Include force groups when serializing forces

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

@@ -42,6 +42,7 @@ 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);
@@ -78,6 +79,7 @@ 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());

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:                                                              *
  *                                                                            *
@@ -42,6 +42,7 @@ void testSerialization() {
     // Create a Force.
 
     NonbondedForce force;
+    force.setForceGroup(3);
     force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
     force.setSwitchingDistance(1.5);
     force.setUseSwitchingFunction(true);
@@ -67,6 +68,7 @@ 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());

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;