Merge branch 'master' into qc

serialization/tests/TestSerializeCMAPTorsion.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CMAPTorsionForce force;
+    force.setForceGroup(3);
     vector<double> map1(9);
     for (int i = 0; i < 9; i++)
         map1[i] = 0.1*i;
@@ -64,6 +65,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CMAPTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumMaps(), force2.getNumMaps());
     for (int i = 0; i < force.getNumMaps(); i++) {
         int size1, size2;

serialization/tests/TestSerializeCMMotionRemover.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CMMotionRemover force(5);
+    force.setForceGroup(3);
 
     // Serialize and then deserialize it.
 
@@ -52,6 +53,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CMMotionRemover& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
 }
 

serialization/tests/TestSerializeCustomAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomAngleForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerAngleParameter("z");
@@ -62,6 +63,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNumPerAngleParameters(), force2.getNumPerAngleParameters());
     for (int i = 0; i < force.getNumPerAngleParameters(); i++)

serialization/tests/TestSerializeCustomBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomBondForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerBondParameter("z");
@@ -62,6 +63,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
     for (int i = 0; i < force.getNumPerBondParameters(); i++)

serialization/tests/TestSerializeCustomCompoundBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomCompoundBondForce force(3, "5*sin(distance(p1,p2))^2+y*z");
+    force.setForceGroup(3);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerBondParameter("z");
@@ -76,6 +77,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomCompoundBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumParticlesPerBond(), force2.getNumParticlesPerBond());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());

serialization/tests/TestSerializeCustomExternalForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomExternalForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerParticleParameter("z");
@@ -62,6 +63,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomExternalForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
     for (int i = 0; i < force.getNumPerParticleParameters(); i++)

serialization/tests/TestSerializeCustomGBForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomGBForce force;
+    force.setForceGroup(3);
     force.setNonbondedMethod(CustomGBForce::CutoffPeriodic);
     force.setCutoffDistance(2.1);
     force.addGlobalParameter("x", 1.3);
@@ -74,6 +75,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomGBForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
     ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());

serialization/tests/TestSerializeCustomHbondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomHbondForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.setNonbondedMethod(CustomHbondForce::CutoffPeriodic);
     force.setCutoffDistance(2.1);
     force.addGlobalParameter("x", 1.3);
@@ -77,6 +78,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomHbondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());

serialization/tests/TestSerializeCustomNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,7 +42,11 @@ void testSerialization() {
     // Create a Force.
 
     CustomNonbondedForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
+    force.setUseSwitchingFunction(true);
+    force.setUseLongRangeCorrection(true);
+    force.setSwitchingDistance(2.0);
     force.setCutoffDistance(2.1);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
@@ -60,6 +64,11 @@ void testSerialization() {
     for (int i = 0; i < 10; i++)
         values[i] = sin((double) i);
     force.addFunction("f", values, 0.5, 1.5);
+    std::set<int> set1, set2;
+    set1.insert(0);
+    set2.insert(1);
+    set2.insert(2);
+    force.addInteractionGroup(set1, set2);
 
     // Serialize and then deserialize it.
 
@@ -70,9 +79,13 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomNonbondedForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
+    ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
+    ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
+    ASSERT_EQUAL(force.getUseLongRangeCorrection(), force2.getUseLongRangeCorrection());
     ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
     for (int i = 0; i < force.getNumPerParticleParameters(); i++)
         ASSERT_EQUAL(force.getPerParticleParameterName(i), force2.getPerParticleParameterName(i));
@@ -111,6 +124,11 @@ void testSerialization() {
         for (int j = 0; j < (int) val1.size(); j++)
             ASSERT_EQUAL(val1[j], val2[j]);
     }
+    ASSERT_EQUAL(force.getNumInteractionGroups(), force2.getNumInteractionGroups());
+    std::set<int> set1c, set2c;
+    force2.getInteractionGroupParameters(0, set1c, set2c);
+    ASSERT_EQUAL_CONTAINERS(set1, set1c);
+    ASSERT_EQUAL_CONTAINERS(set2, set2c);
 }
 
 int main() {

serialization/tests/TestSerializeCustomTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     CustomTorsionForce force("5*sin(x)^2+y*z");
+    force.setForceGroup(3);
     force.addGlobalParameter("x", 1.3);
     force.addGlobalParameter("y", 2.221);
     force.addPerTorsionParameter("z");
@@ -62,6 +63,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     CustomTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
     ASSERT_EQUAL(force.getNumPerTorsionParameters(), force2.getNumPerTorsionParameters());
     for (int i = 0; i < force.getNumPerTorsionParameters(); i++)

serialization/tests/TestSerializeGBSAOBCForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     GBSAOBCForce force;
+    force.setForceGroup(3);
     force.setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
     force.setCutoffDistance(2.0);
     force.setSoluteDielectric(5.1);
@@ -59,6 +60,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     GBSAOBCForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
     ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());

serialization/tests/TestSerializeGBVIForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     GBVIForce force;
+    force.setForceGroup(3);
     force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
     force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
     force.setQuinticLowerLimitFactor(0.123);
@@ -64,6 +65,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     GBVIForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
     ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());

serialization/tests/TestSerializeHarmonicAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     HarmonicAngleForce force;
+    force.setForceGroup(3);
     force.addAngle(0, 1, 2, 1.0, 2.0);
     force.addAngle(0, 2, 3, 2.0, 2.1);
     force.addAngle(2, 3, 4, 3.0, 2.2);
@@ -56,6 +57,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     HarmonicAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
     for (int i = 0; i < force.getNumAngles(); i++) {
         int a1, a2, a3, b1, b2, b3;

serialization/tests/TestSerializeHarmonicBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     HarmonicBondForce force;
+    force.setForceGroup(3);
     force.addBond(0, 1, 1.0, 2.0);
     force.addBond(0, 2, 2.0, 2.1);
     force.addBond(2, 3, 3.0, 2.2);
@@ -56,6 +57,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     HarmonicBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         int a1, a2, b1, b2;

serialization/tests/TestSerializeMonteCarloBarostat.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     MonteCarloBarostat force(25.5, 250.0, 14);
+    force.setForceGroup(3);
     force.setRandomNumberSeed(3);
 
     // Serialize and then deserialize it.
@@ -53,6 +54,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     MonteCarloBarostat& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
     ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
     ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());

serialization/tests/TestSerializeNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,11 +42,17 @@ void testSerialization() {
     // Create a Force.
 
     NonbondedForce force;
+    force.setForceGroup(3);
     force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    force.setSwitchingDistance(1.5);
+    force.setUseSwitchingFunction(true);
     force.setCutoffDistance(2.0);
     force.setEwaldErrorTolerance(1e-3);
     force.setReactionFieldDielectric(50.0);
     force.setUseDispersionCorrection(false);
+    double alpha = 0.5;
+    int nx = 3, ny = 5, nz = 7;
+    force.setPMEParameters(alpha, nx, ny, nz);
     force.addParticle(1, 0.1, 0.01);
     force.addParticle(0.5, 0.2, 0.02);
     force.addParticle(-0.5, 0.3, 0.03);
@@ -62,12 +68,22 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     NonbondedForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
+    ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
+    ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
     ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
     ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
     ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
     ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
     ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    double alpha2;
+    int nx2, ny2, nz2;
+    force2.getPMEParameters(alpha2, nx2, ny2, nz2);
+    ASSERT_EQUAL(alpha, alpha2);
+    ASSERT_EQUAL(nx, nx2);
+    ASSERT_EQUAL(ny, ny2);
+    ASSERT_EQUAL(nz, nz2);    
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge1, sigma1, epsilon1;
         double charge2, sigma2, epsilon2;

serialization/tests/TestSerializePeriodicTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     PeriodicTorsionForce force;
+    force.setForceGroup(3);
     force.addTorsion(0, 1, 2, 3, 2, 1.0, 2.0);
     force.addTorsion(0, 2, 3, 4, 2, 2.0, 2.1);
     force.addTorsion(2, 3, 4, 7, 1, 3.0, 2.2);
@@ -56,6 +57,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     PeriodicTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, a3, a4, b1, b2, b3, b4, perioda, periodb;

serialization/tests/TestSerializeRBTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     RBTorsionForce force;
+    force.setForceGroup(3);
     force.addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
     force.addTorsion(0, 2, 3, 4, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7);
     force.addTorsion(2, 3, 4, 7, -1, -2, -3, 1.1, 2.2, 3.3);
@@ -55,6 +56,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.
 
     RBTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, a3, a4, b1, b2, b3, b4;

wrappers/generateWrappers.py

@@ -68,7 +68,7 @@ class WrapperGenerator:
     
     def __init__(self, inputDirname, output):
         self.skipClasses = ['OpenMM::Vec3', 'OpenMM::XmlSerializer', 'OpenMM::Kernel', 'OpenMM::KernelImpl', 'OpenMM::KernelFactory', 'OpenMM::ContextImpl', 'OpenMM::SerializationNode', 'OpenMM::SerializationProxy']
-        self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint']
+        self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint', 'OpenMM::Context::getMolecules']
         self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
         self.nodeByID={}
 

wrappers/python/CMakeLists.txt

@@ -57,6 +57,8 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
     )
     foreach(file ${STAGING_INPUT_FILES1})
         set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}")
@@ -106,7 +108,7 @@ mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
 set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen")
 file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python)
 
-### Create OpenMM_headers.xml ###
+### Create OpenMMSwigHeaders.i ###
 # Step 1 - Create Doxyfile to point to OpenMM headers
 configure_file(
     ${CMAKE_CURRENT_SOURCE_DIR}/src/swig_doxygen/doxygen/Doxyfile.in
@@ -130,7 +132,7 @@ set(SWIG_INPUT_FILES_REF
     "${SWIG_OPENMM_DIR}/swig_lib/python/pythonprepend.i"
     "${SWIG_OPENMM_DIR}/swig_lib/python/pythonappend.i"
     "${SWIG_OPENMM_DIR}/OpenMM_docstring.i"
-    "${SWIG_OPENMM_DIR}/OpenMM_headers.i"
+    "${SWIG_OPENMM_DIR}/OpenMMSwigHeaders.i"
     # "${SWIG_OPENMM_DIR}/OpenMM.i"
 )
 
@@ -153,7 +155,7 @@ add_custom_command(
         -i "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml"
         -c swigInputConfig.py
         -d OpenMM_docstring.i
-        -o OpenMM_headers.i
+        -o OpenMMSwigHeaders.i
         -a swig_lib/python/pythonprepend.i
         -z swig_lib/python/pythonappend.i
     WORKING_DIRECTORY "${SWIG_OPENMM_DIR}"
@@ -164,6 +166,8 @@ add_custom_command(
     COMMENT "Creating OpenMM Python swig input files..."
 )
 
+INSTALL_FILES(/include FILES "${SWIG_OPENMM_DIR}/OpenMMSwigHeaders.i")
+
 #~ swig -python -c++ \
 #~      -outdir $PYTHON_PACKAGE_DIR \
 #~      -o OpenMMSwig.cxx \