Merge remote-tracking branch 'upstream/master'

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp

@@ -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

@@ -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

@@ -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/src/AmoebaWcaDispersionForceProxy.cpp

@@ -56,7 +56,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
     SerializationNode& particles = node.createChildNode("WcaDispersionParticles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
         double radius, epsilon;
-        force.getParticleParameters( ii,  radius, epsilon );
+        force.getParticleParameters(ii,  radius, epsilon);
         particles.createChildNode("Particle").setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
     }
 
@@ -69,21 +69,21 @@ void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node)
 
     try {
 
-        force->setEpso(    node.getDoubleProperty( "Epso" ) );
-        force->setEpsh(    node.getDoubleProperty( "Epsh" ) );
-        force->setRmino(   node.getDoubleProperty( "Rmino" ) );
-        force->setRminh(   node.getDoubleProperty( "Rminh" ) );
+        force->setEpso(   node.getDoubleProperty("Epso"));
+        force->setEpsh(   node.getDoubleProperty("Epsh"));
+        force->setRmino(  node.getDoubleProperty("Rmino"));
+        force->setRminh(  node.getDoubleProperty("Rminh"));
 
 
-        force->setAwater(  node.getDoubleProperty( "Awater" ) );
-        force->setShctd(   node.getDoubleProperty( "Shctd" ) );
-        force->setDispoff( node.getDoubleProperty( "Dispoff" ) );
-        force->setSlevy(   node.getDoubleProperty( "Slevy" ) );
+        force->setAwater( node.getDoubleProperty("Awater"));
+        force->setShctd(  node.getDoubleProperty("Shctd"));
+        force->setDispoff(node.getDoubleProperty("Dispoff"));
+        force->setSlevy(  node.getDoubleProperty("Slevy"));
 
         const SerializationNode& particles = node.getChildNode("WcaDispersionParticles");
         for (unsigned int ii = 0; ii < particles.getChildren().size(); 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

@@ -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

@@ -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);

plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp

@@ -45,12 +45,12 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaGeneralizedKirkwoodForce force1;
-    force1.setSolventDielectric(   80.0 );
-    force1.setSoluteDielectric(    1.0 );
-    //force1.setDielectricOffset(    0.09 );
-    force1.setProbeRadius(         1.40 );
-    force1.setSurfaceAreaFactor(   0.888 );
-    force1.setIncludeCavityTerm(   1 );
+    force1.setSolventDielectric(  80.0);
+    force1.setSoluteDielectric(   1.0);
+    //force1.setDielectricOffset(   0.09);
+    force1.setProbeRadius(        1.40);
+    force1.setSurfaceAreaFactor(  0.888);
+    force1.setIncludeCavityTerm(  1);
 
     force1.addParticle(1.0, 2.0, 0.9);
     force1.addParticle(-1.1,2.1, 0.8);
@@ -60,14 +60,6 @@ void testSerialization() {
 
     stringstream 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);
 
     // Compare the two forces to see if they are identical.  
@@ -85,8 +77,8 @@ void testSerialization() {
         double radius1, charge1, scaleFactor1;
         double radius2, charge2, scaleFactor2;
 
-        force1.getParticleParameters( ii, charge1, radius1, scaleFactor1 );
-        force2.getParticleParameters( ii, charge2, radius2, scaleFactor2 );
+        force1.getParticleParameters(ii, charge1, radius1, scaleFactor1);
+        force2.getParticleParameters(ii, charge2, radius2, scaleFactor2);
 
         ASSERT_EQUAL(charge1,      charge2);
         ASSERT_EQUAL(radius1,      radius2);

plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp

@@ -46,10 +46,10 @@ void testSerialization() {
 
     AmoebaInPlaneAngleForce force1;
 
-    force1.setAmoebaGlobalInPlaneAngleCubic( 12.3 );
-    force1.setAmoebaGlobalInPlaneAngleQuartic( 98.7 );
-    force1.setAmoebaGlobalInPlaneAnglePentic( 91.7 );
-    force1.setAmoebaGlobalInPlaneAngleSextic( 93.7 );
+    force1.setAmoebaGlobalInPlaneAngleCubic(12.3);
+    force1.setAmoebaGlobalInPlaneAngleQuartic(98.7);
+    force1.setAmoebaGlobalInPlaneAnglePentic(91.7);
+    force1.setAmoebaGlobalInPlaneAngleSextic(93.7);
 
     force1.addAngle(0, 1, 3, 4, 1.0, 2.0);
     force1.addAngle(0, 2, 3, 5, 2.0, 2.1);
@@ -71,7 +71,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleSextic(),   force2.getAmoebaGlobalInPlaneAngleSextic());
     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;
         double da, db, ka, kb;
         force1.getAngleParameters(ii, a1, a2, a3, a4, da, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp

@@ -42,56 +42,56 @@ using namespace std;
 
 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( "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");
 }
 
 void testSerialization() {
     // Create a Force.
 
     AmoebaMultipoleForce force1;
-    force1.setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
-    force1.setCutoffDistance( 0.9 );
-    force1.setAEwald( 0.544 );
-    //force1.setPmeBSplineOrder( 4 );
+    force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
+    force1.setCutoffDistance(0.9);
+    force1.setAEwald(0.544);
+    //force1.setPmeBSplineOrder(4);
 
     std::vector<int> gridDimension;
-    gridDimension.push_back( 64 );
-    gridDimension.push_back( 63 );
-    gridDimension.push_back( 61 );
-    force1.setPmeGridDimensions( gridDimension ); 
-    //force1.setMutualInducedIterationMethod( AmoebaMultipoleForce::SOR ); 
-    force1.setMutualInducedMaxIterations( 200 ); 
-    force1.setMutualInducedTargetEpsilon( 1.0e-05 ); 
-    //force1.setElectricConstant( 138.93 ); 
-    force1.setEwaldErrorTolerance( 1.0e-05 ); 
+    gridDimension.push_back(64);
+    gridDimension.push_back(63);
+    gridDimension.push_back(61);
+    force1.setPmeGridDimensions(gridDimension); 
+    //force1.setMutualInducedIterationMethod(AmoebaMultipoleForce::SOR); 
+    force1.setMutualInducedMaxIterations(200); 
+    force1.setMutualInducedTargetEpsilon(1.0e-05); 
+    //force1.setElectricConstant(138.93); 
+    force1.setEwaldErrorTolerance(1.0e-05); 
 
     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> molecularQuadrupole;
-        molecularDipole.push_back( 0.1 ); molecularDipole.push_back( rand() ); molecularDipole.push_back( rand() );
-        for( unsigned int jj = 0; jj < 9; jj++ ){
-            molecularQuadrupole.push_back( static_cast<double>(rand()) );
+        molecularDipole.push_back(0.1); molecularDipole.push_back(rand()); molecularDipole.push_back(rand());
+        for (unsigned int jj = 0; jj < 9; jj++) {
+            molecularQuadrupole.push_back(static_cast<double>(rand()));
         }
-        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()) );
+        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()));
 
-        for( unsigned int jj = 0; jj < covalentTypes.size(); jj++ ){
+        for (unsigned int jj = 0; jj < covalentTypes.size(); jj++) {
             std::vector< int > covalentMap;
-            covalentMap.push_back( ii*jj ); covalentMap.push_back( rand() ); covalentMap.push_back( rand() );
-            force1.setCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
+            covalentMap.push_back(ii*jj); covalentMap.push_back(rand()); covalentMap.push_back(rand());
+            force1.setCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap);
         }
     }
 
@@ -99,13 +99,6 @@ void testSerialization() {
 
     stringstream 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);
 
@@ -125,10 +118,10 @@ void testSerialization() {
 
     std::vector<int> gridDimension1;
     std::vector<int> gridDimension2;
-    force1.getPmeGridDimensions( gridDimension1 ); 
-    force2.getPmeGridDimensions( gridDimension2 ); 
+    force1.getPmeGridDimensions(gridDimension1); 
+    force2.getPmeGridDimensions(gridDimension2); 
     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]);
     }
     
@@ -147,11 +140,11 @@ void testSerialization() {
         std::vector<double> molecularDipole2;
         std::vector<double> molecularQuadrupole2;
 
-        force1.getMultipoleParameters( ii, charge1, molecularDipole1, molecularQuadrupole1, axisType1, multipoleAtomZ1, multipoleAtomX1, multipoleAtomY1,
-                                       thole1, dampingFactor1, polarity1 );
+        force1.getMultipoleParameters(ii, charge1, molecularDipole1, molecularQuadrupole1, axisType1, multipoleAtomZ1, multipoleAtomX1, multipoleAtomY1,
+                                       thole1, dampingFactor1, polarity1);
 
-        force2.getMultipoleParameters( ii, charge2, molecularDipole2, molecularQuadrupole2, axisType2, multipoleAtomZ2, multipoleAtomX2, multipoleAtomY2,
-                                       thole2, dampingFactor2, polarity2 );
+        force2.getMultipoleParameters(ii, charge2, molecularDipole2, molecularQuadrupole2, axisType2, multipoleAtomZ2, multipoleAtomX2, multipoleAtomY2,
+                                       thole2, dampingFactor2, polarity2);
 
         ASSERT_EQUAL(charge1,                        charge2);
         ASSERT_EQUAL(axisType1,                      axisType2);
@@ -162,25 +155,25 @@ void testSerialization() {
         ASSERT_EQUAL(dampingFactor1,                 dampingFactor2);
         ASSERT_EQUAL(polarity1,                      polarity2);
 
-        ASSERT_EQUAL(molecularDipole1.size(),        molecularDipole2.size() );
-        ASSERT_EQUAL(molecularDipole1.size(),        3 );
+        ASSERT_EQUAL(molecularDipole1.size(),        molecularDipole2.size());
+        ASSERT_EQUAL(molecularDipole1.size(),        3);
         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(),        9 );
+        ASSERT_EQUAL(molecularQuadrupole1.size(),        molecularQuadrupole2.size());
+        ASSERT_EQUAL(molecularQuadrupole1.size(),        9);
         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++) {
             std::vector<int> covalentMap1;
             std::vector<int> covalentMap2;
-            force1.getCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap1 );
-            force2.getCovalentMap( ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap2 );
-            ASSERT_EQUAL(covalentMap1.size(),        covalentMap2.size() );
+            force1.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap1);
+            force2.getCovalentMap(ii, static_cast<AmoebaMultipoleForce::CovalentType>(jj), covalentMap2);
+            ASSERT_EQUAL(covalentMap1.size(),        covalentMap2.size());
             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

@@ -46,10 +46,10 @@ void testSerialization() {
 
     AmoebaOutOfPlaneBendForce force1;
 
-    force1.setAmoebaGlobalOutOfPlaneBendCubic( 12.3 );
-    force1.setAmoebaGlobalOutOfPlaneBendQuartic( 98.7 );
-    force1.setAmoebaGlobalOutOfPlaneBendPentic( 91.7 );
-    force1.setAmoebaGlobalOutOfPlaneBendSextic( 93.7 );
+    force1.setAmoebaGlobalOutOfPlaneBendCubic(12.3);
+    force1.setAmoebaGlobalOutOfPlaneBendQuartic(98.7);
+    force1.setAmoebaGlobalOutOfPlaneBendPentic(91.7);
+    force1.setAmoebaGlobalOutOfPlaneBendSextic(93.7);
 
     force1.addOutOfPlaneBend(0, 1, 3, 4, 2.0);
     force1.addOutOfPlaneBend(0, 2, 3, 5, 2.1);

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -42,27 +42,27 @@ using namespace std;
 
 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;
-    gridVector.resize( gridSize );
-    for( unsigned int ii = 0; ii < gridSize; ii++ ){
-        gridVector[ii].resize( gridSize );
-        for( unsigned int jj = 0; jj < gridSize; jj++ ){
-            gridVector[ii][jj].resize( 6 );
-            for( unsigned int kk = 0; kk < 6; kk++ ){
+    gridVector.resize(gridSize);
+    for (unsigned int ii = 0; ii < gridSize; ii++) {
+        gridVector[ii].resize(gridSize);
+        for (unsigned int jj = 0; jj < gridSize; jj++) {
+            gridVector[ii][jj].resize(6);
+            for (unsigned int kk = 0; kk < 6; kk++) {
                 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][2] = static_cast<double>( rand());
-                gridVector[ii][jj][3] = static_cast<double>( rand());
-                gridVector[ii][jj][4] = static_cast<double>( rand());
-                gridVector[ii][jj][5] = static_cast<double>( rand());
+                gridVector[ii][jj][2] = static_cast<double>(rand());
+                gridVector[ii][jj][3] = static_cast<double>(rand());
+                gridVector[ii][jj][4] = 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());
     for (unsigned int ii = 0; ii < grid1.size(); ii++) {
@@ -81,27 +81,19 @@ void testSerialization() {
 
     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;
-        loadTorsionTorsionGrid( gridVector );
-        force1.setTorsionTorsionGrid( ii, gridVector );
+        loadTorsionTorsionGrid(gridVector);
+        force1.setTorsionTorsionGrid(ii, gridVector);
     }
-    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) );
+    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));
     }
 
     // Serialize and then deserialize it.
 
     stringstream 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);
 
     // Compare the two force1s to see if they are identical.  
@@ -112,8 +104,8 @@ void testSerialization() {
 
         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);
-        force2.getTorsionTorsionParameters( ii, b1, b2, b3, b4, b5, bChiral, bGridIndex);
+        force1.getTorsionTorsionParameters(ii, a1, a2, a3, a4, a5, aChiral, aGridIndex);
+        force2.getTorsionTorsionParameters(ii, b1, b2, b3, b4, b5, bChiral, bGridIndex);
 
         ASSERT_EQUAL(a1, b1);
         ASSERT_EQUAL(a2, b2);
@@ -121,14 +113,14 @@ void testSerialization() {
         ASSERT_EQUAL(a4, b4);
         ASSERT_EQUAL(a5, b5);
         ASSERT_EQUAL(aChiral, bChiral);
-        ASSERT_EQUAL(aGridIndex, bGridIndex );
+        ASSERT_EQUAL(aGridIndex, bGridIndex);
     }
 
     ASSERT_EQUAL(force1.getNumTorsionTorsionGrids(), force2.getNumTorsionTorsionGrids());
     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> > >& grid2 = force2.getTorsionTorsionGrid( ii );
-        compareGrids(grid1, grid2 );
+        const std::vector< std::vector< std::vector<double> > >& grid1 = force1.getTorsionTorsionGrid(ii);
+        const std::vector< std::vector< std::vector<double> > >& grid2 = force2.getTorsionTorsionGrid(ii);
+        compareGrids(grid1, grid2);
     }
 
 }

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -45,34 +45,26 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaVdwForce force1;
-    force1.setSigmaCombiningRule(   "GEOMETRIC" );
-    force1.setEpsilonCombiningRule( "GEOMETRIC" );
-    force1.setCutoff( 0.9 );
+    force1.setSigmaCombiningRule("GEOMETRIC");
+    force1.setEpsilonCombiningRule("GEOMETRIC");
+    force1.setCutoff(0.9);
     force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
 
     force1.addParticle(0, 1.0, 2.0, 0.9);
     force1.addParticle(1, 1.1, 2.1, 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;
-        exclusions.push_back( ii );
-        exclusions.push_back( ii + 1 );
-        exclusions.push_back( ii + 10 );
-        force1.setParticleExclusions( ii, exclusions );
+        exclusions.push_back(ii);
+        exclusions.push_back(ii + 1);
+        exclusions.push_back(ii + 10);
+        force1.setParticleExclusions(ii, exclusions);
     }
 
     // Serialize and then deserialize it.
 
     stringstream 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);
 
     // Compare the two forces to see if they are identical.  
@@ -93,10 +85,10 @@ void testSerialization() {
         double sigma1, epsilon1, reductionFactor1;
         double sigma2, epsilon2, reductionFactor2;
 
-        force1.getParticleParameters( ii, ivIndex1, sigma1, epsilon1, reductionFactor1 );
-        force2.getParticleParameters( ii, ivIndex2, sigma2, epsilon2, reductionFactor2 );
+        force1.getParticleParameters(ii, ivIndex1, sigma1, epsilon1, reductionFactor1);
+        force2.getParticleParameters(ii, ivIndex2, sigma2, epsilon2, reductionFactor2);
 
-        ASSERT_EQUAL(ivIndex1,          ivIndex2 );
+        ASSERT_EQUAL(ivIndex1,          ivIndex2);
         ASSERT_EQUAL(sigma1,            sigma2);
         ASSERT_EQUAL(epsilon1,          epsilon2);
         ASSERT_EQUAL(reductionFactor1,  reductionFactor2);
@@ -106,14 +98,14 @@ void testSerialization() {
         std::vector< int > exclusions1;
         std::vector< int > exclusions2;
 
-        force1.getParticleExclusions( ii, exclusions1 );
-        force2.getParticleExclusions( ii, exclusions2 );
+        force1.getParticleExclusions(ii, exclusions1);
+        force2.getParticleExclusions(ii, exclusions2);
 
         ASSERT_EQUAL(exclusions1.size(), exclusions2.size());
         for (unsigned int jj = 0; jj < exclusions1.size(); jj++) {
             int hit = 0;
             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);
         }

plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp

@@ -45,14 +45,14 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaWcaDispersionForce force1;
-    force1.setEpso(    1.0 );
-    force1.setEpsh(    1.1 );
-    force1.setRmino(   1.2 );
-    force1.setRminh(   1.3 );
-    force1.setAwater(  1.4 );
-    force1.setShctd(   1.5 );
-    force1.setDispoff( 1.6 );
-    force1.setSlevy(   1.7 );
+    force1.setEpso(   1.0);
+    force1.setEpsh(   1.1);
+    force1.setRmino(  1.2);
+    force1.setRminh(  1.3);
+    force1.setAwater( 1.4);
+    force1.setShctd(  1.5);
+    force1.setDispoff(1.6);
+    force1.setSlevy(  1.7);
 
     force1.addParticle(1.0, 2.0);
     force1.addParticle(1.1, 2.1);
@@ -62,14 +62,6 @@ void testSerialization() {
 
     stringstream 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);
 
     // Compare the two forces to see if they are identical.  
@@ -91,8 +83,8 @@ void testSerialization() {
         double radius1, epsilon1;
         double radius2, epsilon2;
 
-        force1.getParticleParameters( ii, radius1, epsilon1 );
-        force2.getParticleParameters( ii, radius2, epsilon2 );
+        force1.getParticleParameters(ii, radius1, epsilon1);
+        force2.getParticleParameters(ii, radius2, epsilon2);
 
         ASSERT_EQUAL(radius1,  radius2);
         ASSERT_EQUAL(epsilon1, epsilon2);

plugins/amoeba/wrappers/generateAmoebaWrappers.py

@@ -327,7 +327,7 @@ extern "C" {
 /* OpenMM_3D_DoubleArray */
 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_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()
 
@@ -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) {
     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);
-    if( array2DInt->size() <= index1 ){
-        array2DInt->resize( index1+1 );
+    if (array2DInt->size() <= index1) {
+        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) {
     vector<vector<int> >* array2DInt = reinterpret_cast<vector<vector<int> >*>(array);
-    if( array2DInt->size() <= index1 ){
-        array2DInt->resize( index1+1 );
+    if (array2DInt->size() <= index1) {
+        array2DInt->resize(index1+1);
     }
-    if( array2DInt[index1].size() <= index2 ){
-        array2DInt[index1].resize( index2+1 );
+    if (array2DInt[index1].size() <= index2) {
+        array2DInt[index1].resize(index2+1);
     }
     (*array2DInt)[index1][index2] = 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);
-    if ( array2DInt->size() <= index1 )
+    if (array2DInt->size() <= index1)
         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.");
     *value = (*array2DInt)[index1][index2];
 }
@@ -618,9 +618,9 @@ OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int siz
     int ii, jj;  
     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);
-        for( jj = 0; jj < size2; jj++ ){
+        for (jj = 0; jj < size2; jj++) {
            (*v3D_Array)[ii][jj].resize(size3);
         }    
     }    
@@ -631,12 +631,12 @@ OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array
     unsigned int ii;
     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);
-    for( ii = 0; ii < (*value_array).size(); ii++ ){
+    for (ii = 0; ii < (*value_array).size(); 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);
 }""", file=self.out)
 

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -99,7 +99,7 @@ void testWater() {
     // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
     // and Drude particles.
     
-    const int gridSize = 4;
+    const int gridSize = 3;
     const int numMolecules = gridSize*gridSize*gridSize;
     const double spacing = 0.6;
     const double boxSize = spacing*(gridSize+1);

plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp

@@ -54,7 +54,7 @@ void testWater() {
     // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
     // and Drude particles.
     
-    const int gridSize = 4;
+    const int gridSize = 3;
     const int numMolecules = gridSize*gridSize*gridSize;
     const double spacing = 0.6;
     const double boxSize = spacing*(gridSize+1);

plugins/rpmd/openmmapi/include/openmm/RPMDMonteCarloBarostat.h

+#ifndef OPENMM_RPMDMONTECARLOBAROSTAT_H_
+#define OPENMM_RPMDMONTECARLOBAROSTAT_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * 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.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/Force.h"
+#include <string>
+#include "internal/windowsExportRpmd.h"
+
+namespace OpenMM {
+
+/**
+ * This class is very similar to MonteCarloBarostat, but it is specifically designed for use
+ * with RPMDIntegrator.  For each trial move, it scales all copies of the system by the same
+ * amount, then accepts or rejects the move based on the change to the total energy of the
+ * ring polymer (as returned by the integrator's getTotalEnergy() method).
+ */
+
+class OPENMM_EXPORT_RPMD RPMDMonteCarloBarostat : public Force {
+public:
+    /**
+     * This is the name of the parameter which stores the current pressure acting on
+     * the system (in bar).
+     */
+    static const std::string& Pressure() {
+        static const std::string key = "RPMDMonteCarloPressure";
+        return key;
+    }
+    /**
+     * Create a MonteCarloBarostat.
+     *
+     * @param defaultPressure   the default pressure acting on the system (in bar)
+     * @param frequency         the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
+     */
+    RPMDMonteCarloBarostat(double defaultPressure, int frequency = 25);
+    /**
+     * Get the default pressure acting on the system (in bar).
+     *
+     * @return the default pressure acting on the system, measured in bar.
+     */
+    double getDefaultPressure() const {
+        return defaultPressure;
+    }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(double pressure) {
+        defaultPressure = pressure;
+    }
+    /**
+     * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
+     * 0, the barostat is disabled.
+     */
+    int getFrequency() const {
+        return frequency;
+    }
+    /**
+     * Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
+     * 0, the barostat is disabled.
+     */
+    void setFrequency(int freq) {
+        frequency = freq;
+    }
+    /**
+     * Get the random number seed.  See setRandomNumberSeed() for details.
+     */
+    int getRandomNumberSeed() const {
+        return randomNumberSeed;
+    }
+    /**
+     * Set the random number seed.  It is guaranteed that if two simulations are run
+     * with different random number seeds, the sequence of Monte Carlo steps will be different.  On
+     * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
+     * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
+     * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
+     */
+    void setRandomNumberSeed(int seed) {
+        randomNumberSeed = seed;
+    }
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return true;
+    }
+protected:
+    ForceImpl* createImpl() const;
+private:
+    double defaultPressure;
+    int frequency, randomNumberSeed;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RPMDMONTECARLOBAROSTAT_H_*/

plugins/rpmd/openmmapi/include/openmm/RPMDUpdater.h

+#ifndef OPENMM_RPMDUPDATER_H_
+#define OPENMM_RPMDUPDATER_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/ForceImpl.h"
+#include "internal/windowsExportRpmd.h"
+
+namespace OpenMM {
+
+/**
+ * This ForceImpl subclass is for forces specifically designed to work with RPMDIntegrator.
+ * It adds an updateRPMDState() method that is invoked at the start of each time step
+ * (in contrast to updateContextState(), which gets invoked many times per time step, once
+ * for each copy).
+ */
+
+class OPENMM_EXPORT_RPMD RPMDUpdater : public ForceImpl {
+public:
+    virtual void updateRPMDState(ContextImpl& context) = 0;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RPMDUPDATER_H_*/

plugins/rpmd/openmmapi/include/openmm/internal/RPMDMonteCarloBarostatImpl.h

+#ifndef OPENMM_RPMDMONTECARLOBAROSTATIMPL_H_
+#define OPENMM_RPMDMONTECARLOBAROSTATIMPL_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * 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.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/RPMDMonteCarloBarostat.h"
+#include "openmm/RPMDUpdater.h"
+#include "openmm/Kernel.h"
+#include "openmm/Vec3.h"
+#include "sfmt/SFMT.h"
+#include <string>
+#include <vector>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of RPMDMonteCarloBarostat.
+ */
+
+class RPMDMonteCarloBarostatImpl : public RPMDUpdater {
+public:
+    RPMDMonteCarloBarostatImpl(const RPMDMonteCarloBarostat& owner);
+    void initialize(ContextImpl& context);
+    const RPMDMonteCarloBarostat& getOwner() const {
+        return owner;
+    }
+    void updateRPMDState(ContextImpl& context);
+    void updateContextState(ContextImpl& context) {
+        // This is unused, since the updating is done in updateRPMDState().
+    }
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+        // This force doesn't apply forces to particles.
+        return 0.0;
+    }
+    std::map<std::string, double> getDefaultParameters();
+    std::vector<std::string> getKernelNames();
+private:
+    const RPMDMonteCarloBarostat& owner;
+    int step, numAttempted, numAccepted;
+    double volumeScale;
+    OpenMM_SFMT::SFMT random;
+    std::vector<std::vector<Vec3> > savedPositions;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RPMDMONTECARLOBAROSTATIMPL_H_*/

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -34,6 +34,7 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/RpmdKernels.h"
+#include "openmm/RPMDUpdater.h"
 #include "SimTKOpenMMRealType.h"
 #include <cmath>
 #include <string>
@@ -190,6 +191,12 @@ void RPMDIntegrator::step(int steps) {
         context->getOwner().setPositions(p);
         isFirstStep = false;
     }
+    vector<ForceImpl*>& forceImpls = context->getForceImpls();
+    for (int i = 0; i < (int) forceImpls.size(); i++) {
+        RPMDUpdater* updater = dynamic_cast<RPMDUpdater*>(forceImpls[i]);
+        if (updater != NULL)
+            updater->updateRPMDState(*context);
+    }
     for (int i = 0; i < steps; ++i) {
         kernel.getAs<IntegrateRPMDStepKernel>().execute(*context, *this, forcesAreValid);
         forcesAreValid = true;