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Commit f11bafd9 authored by peastman's avatar peastman
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Merge pull request #828 from peastman/cleanup 

Cleanup to AMOEBA code
parents 162d69a2 d95b90b9
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Showing with 243 additions and 282 deletions
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ f11bafd9
...@@ -41,29 +41,29 @@ using namespace std; ...@@ -41,29 +41,29 @@ using namespace std;
AmoebaMultipoleForceProxy::AmoebaMultipoleForceProxy() : SerializationProxy("AmoebaMultipoleForce") { 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("Covalent12");
covalentTypes.push_back( "Covalent13" ); covalentTypes.push_back("Covalent13");
covalentTypes.push_back( "Covalent14" ); covalentTypes.push_back("Covalent14");
covalentTypes.push_back( "Covalent15" ); covalentTypes.push_back("Covalent15");
covalentTypes.push_back( "PolarizationCovalent11" ); covalentTypes.push_back("PolarizationCovalent11");
covalentTypes.push_back( "PolarizationCovalent12" ); covalentTypes.push_back("PolarizationCovalent12");
covalentTypes.push_back( "PolarizationCovalent13" ); covalentTypes.push_back("PolarizationCovalent13");
covalentTypes.push_back( "PolarizationCovalent14" ); 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); SerializationNode& map = particleExclusions.createChildNode(mapName);
for (unsigned int ii = 0; ii < covalentMap.size(); ii++) { 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++) { 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& ...@@ -84,12 +84,12 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance()); node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance());
std::vector<int> gridDimensions; std::vector<int> gridDimensions;
force.getPmeGridDimensions( gridDimensions ); force.getPmeGridDimensions(gridDimensions);
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension"); 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; std::vector<std::string> covalentTypes;
getCovalentTypes( covalentTypes ); getCovalentTypes(covalentTypes);
SerializationNode& particles = node.createChildNode("MultipoleParticles"); SerializationNode& particles = node.createChildNode("MultipoleParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
...@@ -100,25 +100,25 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& ...@@ -100,25 +100,25 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole; std::vector<double> molecularQuadrupole;
force.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, force.getMultipoleParameters(ii, charge, molecularDipole, molecularQuadrupole,
axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity ); axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity);
SerializationNode& particle = particles.createChildNode("Particle"); SerializationNode& particle = particles.createChildNode("Particle");
particle.setIntProperty("axisType", axisType).setIntProperty("multipoleAtomZ", multipoleAtomZ).setIntProperty("multipoleAtomX", multipoleAtomX).setIntProperty("multipoleAtomY", multipoleAtomY); 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); particle.setDoubleProperty("charge", charge).setDoubleProperty("thole", thole).setDoubleProperty("damp", dampingFactor).setDoubleProperty("polarity", polarity);
SerializationNode& dipole = particle.createChildNode("Dipole"); 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"); SerializationNode& quadrupole = particle.createChildNode("Quadrupole");
quadrupole.setDoubleProperty( "q0", molecularQuadrupole[0] ).setDoubleProperty( "q1", molecularQuadrupole[1] ).setDoubleProperty( "q2", molecularQuadrupole[2] ); 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("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("q6", molecularQuadrupole[6]).setDoubleProperty("q7", molecularQuadrupole[7]).setDoubleProperty("q8", molecularQuadrupole[8]);
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) { for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap; std::vector< int > covalentMap;
force.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap ); force.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
addCovalentMap( particle, ii, covalentTypes[jj], covalentMap ); addCovalentMap(particle, ii, covalentTypes[jj], covalentMap);
} }
} }
} }
...@@ -130,54 +130,54 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons ...@@ -130,54 +130,54 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
try { try {
force->setNonbondedMethod( static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty( "nonbondedMethod" )) ); force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
if( node.getIntProperty("version") == 2 ){ if (node.getIntProperty("version") == 2) {
force->setPolarizationType( static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty( "polarizationType" )) ); force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
} }
//force->setPmeBSplineOrder( node.getIntProperty( "pmeBSplineOrder" ) ); //force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
//force->setMutualInducedIterationMethod( static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty( "mutualInducedIterationMethod" ) ) ); //force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
force->setMutualInducedMaxIterations( node.getIntProperty( "mutualInducedMaxIterations" ) ); force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
force->setCutoffDistance( node.getDoubleProperty( "cutoffDistance" ) ); force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
force->setAEwald( node.getDoubleProperty( "aEwald" ) ); force->setAEwald(node.getDoubleProperty("aEwald"));
force->setMutualInducedTargetEpsilon( node.getDoubleProperty( "mutualInducedTargetEpsilon" ) ); force->setMutualInducedTargetEpsilon(node.getDoubleProperty("mutualInducedTargetEpsilon"));
//force->setElectricConstant( node.getDoubleProperty( "electricConstant" ) ); //force->setElectricConstant(node.getDoubleProperty("electricConstant"));
force->setEwaldErrorTolerance( node.getDoubleProperty( "ewaldErrorTolerance" ) ); force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldErrorTolerance"));
std::vector<int> gridDimensions; std::vector<int> gridDimensions;
const SerializationNode& gridDimensionsNode = node.getChildNode("MultipoleParticleGridDimension"); const SerializationNode& gridDimensionsNode = node.getChildNode("MultipoleParticleGridDimension");
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d0" )); gridDimensions.push_back(gridDimensionsNode.getIntProperty("d0"));
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d1" )); gridDimensions.push_back(gridDimensionsNode.getIntProperty("d1"));
gridDimensions.push_back( gridDimensionsNode.getIntProperty( "d2" )); gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
force->setPmeGridDimensions( gridDimensions ); force->setPmeGridDimensions(gridDimensions);
std::vector<std::string> covalentTypes; std::vector<std::string> covalentTypes;
getCovalentTypes( covalentTypes ); getCovalentTypes(covalentTypes);
const SerializationNode& particles = node.getChildNode("MultipoleParticles"); 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]; const SerializationNode& particle = particles.getChildren()[ii];
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
const SerializationNode& dipole = particle.getChildNode("Dipole"); const SerializationNode& dipole = particle.getChildNode("Dipole");
molecularDipole.push_back( dipole.getDoubleProperty( "d0" ) ); molecularDipole.push_back(dipole.getDoubleProperty("d0"));
molecularDipole.push_back( dipole.getDoubleProperty( "d1" ) ); molecularDipole.push_back(dipole.getDoubleProperty("d1"));
molecularDipole.push_back( dipole.getDoubleProperty( "d2" ) ); molecularDipole.push_back(dipole.getDoubleProperty("d2"));
std::vector<double> molecularQuadrupole; std::vector<double> molecularQuadrupole;
const SerializationNode& quadrupole = particle.getChildNode("Quadrupole"); const SerializationNode& quadrupole = particle.getChildNode("Quadrupole");
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q0" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q0"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q1" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q1"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q2" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q2"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q3" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q3"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q4" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q4"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q5" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q5"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q6" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q6"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q7" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q7"));
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q8" ) ); molecularQuadrupole.push_back(quadrupole.getDoubleProperty("q8"));
force->addMultipole( particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole, force->addMultipole(particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole,
particle.getIntProperty("axisType"), particle.getIntProperty("axisType"),
particle.getIntProperty("multipoleAtomZ"), particle.getIntProperty("multipoleAtomZ"),
particle.getIntProperty("multipoleAtomX"), particle.getIntProperty("multipoleAtomX"),
...@@ -189,8 +189,8 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons ...@@ -189,8 +189,8 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) { for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap; std::vector< int > covalentMap;
loadCovalentMap( particle.getChildNode(covalentTypes[jj]), covalentMap ); loadCovalentMap(particle.getChildNode(covalentTypes[jj]), covalentMap);
force->setCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap ); force->setCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
} }
} }
......
plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp
View file @ f11bafd9
...@@ -64,10 +64,10 @@ void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node) ...@@ -64,10 +64,10 @@ void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node)
AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce(); AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
try { try {
force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty( "cubic")); force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("cubic"));
force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic")); force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty( "pentic")); force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("pentic"));
force->setAmoebaGlobalOutOfPlaneBendSextic(node.getDoubleProperty( "sextic")); force->setAmoebaGlobalOutOfPlaneBendSextic(node.getDoubleProperty("sextic"));
const SerializationNode& bonds = node.getChildNode("OutOfPlaneBend"); const SerializationNode& bonds = node.getChildNode("OutOfPlaneBend");
for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) { for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
......
plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp
View file @ f11bafd9
...@@ -45,7 +45,7 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& ...@@ -45,7 +45,7 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
node.setIntProperty("version", 1); node.setIntProperty("version", 1);
const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object); const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
SerializationNode& bonds = node.createChildNode("PiTorsion"); 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; int particle1, particle2, particle3, particle4, particle5, particle6;
double k; double k;
force.getPiTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, particle6, k); force.getPiTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, particle6, k);
......
plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp
View file @ f11bafd9
...@@ -60,7 +60,7 @@ void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) co ...@@ -60,7 +60,7 @@ void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) co
AmoebaStretchBendForce* force = new AmoebaStretchBendForce(); AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
try { try {
const SerializationNode& bonds = node.getChildNode("StretchBendAngles"); 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]; 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")); 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 @ f11bafd9
...@@ -41,23 +41,23 @@ using namespace std; ...@@ -41,23 +41,23 @@ using namespace std;
AmoebaTorsionTorsionForceProxy::AmoebaTorsionTorsionForceProxy() : SerializationProxy("AmoebaTorsionTorsionForce") { 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(); 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(); const std::vector<SerializationNode>& gridSerializationColumns = gridSerializationRows[ii].getChildren();
gridVector[ii].resize( gridSerializationColumns.size() ); gridVector[ii].resize(gridSerializationColumns.size());
for( unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) { for (unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) {
const SerializationNode& gridSerializationColumnNode = gridSerializationColumns[jj]; const SerializationNode& gridSerializationColumnNode = gridSerializationColumns[jj];
gridVector[ii][jj].resize( 6 ); gridVector[ii][jj].resize(6);
gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty( "x" ); gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty("x");
gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty( "y" ); gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty("y");
gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty( "f" ); gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty("f");
gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty( "fx" ); gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty("fx");
gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty( "fy" ); gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty("fy");
gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty( "fxy" ); gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty("fxy");
} }
} }
} }
...@@ -78,28 +78,28 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization ...@@ -78,28 +78,28 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
SerializationNode& grids = node.createChildNode("TorsionTorsionGrids"); SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) { 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 gridCount = 0;
unsigned int gridYsize = grid[0].size(); 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(); gridCount += grid[ii].size();
} }
SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid"); 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"); SerializationNode& gridSerializationRow = gridNode.createChildNode("RowNode");
gridSerializationRow.setIntProperty("dim", ii ); gridSerializationRow.setIntProperty("dim", ii);
for ( unsigned int jj = 0; jj < grid[ii].size(); jj++) { for (unsigned int jj = 0; jj < grid[ii].size(); jj++) {
SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode"); SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode");
gridSerializationColumnNode.setIntProperty("dim", jj ); gridSerializationColumnNode.setIntProperty("dim", jj);
unsigned int index = 0; unsigned int index = 0;
gridSerializationColumnNode.setDoubleProperty("x", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("x", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("y", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("y", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("f", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("f", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fx", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("fx", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fy", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("fy", grid[ii][jj][index++]);
gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++] ); gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++]);
} }
} }
} }
...@@ -108,8 +108,8 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization ...@@ -108,8 +108,8 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5; int particle1, particle2, particle3, particle4, particle5;
int chiralCheckAtomIndex, gridIndex; int chiralCheckAtomIndex, gridIndex;
force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, 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 ); 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) ...@@ -124,10 +124,10 @@ void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node)
const SerializationNode& grids = node.getChildNode("TorsionTorsionGrids"); const SerializationNode& grids = node.getChildNode("TorsionTorsionGrids");
const std::vector<SerializationNode>& gridList = grids.getChildren(); 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; std::vector< std::vector< std::vector<double> > > gridVector;
loadGrid( gridList[ii], gridVector ); loadGrid(gridList[ii], gridVector);
force->setTorsionTorsionGrid( ii, gridVector ); force->setTorsionTorsionGrid(ii, gridVector);
} }
const SerializationNode& bonds = node.getChildNode("TorsionTorsion"); const SerializationNode& bonds = node.getChildNode("TorsionTorsion");
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ f11bafd9
...@@ -56,17 +56,17 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) ...@@ -56,17 +56,17 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
int ivIndex; int ivIndex;
double sigma, epsilon, reductionFactor; double sigma, epsilon, reductionFactor;
force.getParticleParameters( ii, ivIndex, sigma, epsilon, reductionFactor ); force.getParticleParameters(ii, ivIndex, sigma, epsilon, reductionFactor);
SerializationNode& particle = particles.createChildNode("Particle"); SerializationNode& particle = particles.createChildNode("Particle");
particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor); particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor);
std::vector< int > exclusions; std::vector< int > exclusions;
force.getParticleExclusions( ii, exclusions ); force.getParticleExclusions(ii, exclusions);
SerializationNode& particleExclusions = particle.createChildNode("ParticleExclusions"); SerializationNode& particleExclusions = particle.createChildNode("ParticleExclusions");
for (unsigned int jj = 0; jj < exclusions.size(); jj++) { 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 { ...@@ -77,9 +77,9 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
AmoebaVdwForce* force = new AmoebaVdwForce(); AmoebaVdwForce* force = new AmoebaVdwForce();
try { try {
force->setSigmaCombiningRule(node.getStringProperty( "SigmaCombiningRule" ) ); force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
force->setEpsilonCombiningRule(node.getStringProperty( "EpsilonCombiningRule" ) ); force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
force->setCutoff(node.getDoubleProperty( "VdwCutoff" ) ); force->setCutoff(node.getDoubleProperty("VdwCutoff"));
force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method")); force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));
const SerializationNode& particles = node.getChildNode("VdwParticles"); const SerializationNode& particles = node.getChildNode("VdwParticles");
...@@ -92,9 +92,9 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const { ...@@ -92,9 +92,9 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& particleExclusions = particle.getChildNode("ParticleExclusions"); const SerializationNode& particleExclusions = particle.getChildNode("ParticleExclusions");
std::vector< int > exclusions; std::vector< int > exclusions;
for (unsigned int jj = 0; jj < particleExclusions.getChildren().size(); jj++) { 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/src/AmoebaWcaDispersionForceProxy.cpp
View file @ f11bafd9
...@@ -56,7 +56,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN ...@@ -56,7 +56,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
SerializationNode& particles = node.createChildNode("WcaDispersionParticles"); SerializationNode& particles = node.createChildNode("WcaDispersionParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
double radius, epsilon; double radius, epsilon;
force.getParticleParameters( ii, radius, epsilon ); force.getParticleParameters(ii, radius, epsilon);
particles.createChildNode("Particle").setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon); particles.createChildNode("Particle").setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
} }
...@@ -69,21 +69,21 @@ void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node) ...@@ -69,21 +69,21 @@ void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node)
try { try {
force->setEpso( node.getDoubleProperty( "Epso" ) ); force->setEpso( node.getDoubleProperty("Epso"));
force->setEpsh( node.getDoubleProperty( "Epsh" ) ); force->setEpsh( node.getDoubleProperty("Epsh"));
force->setRmino( node.getDoubleProperty( "Rmino" ) ); force->setRmino( node.getDoubleProperty("Rmino"));
force->setRminh( node.getDoubleProperty( "Rminh" ) ); force->setRminh( node.getDoubleProperty("Rminh"));
force->setAwater( node.getDoubleProperty( "Awater" ) ); force->setAwater( node.getDoubleProperty("Awater"));
force->setShctd( node.getDoubleProperty( "Shctd" ) ); force->setShctd( node.getDoubleProperty("Shctd"));
force->setDispoff( node.getDoubleProperty( "Dispoff" ) ); force->setDispoff(node.getDoubleProperty("Dispoff"));
force->setSlevy( node.getDoubleProperty( "Slevy" ) ); force->setSlevy( node.getDoubleProperty("Slevy"));
const SerializationNode& particles = node.getChildNode("WcaDispersionParticles"); const SerializationNode& particles = node.getChildNode("WcaDispersionParticles");
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]; const SerializationNode& particle = particles.getChildren()[ii];
force->addParticle( particle.getDoubleProperty("radius"), particle.getDoubleProperty("epsilon")); force->addParticle(particle.getDoubleProperty("radius"), particle.getDoubleProperty("epsilon"));
} }
} }
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp
View file @ f11bafd9
...@@ -45,10 +45,10 @@ void testSerialization() { ...@@ -45,10 +45,10 @@ void testSerialization() {
// Create a Force. // Create a Force.
AmoebaAngleForce force1; AmoebaAngleForce force1;
force1.setAmoebaGlobalAngleCubic( 12.3 ); force1.setAmoebaGlobalAngleCubic(12.3);
force1.setAmoebaGlobalAngleQuartic( 98.7 ); force1.setAmoebaGlobalAngleQuartic(98.7);
force1.setAmoebaGlobalAnglePentic( 91.7 ); force1.setAmoebaGlobalAnglePentic(91.7);
force1.setAmoebaGlobalAngleSextic( 93.7 ); force1.setAmoebaGlobalAngleSextic(93.7);
force1.addAngle(0, 1, 3, 1.0, 2.0); force1.addAngle(0, 1, 3, 1.0, 2.0);
force1.addAngle(0, 2, 3, 2.0, 2.1); force1.addAngle(0, 2, 3, 2.0, 2.1);
force1.addAngle(2, 3, 5, 3.0, 2.2); force1.addAngle(2, 3, 5, 3.0, 2.2);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp
View file @ f11bafd9
...@@ -45,8 +45,8 @@ void testSerialization() { ...@@ -45,8 +45,8 @@ void testSerialization() {
// Create a Force. // Create a Force.
AmoebaBondForce force1; AmoebaBondForce force1;
force1.setAmoebaGlobalBondCubic( 12.3 ); force1.setAmoebaGlobalBondCubic(12.3);
force1.setAmoebaGlobalBondQuartic( 98.7 ); force1.setAmoebaGlobalBondQuartic(98.7);
force1.addBond(0, 1, 1.0, 2.0); force1.addBond(0, 1, 1.0, 2.0);
force1.addBond(0, 2, 2.0, 2.1); force1.addBond(0, 2, 2.0, 2.1);
force1.addBond(2, 3, 3.0, 2.2); force1.addBond(2, 3, 3.0, 2.2);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp
View file @ f11bafd9
...@@ -45,12 +45,12 @@ void testSerialization() { ...@@ -45,12 +45,12 @@ void testSerialization() {
// Create a Force. // Create a Force.
AmoebaGeneralizedKirkwoodForce force1; AmoebaGeneralizedKirkwoodForce force1;
force1.setSolventDielectric( 80.0 ); force1.setSolventDielectric( 80.0);
force1.setSoluteDielectric( 1.0 ); force1.setSoluteDielectric( 1.0);
//force1.setDielectricOffset( 0.09 ); //force1.setDielectricOffset( 0.09);
force1.setProbeRadius( 1.40 ); force1.setProbeRadius( 1.40);
force1.setSurfaceAreaFactor( 0.888 ); force1.setSurfaceAreaFactor( 0.888);
force1.setIncludeCavityTerm( 1 ); force1.setIncludeCavityTerm( 1);
force1.addParticle(1.0, 2.0, 0.9); force1.addParticle(1.0, 2.0, 0.9);
force1.addParticle(-1.1,2.1, 0.8); force1.addParticle(-1.1,2.1, 0.8);
...@@ -60,14 +60,6 @@ void testSerialization() { ...@@ -60,14 +60,6 @@ void testSerialization() {
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaGeneralizedKirkwoodForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaGeneralizedKirkwoodForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("GeneralizedKirkwood.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaGeneralizedKirkwoodForce* copy = XmlSerializer::deserialize<AmoebaGeneralizedKirkwoodForce>(buffer); AmoebaGeneralizedKirkwoodForce* copy = XmlSerializer::deserialize<AmoebaGeneralizedKirkwoodForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
...@@ -85,8 +77,8 @@ void testSerialization() { ...@@ -85,8 +77,8 @@ void testSerialization() {
double radius1, charge1, scaleFactor1; double radius1, charge1, scaleFactor1;
double radius2, charge2, scaleFactor2; double radius2, charge2, scaleFactor2;
force1.getParticleParameters( ii, charge1, radius1, scaleFactor1 ); force1.getParticleParameters(ii, charge1, radius1, scaleFactor1);
force2.getParticleParameters( ii, charge2, radius2, scaleFactor2 ); force2.getParticleParameters(ii, charge2, radius2, scaleFactor2);
ASSERT_EQUAL(charge1, charge2); ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(radius1, radius2); ASSERT_EQUAL(radius1, radius2);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp
View file @ f11bafd9
...@@ -46,10 +46,10 @@ void testSerialization() { ...@@ -46,10 +46,10 @@ void testSerialization() {
AmoebaInPlaneAngleForce force1; AmoebaInPlaneAngleForce force1;
force1.setAmoebaGlobalInPlaneAngleCubic( 12.3 ); force1.setAmoebaGlobalInPlaneAngleCubic(12.3);
force1.setAmoebaGlobalInPlaneAngleQuartic( 98.7 ); force1.setAmoebaGlobalInPlaneAngleQuartic(98.7);
force1.setAmoebaGlobalInPlaneAnglePentic( 91.7 ); force1.setAmoebaGlobalInPlaneAnglePentic(91.7);
force1.setAmoebaGlobalInPlaneAngleSextic( 93.7 ); force1.setAmoebaGlobalInPlaneAngleSextic(93.7);
force1.addAngle(0, 1, 3, 4, 1.0, 2.0); force1.addAngle(0, 1, 3, 4, 1.0, 2.0);
force1.addAngle(0, 2, 3, 5, 2.0, 2.1); force1.addAngle(0, 2, 3, 5, 2.0, 2.1);
...@@ -71,7 +71,7 @@ void testSerialization() { ...@@ -71,7 +71,7 @@ void testSerialization() {
ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleSextic(), force2.getAmoebaGlobalInPlaneAngleSextic()); ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleSextic(), force2.getAmoebaGlobalInPlaneAngleSextic());
ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles()); ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles());
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) {
int a1, a2, a3, a4, b1, b2, b3, b4; int a1, a2, a3, a4, b1, b2, b3, b4;
double da, db, ka, kb; double da, db, ka, kb;
force1.getAngleParameters(ii, a1, a2, a3, a4, da, ka); force1.getAngleParameters(ii, a1, a2, a3, a4, da, ka);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ f11bafd9
...@@ -42,56 +42,56 @@ using namespace std; ...@@ -42,56 +42,56 @@ using namespace std;
extern "C" void registerAmoebaSerializationProxies(); extern "C" void registerAmoebaSerializationProxies();
static void getCovalentTypes( std::vector<std::string>& covalentTypes ){ static void getCovalentTypes(std::vector<std::string>& covalentTypes) {
covalentTypes.push_back( "Covalent12" ); covalentTypes.push_back("Covalent12");
covalentTypes.push_back( "Covalent13" ); covalentTypes.push_back("Covalent13");
covalentTypes.push_back( "Covalent14" ); covalentTypes.push_back("Covalent14");
covalentTypes.push_back( "Covalent15" ); covalentTypes.push_back("Covalent15");
covalentTypes.push_back( "PolarizationCovalent11" ); covalentTypes.push_back("PolarizationCovalent11");
covalentTypes.push_back( "PolarizationCovalent12" ); covalentTypes.push_back("PolarizationCovalent12");
covalentTypes.push_back( "PolarizationCovalent13" ); covalentTypes.push_back("PolarizationCovalent13");
covalentTypes.push_back( "PolarizationCovalent14" ); covalentTypes.push_back("PolarizationCovalent14");
} }
void testSerialization() { void testSerialization() {
// Create a Force. // Create a Force.
AmoebaMultipoleForce force1; AmoebaMultipoleForce force1;
force1.setNonbondedMethod( AmoebaMultipoleForce::NoCutoff ); force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
force1.setCutoffDistance( 0.9 ); force1.setCutoffDistance(0.9);
force1.setAEwald( 0.544 ); force1.setAEwald(0.544);
//force1.setPmeBSplineOrder( 4 ); //force1.setPmeBSplineOrder(4);
std::vector<int> gridDimension; std::vector<int> gridDimension;
gridDimension.push_back( 64 ); gridDimension.push_back(64);
gridDimension.push_back( 63 ); gridDimension.push_back(63);
gridDimension.push_back( 61 ); gridDimension.push_back(61);
force1.setPmeGridDimensions( gridDimension ); force1.setPmeGridDimensions(gridDimension);
//force1.setMutualInducedIterationMethod( AmoebaMultipoleForce::SOR ); //force1.setMutualInducedIterationMethod(AmoebaMultipoleForce::SOR);
force1.setMutualInducedMaxIterations( 200 ); force1.setMutualInducedMaxIterations(200);
force1.setMutualInducedTargetEpsilon( 1.0e-05 ); force1.setMutualInducedTargetEpsilon(1.0e-05);
//force1.setElectricConstant( 138.93 ); //force1.setElectricConstant(138.93);
force1.setEwaldErrorTolerance( 1.0e-05 ); force1.setEwaldErrorTolerance(1.0e-05);
std::vector<std::string> covalentTypes; std::vector<std::string> covalentTypes;
getCovalentTypes( covalentTypes ); getCovalentTypes(covalentTypes);
for( unsigned int ii = 0; ii < 3; ii++ ){ for (unsigned int ii = 0; ii < 3; ii++) {
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole; std::vector<double> molecularQuadrupole;
molecularDipole.push_back( 0.1 ); molecularDipole.push_back( rand() ); molecularDipole.push_back( rand() ); molecularDipole.push_back(0.1); molecularDipole.push_back(rand()); molecularDipole.push_back(rand());
for( unsigned int jj = 0; jj < 9; jj++ ){ for (unsigned int jj = 0; jj < 9; jj++) {
molecularQuadrupole.push_back( static_cast<double>(rand()) ); molecularQuadrupole.push_back(static_cast<double>(rand()));
} }
force1.addMultipole( static_cast<double>(ii+1), molecularDipole, molecularQuadrupole, AmoebaMultipoleForce::Bisector, force1.addMultipole(static_cast<double>(ii+1), molecularDipole, molecularQuadrupole, AmoebaMultipoleForce::Bisector,
ii+1, ii+2, ii+3, static_cast<double>(rand()), static_cast<double>(rand()), static_cast<double>(rand()) ); ii+1, ii+2, ii+3, static_cast<double>(rand()), static_cast<double>(rand()), static_cast<double>(rand()));
for( unsigned int jj = 0; jj < covalentTypes.size(); jj++ ){ for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector< int > covalentMap; std::vector< int > covalentMap;
covalentMap.push_back( ii*jj ); covalentMap.push_back( rand() ); covalentMap.push_back( rand() ); covalentMap.push_back(ii*jj); covalentMap.push_back(rand()); covalentMap.push_back(rand());
force1.setCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap); force1.setCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
} }
} }
...@@ -99,13 +99,6 @@ void testSerialization() { ...@@ -99,13 +99,6 @@ void testSerialization() {
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaMultipoleForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaMultipoleForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("Multipole.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaMultipoleForce* copy = XmlSerializer::deserialize<AmoebaMultipoleForce>(buffer); AmoebaMultipoleForce* copy = XmlSerializer::deserialize<AmoebaMultipoleForce>(buffer);
...@@ -125,10 +118,10 @@ void testSerialization() { ...@@ -125,10 +118,10 @@ void testSerialization() {
std::vector<int> gridDimension1; std::vector<int> gridDimension1;
std::vector<int> gridDimension2; std::vector<int> gridDimension2;
force1.getPmeGridDimensions( gridDimension1 ); force1.getPmeGridDimensions(gridDimension1);
force2.getPmeGridDimensions( gridDimension2 ); force2.getPmeGridDimensions(gridDimension2);
ASSERT_EQUAL(gridDimension1.size(), gridDimension2.size()); ASSERT_EQUAL(gridDimension1.size(), gridDimension2.size());
for( unsigned int jj = 0; jj < gridDimension1.size(); jj++ ){ for (unsigned int jj = 0; jj < gridDimension1.size(); jj++) {
ASSERT_EQUAL(gridDimension1[jj], gridDimension2[jj]); ASSERT_EQUAL(gridDimension1[jj], gridDimension2[jj]);
} }
...@@ -147,11 +140,11 @@ void testSerialization() { ...@@ -147,11 +140,11 @@ void testSerialization() {
std::vector<double> molecularDipole2; std::vector<double> molecularDipole2;
std::vector<double> molecularQuadrupole2; std::vector<double> molecularQuadrupole2;
force1.getMultipoleParameters( ii, charge1, molecularDipole1, molecularQuadrupole1, axisType1, multipoleAtomZ1, multipoleAtomX1, multipoleAtomY1, force1.getMultipoleParameters(ii, charge1, molecularDipole1, molecularQuadrupole1, axisType1, multipoleAtomZ1, multipoleAtomX1, multipoleAtomY1,
thole1, dampingFactor1, polarity1 ); thole1, dampingFactor1, polarity1);
force2.getMultipoleParameters( ii, charge2, molecularDipole2, molecularQuadrupole2, axisType2, multipoleAtomZ2, multipoleAtomX2, multipoleAtomY2, force2.getMultipoleParameters(ii, charge2, molecularDipole2, molecularQuadrupole2, axisType2, multipoleAtomZ2, multipoleAtomX2, multipoleAtomY2,
thole2, dampingFactor2, polarity2 ); thole2, dampingFactor2, polarity2);
ASSERT_EQUAL(charge1, charge2); ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(axisType1, axisType2); ASSERT_EQUAL(axisType1, axisType2);
...@@ -162,25 +155,25 @@ void testSerialization() { ...@@ -162,25 +155,25 @@ void testSerialization() {
ASSERT_EQUAL(dampingFactor1, dampingFactor2); ASSERT_EQUAL(dampingFactor1, dampingFactor2);
ASSERT_EQUAL(polarity1, polarity2); ASSERT_EQUAL(polarity1, polarity2);
ASSERT_EQUAL(molecularDipole1.size(), molecularDipole2.size() ); ASSERT_EQUAL(molecularDipole1.size(), molecularDipole2.size());
ASSERT_EQUAL(molecularDipole1.size(), 3 ); ASSERT_EQUAL(molecularDipole1.size(), 3);
for (unsigned int jj = 0; jj < molecularDipole1.size(); jj++) { for (unsigned int jj = 0; jj < molecularDipole1.size(); jj++) {
ASSERT_EQUAL(molecularDipole1[jj], molecularDipole2[jj] ); ASSERT_EQUAL(molecularDipole1[jj], molecularDipole2[jj]);
} }
ASSERT_EQUAL(molecularQuadrupole1.size(), molecularQuadrupole2.size() ); ASSERT_EQUAL(molecularQuadrupole1.size(), molecularQuadrupole2.size());
ASSERT_EQUAL(molecularQuadrupole1.size(), 9 ); ASSERT_EQUAL(molecularQuadrupole1.size(), 9);
for (unsigned int jj = 0; jj < molecularQuadrupole1.size(); jj++) { for (unsigned int jj = 0; jj < molecularQuadrupole1.size(); jj++) {
ASSERT_EQUAL(molecularQuadrupole1[jj], molecularQuadrupole2[jj] ); ASSERT_EQUAL(molecularQuadrupole1[jj], molecularQuadrupole2[jj]);
} }
for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) { for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
std::vector<int> covalentMap1; std::vector<int> covalentMap1;
std::vector<int> covalentMap2; std::vector<int> covalentMap2;
force1.getCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap1 ); force1.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap1);
force2.getCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap2 ); force2.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap2);
ASSERT_EQUAL(covalentMap1.size(), covalentMap2.size() ); ASSERT_EQUAL(covalentMap1.size(), covalentMap2.size());
for (unsigned int kk = 0; kk < covalentMap1.size(); kk++) { for (unsigned int kk = 0; kk < covalentMap1.size(); kk++) {
ASSERT_EQUAL(covalentMap1[kk], covalentMap2[kk] ); ASSERT_EQUAL(covalentMap1[kk], covalentMap2[kk]);
} }
} }
} }
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp
View file @ f11bafd9
...@@ -46,10 +46,10 @@ void testSerialization() { ...@@ -46,10 +46,10 @@ void testSerialization() {
AmoebaOutOfPlaneBendForce force1; AmoebaOutOfPlaneBendForce force1;
force1.setAmoebaGlobalOutOfPlaneBendCubic( 12.3 ); force1.setAmoebaGlobalOutOfPlaneBendCubic(12.3);
force1.setAmoebaGlobalOutOfPlaneBendQuartic( 98.7 ); force1.setAmoebaGlobalOutOfPlaneBendQuartic(98.7);
force1.setAmoebaGlobalOutOfPlaneBendPentic( 91.7 ); force1.setAmoebaGlobalOutOfPlaneBendPentic(91.7);
force1.setAmoebaGlobalOutOfPlaneBendSextic( 93.7 ); force1.setAmoebaGlobalOutOfPlaneBendSextic(93.7);
force1.addOutOfPlaneBend(0, 1, 3, 4, 2.0); force1.addOutOfPlaneBend(0, 1, 3, 4, 2.0);
force1.addOutOfPlaneBend(0, 2, 3, 5, 2.1); force1.addOutOfPlaneBend(0, 2, 3, 5, 2.1);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp
View file @ f11bafd9
...@@ -42,27 +42,27 @@ using namespace std; ...@@ -42,27 +42,27 @@ using namespace std;
extern "C" void registerAmoebaSerializationProxies(); extern "C" void registerAmoebaSerializationProxies();
static void loadTorsionTorsionGrid( std::vector< std::vector< std::vector<double> > >& gridVector ){ static void loadTorsionTorsionGrid(std::vector< std::vector< std::vector<double> > >& gridVector) {
static const int gridSize = 25; static const int gridSize = 25;
gridVector.resize( gridSize ); gridVector.resize(gridSize);
for( unsigned int ii = 0; ii < gridSize; ii++ ){ for (unsigned int ii = 0; ii < gridSize; ii++) {
gridVector[ii].resize( gridSize ); gridVector[ii].resize(gridSize);
for( unsigned int jj = 0; jj < gridSize; jj++ ){ for (unsigned int jj = 0; jj < gridSize; jj++) {
gridVector[ii][jj].resize( 6 ); gridVector[ii][jj].resize(6);
for( unsigned int kk = 0; kk < 6; kk++ ){ for (unsigned int kk = 0; kk < 6; kk++) {
gridVector[ii][jj][0] = -180.0 + 15.0*static_cast<double>(ii); gridVector[ii][jj][0] = -180.0 + 15.0*static_cast<double>(ii);
gridVector[ii][jj][1] = -180.0 + 15.0*static_cast<double>(jj); gridVector[ii][jj][1] = -180.0 + 15.0*static_cast<double>(jj);
gridVector[ii][jj][2] = static_cast<double>( rand()); gridVector[ii][jj][2] = static_cast<double>(rand());
gridVector[ii][jj][3] = static_cast<double>( rand()); gridVector[ii][jj][3] = static_cast<double>(rand());
gridVector[ii][jj][4] = static_cast<double>( rand()); gridVector[ii][jj][4] = static_cast<double>(rand());
gridVector[ii][jj][5] = static_cast<double>( rand()); gridVector[ii][jj][5] = static_cast<double>(rand());
} }
} }
} }
} }
static void compareGrids( const std::vector< std::vector< std::vector<double> > >& grid1, const std::vector< std::vector< std::vector<double> > >& grid2 ) { static void compareGrids(const std::vector< std::vector< std::vector<double> > >& grid1, const std::vector< std::vector< std::vector<double> > >& grid2) {
ASSERT_EQUAL(grid1.size(), grid2.size()); ASSERT_EQUAL(grid1.size(), grid2.size());
for (unsigned int ii = 0; ii < grid1.size(); ii++) { for (unsigned int ii = 0; ii < grid1.size(); ii++) {
...@@ -81,27 +81,19 @@ void testSerialization() { ...@@ -81,27 +81,19 @@ void testSerialization() {
AmoebaTorsionTorsionForce force1; AmoebaTorsionTorsionForce force1;
for( unsigned int ii = 0; ii < 5; ii++ ){ for (unsigned int ii = 0; ii < 5; ii++) {
std::vector< std::vector< std::vector<double> > > gridVector; std::vector< std::vector< std::vector<double> > > gridVector;
loadTorsionTorsionGrid( gridVector ); loadTorsionTorsionGrid(gridVector);
force1.setTorsionTorsionGrid( ii, gridVector ); force1.setTorsionTorsionGrid(ii, gridVector);
} }
for( unsigned int ii = 0; ii < 5; ii++ ){ for (unsigned int ii = 0; ii < 5; ii++) {
force1.addTorsionTorsion( ii, ii+1,ii+3, ii+4, ii+5, ( (ii % 2 ) ? 1 : 0), (ii % 4) ); force1.addTorsionTorsion(ii, ii+1,ii+3, ii+4, ii+5, ((ii % 2) ? 1 : 0), (ii % 4));
} }
// Serialize and then deserialize it. // Serialize and then deserialize it.
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaTorsionTorsionForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaTorsionTorsionForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("TorsionTorsion.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaTorsionTorsionForce* copy = XmlSerializer::deserialize<AmoebaTorsionTorsionForce>(buffer); AmoebaTorsionTorsionForce* copy = XmlSerializer::deserialize<AmoebaTorsionTorsionForce>(buffer);
// Compare the two force1s to see if they are identical. // Compare the two force1s to see if they are identical.
...@@ -112,8 +104,8 @@ void testSerialization() { ...@@ -112,8 +104,8 @@ void testSerialization() {
int a1, a2, a3, a4, a5, aChiral, aGridIndex, b1, b2, b3, b4, b5, bChiral, bGridIndex; int a1, a2, a3, a4, a5, aChiral, aGridIndex, b1, b2, b3, b4, b5, bChiral, bGridIndex;
force1.getTorsionTorsionParameters( ii, a1, a2, a3, a4, a5, aChiral, aGridIndex); force1.getTorsionTorsionParameters(ii, a1, a2, a3, a4, a5, aChiral, aGridIndex);
force2.getTorsionTorsionParameters( ii, b1, b2, b3, b4, b5, bChiral, bGridIndex); force2.getTorsionTorsionParameters(ii, b1, b2, b3, b4, b5, bChiral, bGridIndex);
ASSERT_EQUAL(a1, b1); ASSERT_EQUAL(a1, b1);
ASSERT_EQUAL(a2, b2); ASSERT_EQUAL(a2, b2);
...@@ -121,14 +113,14 @@ void testSerialization() { ...@@ -121,14 +113,14 @@ void testSerialization() {
ASSERT_EQUAL(a4, b4); ASSERT_EQUAL(a4, b4);
ASSERT_EQUAL(a5, b5); ASSERT_EQUAL(a5, b5);
ASSERT_EQUAL(aChiral, bChiral); ASSERT_EQUAL(aChiral, bChiral);
ASSERT_EQUAL(aGridIndex, bGridIndex ); ASSERT_EQUAL(aGridIndex, bGridIndex);
} }
ASSERT_EQUAL(force1.getNumTorsionTorsionGrids(), force2.getNumTorsionTorsionGrids()); ASSERT_EQUAL(force1.getNumTorsionTorsionGrids(), force2.getNumTorsionTorsionGrids());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsionGrids()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsionGrids()); ii++) {
const std::vector< std::vector< std::vector<double> > >& grid1 = force1.getTorsionTorsionGrid( ii ); const std::vector< std::vector< std::vector<double> > >& grid1 = force1.getTorsionTorsionGrid(ii);
const std::vector< std::vector< std::vector<double> > >& grid2 = force2.getTorsionTorsionGrid( ii ); const std::vector< std::vector< std::vector<double> > >& grid2 = force2.getTorsionTorsionGrid(ii);
compareGrids(grid1, grid2 ); compareGrids(grid1, grid2);
} }
} }
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp
View file @ f11bafd9
...@@ -45,34 +45,26 @@ void testSerialization() { ...@@ -45,34 +45,26 @@ void testSerialization() {
// Create a Force. // Create a Force.
AmoebaVdwForce force1; AmoebaVdwForce force1;
force1.setSigmaCombiningRule( "GEOMETRIC" ); force1.setSigmaCombiningRule("GEOMETRIC");
force1.setEpsilonCombiningRule( "GEOMETRIC" ); force1.setEpsilonCombiningRule("GEOMETRIC");
force1.setCutoff( 0.9 ); force1.setCutoff(0.9);
force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic); force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
force1.addParticle(0, 1.0, 2.0, 0.9); force1.addParticle(0, 1.0, 2.0, 0.9);
force1.addParticle(1, 1.1, 2.1, 0.9); force1.addParticle(1, 1.1, 2.1, 0.9);
force1.addParticle(2, 1.3, 4.1, 0.9); force1.addParticle(2, 1.3, 4.1, 0.9);
for( unsigned int ii = 0; ii < 3; ii++ ){ for (unsigned int ii = 0; ii < 3; ii++) {
std::vector< int > exclusions; std::vector< int > exclusions;
exclusions.push_back( ii ); exclusions.push_back(ii);
exclusions.push_back( ii + 1 ); exclusions.push_back(ii + 1);
exclusions.push_back( ii + 10 ); exclusions.push_back(ii + 10);
force1.setParticleExclusions( ii, exclusions ); force1.setParticleExclusions(ii, exclusions);
} }
// Serialize and then deserialize it. // Serialize and then deserialize it.
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("Vdw.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer); AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
...@@ -93,10 +85,10 @@ void testSerialization() { ...@@ -93,10 +85,10 @@ void testSerialization() {
double sigma1, epsilon1, reductionFactor1; double sigma1, epsilon1, reductionFactor1;
double sigma2, epsilon2, reductionFactor2; double sigma2, epsilon2, reductionFactor2;
force1.getParticleParameters( ii, ivIndex1, sigma1, epsilon1, reductionFactor1 ); force1.getParticleParameters(ii, ivIndex1, sigma1, epsilon1, reductionFactor1);
force2.getParticleParameters( ii, ivIndex2, sigma2, epsilon2, reductionFactor2 ); force2.getParticleParameters(ii, ivIndex2, sigma2, epsilon2, reductionFactor2);
ASSERT_EQUAL(ivIndex1, ivIndex2 ); ASSERT_EQUAL(ivIndex1, ivIndex2);
ASSERT_EQUAL(sigma1, sigma2); ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2); ASSERT_EQUAL(epsilon1, epsilon2);
ASSERT_EQUAL(reductionFactor1, reductionFactor2); ASSERT_EQUAL(reductionFactor1, reductionFactor2);
...@@ -106,14 +98,14 @@ void testSerialization() { ...@@ -106,14 +98,14 @@ void testSerialization() {
std::vector< int > exclusions1; std::vector< int > exclusions1;
std::vector< int > exclusions2; std::vector< int > exclusions2;
force1.getParticleExclusions( ii, exclusions1 ); force1.getParticleExclusions(ii, exclusions1);
force2.getParticleExclusions( ii, exclusions2 ); force2.getParticleExclusions(ii, exclusions2);
ASSERT_EQUAL(exclusions1.size(), exclusions2.size()); ASSERT_EQUAL(exclusions1.size(), exclusions2.size());
for (unsigned int jj = 0; jj < exclusions1.size(); jj++) { for (unsigned int jj = 0; jj < exclusions1.size(); jj++) {
int hit = 0; int hit = 0;
for (unsigned int kk = 0; kk < exclusions2.size(); kk++) { for (unsigned int kk = 0; kk < exclusions2.size(); kk++) {
if( exclusions2[jj] == exclusions1[kk] )hit++; if (exclusions2[jj] == exclusions1[kk])hit++;
} }
ASSERT_EQUAL(hit, 1); ASSERT_EQUAL(hit, 1);
} }
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp
View file @ f11bafd9
...@@ -45,14 +45,14 @@ void testSerialization() { ...@@ -45,14 +45,14 @@ void testSerialization() {
// Create a Force. // Create a Force.
AmoebaWcaDispersionForce force1; AmoebaWcaDispersionForce force1;
force1.setEpso( 1.0 ); force1.setEpso( 1.0);
force1.setEpsh( 1.1 ); force1.setEpsh( 1.1);
force1.setRmino( 1.2 ); force1.setRmino( 1.2);
force1.setRminh( 1.3 ); force1.setRminh( 1.3);
force1.setAwater( 1.4 ); force1.setAwater( 1.4);
force1.setShctd( 1.5 ); force1.setShctd( 1.5);
force1.setDispoff( 1.6 ); force1.setDispoff(1.6);
force1.setSlevy( 1.7 ); force1.setSlevy( 1.7);
force1.addParticle(1.0, 2.0); force1.addParticle(1.0, 2.0);
force1.addParticle(1.1, 2.1); force1.addParticle(1.1, 2.1);
...@@ -62,14 +62,6 @@ void testSerialization() { ...@@ -62,14 +62,6 @@ void testSerialization() {
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaWcaDispersionForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaWcaDispersionForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("WcaDispersion.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaWcaDispersionForce* copy = XmlSerializer::deserialize<AmoebaWcaDispersionForce>(buffer); AmoebaWcaDispersionForce* copy = XmlSerializer::deserialize<AmoebaWcaDispersionForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
...@@ -91,8 +83,8 @@ void testSerialization() { ...@@ -91,8 +83,8 @@ void testSerialization() {
double radius1, epsilon1; double radius1, epsilon1;
double radius2, epsilon2; double radius2, epsilon2;
force1.getParticleParameters( ii, radius1, epsilon1 ); force1.getParticleParameters(ii, radius1, epsilon1);
force2.getParticleParameters( ii, radius2, epsilon2 ); force2.getParticleParameters(ii, radius2, epsilon2);
ASSERT_EQUAL(radius1, radius2); ASSERT_EQUAL(radius1, radius2);
ASSERT_EQUAL(epsilon1, epsilon2); ASSERT_EQUAL(epsilon1, epsilon2);
......
plugins/amoeba/wrappers/generateAmoebaWrappers.py
View file @ f11bafd9
...@@ -327,7 +327,7 @@ extern "C" { ...@@ -327,7 +327,7 @@ extern "C" {
/* OpenMM_3D_DoubleArray */ /* OpenMM_3D_DoubleArray */
OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int size1, int size2, int size3); OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int size1, int size2, int size3);
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array, int index1, int index2, OpenMM_DoubleArray* values); OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array, int index1, int index2, OpenMM_DoubleArray* values);
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array);""", file=self.out) OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy(OpenMM_3D_DoubleArray* array);""", file=self.out)
self.writeClasses() self.writeClasses()
...@@ -586,29 +586,29 @@ OPENMM_EXPORT_AMOEBA int OpenMM_2D_IntArray_getSize(const OpenMM_2D_IntArray* ar ...@@ -586,29 +586,29 @@ OPENMM_EXPORT_AMOEBA int OpenMM_2D_IntArray_getSize(const OpenMM_2D_IntArray* ar
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_resize(OpenMM_2D_IntArray* array, int size) { OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_resize(OpenMM_2D_IntArray* array, int size) {
reinterpret_cast<vector<vector<int> >*>(array)->resize(size); reinterpret_cast<vector<vector<int> >*>(array)->resize(size);
} }
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_append(OpenMM_2D_IntArray* array, int index1, int value ) { OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_append(OpenMM_2D_IntArray* array, int index1, int value) {
vector<vector<int> >* array2DInt = reinterpret_cast<vector<vector<int> >*>(array); vector<vector<int> >* array2DInt = reinterpret_cast<vector<vector<int> >*>(array);
if( array2DInt->size() <= index1 ){ if (array2DInt->size() <= index1) {
array2DInt->resize( index1+1 ); array2DInt->resize(index1+1);
} }
(*array2DInt)[index1].push_back( value ); (*array2DInt)[index1].push_back(value);
} }
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_set(OpenMM_2D_IntArray* array, int index1, int index2, int value) { OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_set(OpenMM_2D_IntArray* array, int index1, int index2, int value) {
vector<vector<int> >* array2DInt = reinterpret_cast<vector<vector<int> >*>(array); vector<vector<int> >* array2DInt = reinterpret_cast<vector<vector<int> >*>(array);
if( array2DInt->size() <= index1 ){ if (array2DInt->size() <= index1) {
array2DInt->resize( index1+1 ); array2DInt->resize(index1+1);
} }
if( array2DInt[index1].size() <= index2 ){ if (array2DInt[index1].size() <= index2) {
array2DInt[index1].resize( index2+1 ); array2DInt[index1].resize(index2+1);
} }
(*array2DInt)[index1][index2] = value; (*array2DInt)[index1][index2] = value;
} }
OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_get(const OpenMM_2D_IntArray* array, int index1, int index2, int* value) { OPENMM_EXPORT_AMOEBA void OpenMM_2D_IntArray_get(const OpenMM_2D_IntArray* array, int index1, int index2, int* value) {
const vector<vector<int> >* array2DInt = reinterpret_cast<const vector<vector<int> >*>(array); const vector<vector<int> >* array2DInt = reinterpret_cast<const vector<vector<int> >*>(array);
if ( array2DInt->size() <= index1 ) if (array2DInt->size() <= index1)
throw OpenMMException("OpenMM_2D_IntArray_get: first index out of range."); throw OpenMMException("OpenMM_2D_IntArray_get: first index out of range.");
if ( (*array2DInt)[index1].size() <= index2 ) if ((*array2DInt)[index1].size() <= index2)
throw OpenMMException("OpenMM_2D_IntArray_get: second index out of range."); throw OpenMMException("OpenMM_2D_IntArray_get: second index out of range.");
*value = (*array2DInt)[index1][index2]; *value = (*array2DInt)[index1][index2];
} }
...@@ -618,9 +618,9 @@ OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int siz ...@@ -618,9 +618,9 @@ OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int siz
int ii, jj; int ii, jj;
std::vector< std::vector< std::vector<double> > >* v3D_Array = new std::vector<std::vector<std::vector<double> > >(size1); std::vector< std::vector< std::vector<double> > >* v3D_Array = new std::vector<std::vector<std::vector<double> > >(size1);
for( ii = 0; ii < size1; ii++ ){ for (ii = 0; ii < size1; ii++) {
(*v3D_Array)[ii].resize(size2); (*v3D_Array)[ii].resize(size2);
for( jj = 0; jj < size2; jj++ ){ for (jj = 0; jj < size2; jj++) {
(*v3D_Array)[ii][jj].resize(size3); (*v3D_Array)[ii][jj].resize(size3);
} }
} }
...@@ -631,12 +631,12 @@ OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array ...@@ -631,12 +631,12 @@ OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array
unsigned int ii; unsigned int ii;
std::vector< std::vector< std::vector<double> > >* v3D_Array = reinterpret_cast<std::vector<std::vector<std::vector<double> > >*>(array); std::vector< std::vector< std::vector<double> > >* v3D_Array = reinterpret_cast<std::vector<std::vector<std::vector<double> > >*>(array);
std::vector<double> * value_array = reinterpret_cast<std::vector<double> *>(values); std::vector<double> * value_array = reinterpret_cast<std::vector<double> *>(values);
for( ii = 0; ii < (*value_array).size(); ii++ ){ for (ii = 0; ii < (*value_array).size(); ii++) {
(*v3D_Array)[index1][index2][ii] = (*value_array)[ii]; (*v3D_Array)[index1][index2][ii] = (*value_array)[ii];
} }
} }
OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array) { OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy(OpenMM_3D_DoubleArray* array) {
delete reinterpret_cast<std::vector<std::vector<std::vector<double> > >*>(array); delete reinterpret_cast<std::vector<std::vector<std::vector<double> > >*>(array);
}""", file=self.out) }""", file=self.out)
......
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