubleProperty( "d1", molecularDipole[1] ).setDoubleProperty( "d2", molecularDipole[2] );
dipole.setDoubleProperty("d0", molecularDipole[0]).setDoubleProperty("d1", molecularDipole[1]).setDoubleProperty("d2", molecularDipole[2]);
SerializationNode& quadrupole = particle.createChildNode("Quadrupole");
quadrupole.setDoubleProperty( "q0", molecularQuadrupole[0] ).setDoubleProperty( "q1", molecularQuadrupole[1] ).setDoubleProperty( "q2", molecularQuadrupole[2] );
quadrupole.setDoubleProperty( "q3", molecularQuadrupole[3] ).setDoubleProperty( "q4", molecularQuadrupole[4] ).setDoubleProperty( "q5", molecularQuadrupole[5] );
quadrupole.setDoubleProperty( "q6", molecularQuadrupole[6] ).setDoubleProperty( "q7", molecularQuadrupole[7] ).setDoubleProperty( "q8", molecularQuadrupole[8] );
quadrupole.setDoubleProperty("q0", molecularQuadrupole[0]).setDoubleProperty("q1", molecularQuadrupole[1]).setDoubleProperty("q2", molecularQuadrupole[2]);
quadrupole.setDoubleProperty("q3", molecularQuadrupole[3]).setDoubleProperty("q4", molecularQuadrupole[4]).setDoubleProperty("q5", molecularQuadrupole[5]);
quadrupole.setDoubleProperty("q6", molecularQuadrupole[6]).setDoubleProperty("q7", molecularQuadrupole[7]).setDoubleProperty("q8", molecularQuadrupole[8]);
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap;
force.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap );
addCovalentMap( particle, ii, covalentTypes[jj], covalentMap );
force.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
addCovalentMap(particle, ii, covalentTypes[jj], covalentMap);
}
}
}
......@@ -130,54 +130,54 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
try {
force->setNonbondedMethod( static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty( "nonbondedMethod" )) );
if( node.getIntProperty("version") == 2 ){
force->setPolarizationType( static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty( "polarizationType" )) );
force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
if (node.getIntProperty("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" ) );
//force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
//force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
force->setCutoffDistance( node.getDoubleProperty( "cutoffDistance" ) );
force->setAEwald( node.getDoubleProperty( "aEwald" ) );
force->setMutualInducedTargetEpsilon( node.getDoubleProperty( "mutualInducedTargetEpsilon" ) );
//force->setElectricConstant( node.getDoubleProperty( "electricConstant" ) );
force->setEwaldErrorTolerance( node.getDoubleProperty( "ewaldErrorTolerance" ) );
force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
force->setAEwald(node.getDoubleProperty("aEwald"));
force->setMutualInducedTargetEpsilon(node.getDoubleProperty("mutualInducedTargetEpsilon"));
//force->setElectricConstant(node.getDoubleProperty("electricConstant"));
force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldErrorTolerance"));
std::vector<int> gridDimensions;
const SerializationNode& gridDimensionsNode = node.getChildNode("MultipoleParticleGridDimension");
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d0" ));
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d1" ));
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d2" ));
force->setPmeGridDimensions( gridDimensions );
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d0"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d1"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
force->setPmeGridDimensions(gridDimensions);
std::vector<std::string> covalentTypes;
getCovalentTypes( covalentTypes );
getCovalentTypes(covalentTypes);
const SerializationNode& particles = node.getChildNode("MultipoleParticles");
for ( unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
for (unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
const SerializationNode& particle = particles.getChildren()[ii];
std::vector<double> molecularDipole;
const SerializationNode& dipole = particle.getChildNode("Dipole");
molecularDipole.push_back( dipole.getDoubleProperty( "d0" ) );
molecularDipole.push_back( dipole.getDoubleProperty( "d1" ) );
molecularDipole.push_back( dipole.getDoubleProperty( "d2" ) );
molecularDipole.push_back(dipole.getDoubleProperty("d0"));
molecularDipole.push_back(dipole.getDoubleProperty("d1"));
molecularDipole.push_back(dipole.getDoubleProperty("d2"));
std::vector<double> molecularQuadrupole;
const SerializationNode& quadrupole = particle.getChildNode("Quadrupole");
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q0" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q1" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q2" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q3" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q4" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q5" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q6" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q7" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q8" ) );
force->addMultipole( particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole,
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q0"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q1"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q2"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q3"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q4"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q5"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q6"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q7"));
molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q8"));
force->addMultipole(particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole,
particle.getIntProperty("axisType"),
particle.getIntProperty("multipoleAtomZ"),
particle.getIntProperty("multipoleAtomX"),
......@@ -189,8 +189,8 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap;
loadCovalentMap( particle.getChildNode(covalentTypes[jj]), covalentMap );
force->setCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap );
loadCovalentMap(particle.getChildNode(covalentTypes[jj]), covalentMap);
force->setCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
}
}
......
plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp
View file @ d95b90b9
......@@ -64,10 +64,10 @@ void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node)
AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
try {
force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty( "cubic"));
force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("cubic"));
force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty( "pentic"));
force->setAmoebaGlobalOutOfPlaneBendSextic(node.getDoubleProperty( "sextic"));
force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("pentic"));
force->setAmoebaGlobalOutOfPlaneBendSextic(node.getDoubleProperty("sextic"));
const SerializationNode& bonds = node.getChildNode("OutOfPlaneBend");
for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
......
plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp
View file @ d95b90b9
......@@ -45,7 +45,7 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
node.setIntProperty("version", 1);
const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
SerializationNode& bonds = node.createChildNode("PiTorsion");
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5, particle6;
double k;
force.getPiTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, particle6, k);
......
plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp
View file @ d95b90b9
......@@ -60,7 +60,7 @@ void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) co
AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
try {
const SerializationNode& bonds = node.getChildNode("StretchBendAngles");
for ( unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii];
force->addStretchBend(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"), bond.getDoubleProperty("dAB"), bond.getDoubleProperty("dCB"), bond.getDoubleProperty("angle"), bond.getDoubleProperty("k1"), bond.getDoubleProperty("k2"));
......
plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp
View file @ d95b90b9
......@@ -41,23 +41,23 @@ using namespace std;
AmoebaTorsionTorsionForceProxy::AmoebaTorsionTorsionForceProxy() : SerializationProxy("AmoebaTorsionTorsionForce") {
}
static void loadGrid( const SerializationNode& grid, std::vector< std::vector< std::vector<double> > >& gridVector ){
static void loadGrid(const SerializationNode& grid, std::vector< std::vector< std::vector<double> > >& gridVector) {
const std::vector<SerializationNode>& gridSerializationRows = grid.getChildren();
gridVector.resize( gridSerializationRows.size() );
gridVector.resize(gridSerializationRows.size());
for( unsigned int ii = 0; ii < gridSerializationRows.size(); ii++) {
for (unsigned int ii = 0; ii < gridSerializationRows.size(); ii++) {
const std::vector<SerializationNode>& gridSerializationColumns = gridSerializationRows[ii].getChildren();
gridVector[ii].resize( gridSerializationColumns.size() );
for( unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) {
gridVector[ii].resize(gridSerializationColumns.size());
for (unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) {
const SerializationNode& gridSerializationColumnNode = gridSerializationColumns[jj];
gridVector[ii][jj].resize( 6 );
gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty( "x" );
gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty( "y" );
gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty( "f" );
gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty( "fx" );
gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty( "fy" );
gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty( "fxy" );
gridVector[ii][jj].resize(6);
gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty("x");
gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty("y");
gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty("f");
gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty("fx");
gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty("fy");
gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty("fxy");
}
}
}
......@@ -78,28 +78,28 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) {
const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( kk );
const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid(kk);
unsigned int gridCount = 0;
unsigned int gridYsize = grid[0].size();
for ( unsigned int ii = 0; ii < grid.size(); ii++) {
for (unsigned int ii = 0; ii < grid.size(); ii++) {
gridCount += grid[ii].size();
}
SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid");
for ( unsigned int ii = 0; ii < grid.size(); ii++) {
for (unsigned int ii = 0; ii < grid.size(); ii++) {
SerializationNode& gridSerializationRow = gridNode.createChildNode("RowNode");
gridSerializationRow.setIntProperty("dim", ii );
for ( unsigned int jj = 0; jj < grid[ii].size(); jj++) {
gridSerializationRow.setIntProperty("dim", ii);
for (unsigned int jj = 0; jj < grid[ii].size(); jj++) {
SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode");
gridSerializationColumnNode.setIntProperty("dim", jj );
gridSerializationColumnNode.setIntProperty("dim", jj);
unsigned int index = 0;
gridSerializationColumnNode.setDoubleProperty("x", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("y", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("f", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("fx", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("fy", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++] );
gridSerializationColumnNode.setDoubleProperty("x", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("y", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("f", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fx", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fy", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++]);
}
}
}
......@@ -108,8 +108,8 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5;
int chiralCheckAtomIndex, gridIndex;
force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex );
bonds.createChildNode("TorsionTorsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("p5", particle5).setIntProperty("chiralCheckAtomIndex", chiralCheckAtomIndex).setIntProperty("gridIndex", gridIndex );
force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex);
bonds.createChildNode("TorsionTorsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("p5", particle5).setIntProperty("chiralCheckAtomIndex", chiralCheckAtomIndex).setIntProperty("gridIndex", gridIndex);
}
}
......@@ -124,10 +124,10 @@ void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node)
const SerializationNode& grids = node.getChildNode("TorsionTorsionGrids");
const std::vector<SerializationNode>& gridList = grids.getChildren();
for( unsigned int ii = 0; ii < gridList.size(); ii++) {
for (unsigned int ii = 0; ii < gridList.size(); ii++) {
std::vector< std::vector< std::vector<double> > > gridVector;
loadGrid( gridList[ii], gridVector );
force->setTorsionTorsionGrid( ii, gridVector );
loadGrid(gridList[ii], gridVector);
force->setTorsionTorsionGrid(ii, gridVector);
}
const SerializationNode& bonds = node.getChildNode("TorsionTorsion");
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ d95b90b9
......@@ -56,17 +56,17 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
int ivIndex;
double sigma, epsilon, reductionFactor;
force.getParticleParameters( ii, ivIndex, sigma, epsilon, reductionFactor );
force.getParticleParameters(ii, ivIndex, sigma, epsilon, reductionFactor);
SerializationNode& particle = particles.createChildNode("Particle");
particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor);
std::vector< int > exclusions;
force.getParticleExclusions( ii, exclusions );
force.getParticleExclusions(ii, exclusions);
SerializationNode& particleExclusions = particle.createChildNode("ParticleExclusions");
for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
particleExclusions.createChildNode( "excl" ).setIntProperty( "index", exclusions[jj] );
particleExclusions.createChildNode("excl").setIntProperty("index", exclusions[jj]);
}
}
}
......@@ -77,9 +77,9 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
AmoebaVdwForce* force = new AmoebaVdwForce();
try {
force->setSigmaCombiningRule(node.getStringProperty( "SigmaCombiningRule" ) );
force->setEpsilonCombiningRule(node.getStringProperty( "EpsilonCombiningRule" ) );
force->setCutoff(node.getDoubleProperty( "VdwCutoff" ) );
force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
force->setCutoff(node.getDoubleProperty("VdwCutoff"));
force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));
const SerializationNode& particles = node.getChildNode("VdwParticles");
......@@ -92,9 +92,9 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& particleExclusions = particle.getChildNode("ParticleExclusions");
std::vector< int > exclusions;
for (unsigned int jj = 0; jj < particleExclusions.getChildren().size(); jj++) {
exclusions.push_back( particleExclusions.getChildren()[jj].getIntProperty("index") );
exclusions.push_back(particleExclusions.getChildren()[jj].getIntProperty("index"));
}
force->setParticleExclusions( ii, exclusions );
force->setParticleExclusions(ii, exclusions);
}
}
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp
View file @ d95b90b9
......@@ -45,10 +45,10 @@ void testSerialization() {
// Create a Force.
AmoebaAngleForce force1;
force1.setAmoebaGlobalAngleCubic( 12.3 );
force1.setAmoebaGlobalAngleQuartic( 98.7 );
force1.setAmoebaGlobalAnglePentic( 91.7 );
force1.setAmoebaGlobalAngleSextic( 93.7 );
force1.setAmoebaGlobalAngleCubic(12.3);
force1.setAmoebaGlobalAngleQuartic(98.7);
force1.setAmoebaGlobalAnglePentic(91.7);
force1.setAmoebaGlobalAngleSextic(93.7);
force1.addAngle(0, 1, 3, 1.0, 2.0);
force1.addAngle(0, 2, 3, 2.0, 2.1);
force1.addAngle(2, 3, 5, 3.0, 2.2);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp
View file @ d95b90b9
......@@ -45,8 +45,8 @@ void testSerialization() {
// Create a Force.
AmoebaBondForce force1;
force1.setAmoebaGlobalBondCubic( 12.3 );
force1.setAmoebaGlobalBondQuartic( 98.7 );
force1.setAmoebaGlobalBondCubic(12.3);
force1.setAmoebaGlobalBondQuartic(98.7);
force1.addBond(0, 1, 1.0, 2.0);
force1.addBond(0, 2, 2.0, 2.1);
force1.addBond(2, 3, 3.0, 2.2);
......
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