Merge pull request #1146 from peastman/params

Added default values for some arguments

openmmapi/include/openmm/CustomAngleForce.h

@@ -171,7 +171,7 @@ public:
      * @param parameters    the list of parameters for the new angle
      * @return the index of the angle that was added
      */
-    int addAngle(int particle1, int particle2, int particle3, const std::vector<double>& parameters);
+    int addAngle(int particle1, int particle2, int particle3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for an angle term.
      *
@@ -191,7 +191,7 @@ public:
      * @param particle3     the index of the third particle connected by the angle
      * @param parameters    the list of parameters for the angle
      */
-    void setAngleParameters(int index, int particle1, int particle2, int particle3, const std::vector<double>& parameters);
+    void setAngleParameters(int index, int particle1, int particle2, int particle3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/CustomBondForce.h

@@ -170,7 +170,7 @@ public:
      * @param parameters    the list of parameters for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(int particle1, int particle2, const std::vector<double>& parameters);
+    int addBond(int particle1, int particle2, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a bond term.
      *
@@ -188,7 +188,7 @@ public:
      * @param particle2     the index of the second particle connected by the bond
      * @param parameters    the list of parameters for the bond
      */
-    void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
+    void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -237,7 +237,7 @@ public:
      *                    If this is omitted, then particle masses will be used as weights.
      * @return the index of the group that was added
      */
-    int addGroup(const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    int addGroup(const std::vector<int>& particles, const std::vector<double>& weights=std::vector<double>());
     /**
      * Get the properties of a group.
      *
@@ -256,7 +256,7 @@ public:
      * @param weights     the weight to use for each particle when computing the center position.
      *                    If this is omitted, then particle masses will be used as weights.
      */
-    void setGroupParameters(int index, const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    void setGroupParameters(int index, const std::vector<int>& particles, const std::vector<double>& weights=std::vector<double>());
     /**
      * Add a bond to the force
      *
@@ -264,7 +264,7 @@ public:
      * @param parameters  the list of per-bond parameter values for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(const std::vector<int>& groups, const std::vector<double>& parameters);
+    int addBond(const std::vector<int>& groups, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a bond.
      *
@@ -280,7 +280,7 @@ public:
      * @param groups      the indices of the groups in the bond
      * @param parameters  the list of per-bond parameter values for the bond
      */
-    void setBondParameters(int index, const std::vector<int>& groups, const std::vector<double>& parameters);
+    void setBondParameters(int index, const std::vector<int>& groups, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a tabulated function that may appear in the energy expression.
      *

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -219,7 +219,7 @@ public:
      * @param parameters  the list of per-bond parameter values for the new bond
      * @return the index of the bond that was added
      */
-    int addBond(const std::vector<int>& particles, const std::vector<double>& parameters);
+    int addBond(const std::vector<int>& particles, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a bond.
      *
@@ -235,7 +235,7 @@ public:
      * @param particles   the indices of the particles in the bond
      * @param parameters  the list of per-bond parameter values for the bond
      */
-    void setBondParameters(int index, const std::vector<int>& particles, const std::vector<double>& parameters);
+    void setBondParameters(int index, const std::vector<int>& particles, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a tabulated function that may appear in the energy expression.
      *

openmmapi/include/openmm/CustomExternalForce.h

@@ -180,7 +180,7 @@ public:
      * @param parameters   the list of parameters for the new force term
      * @return the index of the particle term that was added
      */
-    int addParticle(int particle, const std::vector<double>& parameters);
+    int addParticle(int particle, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a force field term.
      *
@@ -196,7 +196,7 @@ public:
      * @param particle      the index of the particle this term is applied to
      * @param parameters    the list of parameters for the force field term
      */
-    void setParticleParameters(int index, int particle, const std::vector<double>& parameters);
+    void setParticleParameters(int index, int particle, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

openmmapi/include/openmm/CustomGBForce.h

@@ -319,7 +319,7 @@ public:
      * @param parameters    the list of parameters for the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomHbondForce.h

@@ -296,7 +296,7 @@ public:
      * @param parameters  the list of per-donor parameter values for the new donor
      * @return the index of the donor that was added
      */
-    int addDonor(int d1, int d2, int d3, const std::vector<double>& parameters);
+    int addDonor(int d1, int d2, int d3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of a donor group.
      *
@@ -320,7 +320,7 @@ public:
      *                    less than three particles, this must be -1.
      * @param parameters  the list of per-donor parameter values for the donor
      */
-    void setDonorParameters(int index, int d1, int d2, int d3, const std::vector<double>& parameters);
+    void setDonorParameters(int index, int d1, int d2, int d3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add an acceptor group to the force
      *
@@ -332,7 +332,7 @@ public:
      * @param parameters  the list of per-acceptor parameter values for the new acceptor
      * @return the index of the acceptor that was added
      */
-    int addAcceptor(int a1, int a2, int a3, const std::vector<double>& parameters);
+    int addAcceptor(int a1, int a2, int a3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the properties of an acceptor group.
      *
@@ -356,7 +356,7 @@ public:
      *                    less than three particles, this must be -1.
      * @param parameters  the list of per-acceptor parameter values for the acceptor
      */
-    void setAcceptorParameters(int index, int a1, int a2, int a3, const std::vector<double>& parameters);
+    void setAcceptorParameters(int index, int a1, int a2, int a3, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Add a donor-acceptor pair to the list of interactions that should be excluded.
      *

openmmapi/include/openmm/CustomManyParticleForce.h

@@ -348,7 +348,7 @@ public:
      * @param type          the type of the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters, int type=0);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>(), int type=0);
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -328,7 +328,7 @@ public:
      * @param parameters    the list of parameters for the new particle
      * @return the index of the particle that was added
      */
-    int addParticle(const std::vector<double>& parameters);
+    int addParticle(const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the nonbonded force parameters for a particle.
      *

openmmapi/include/openmm/CustomTorsionForce.h

@@ -172,7 +172,7 @@ public:
      * @param parameters    the list of parameters for the new torsion
      * @return the index of the torsion that was added
      */
-    int addTorsion(int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters);
+    int addTorsion(int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Get the force field parameters for a torsion term.
      *
@@ -194,7 +194,7 @@ public:
      * @param particle4     the index of the fourth particle connected by the torsion
      * @param parameters    the list of parameters for the torsion
      */
-    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters);
+    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters=std::vector<double>());
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.

tests/TestCustomAngleForce.h

@@ -132,8 +132,7 @@ void testIllegalVariable() {
     system.addParticle(1.0);
     system.addParticle(1.0);
     CustomAngleForce* force = new CustomAngleForce("theta+none");
-    vector<double> params;
-    force->addAngle(0, 1, 2, params);
+    force->addAngle(0, 1, 2);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomBondForce.h

@@ -135,8 +135,7 @@ void testIllegalVariable() {
     system.addParticle(1.0);
     system.addParticle(1.0);
     CustomBondForce* force = new CustomBondForce("r+none");
-    vector<double> params;
-    force->addBond(0, 1, params);
+    force->addBond(0, 1);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomCentroidBondForce.h

@@ -264,8 +264,7 @@ void testIllegalVariable() {
     vector<int> groups;
     groups.push_back(0);
     groups.push_back(1);
-    vector<double> params;
-    force->addBond(groups, params);
+    force->addBond(groups);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomCompoundBondForce.h

@@ -317,8 +317,7 @@ void testIllegalVariable() {
     vector<int> particles;
     particles.push_back(0);
     particles.push_back(1);
-    vector<double> params;
-    force->addBond(particles, params);
+    force->addBond(particles);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomExternalForce.h

@@ -171,8 +171,7 @@ void testIllegalVariable() {
     System system;
     system.addParticle(1.0);
     CustomExternalForce* force = new CustomExternalForce("x+none");
-    vector<double> params;
-    force->addParticle(0, params);
+    force->addParticle(0);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomGBForce.h

@@ -475,8 +475,7 @@ void testIllegalVariable() {
     system.addParticle(1.0);
     CustomGBForce* force = new CustomGBForce();
     force->addComputedValue("a", "r+none", CustomGBForce::ParticlePair);
-    vector<double> params;
-    force->addParticle(params);
+    force->addParticle();
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomHbondForce.h

@@ -230,9 +230,8 @@ void testIllegalVariable() {
     system.addParticle(1.0);
     system.addParticle(1.0);
     CustomHbondForce* force = new CustomHbondForce("1+none");
-    vector<double> params;
-    force->addDonor(0, -1, -1, params);
-    force->addAcceptor(1, -1, -1, params);
+    force->addDonor(0, -1, -1);
+    force->addAcceptor(1, -1, -1);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomManyParticleForce.h

@@ -711,8 +711,7 @@ void testIllegalVariable() {
     System system;
     system.addParticle(1.0);
     CustomManyParticleForce* force = new CustomManyParticleForce(2, "x1+y2+none");
-    vector<double> params;
-    force->addParticle(params);
+    force->addParticle();
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomNonbondedForce.h

@@ -997,8 +997,7 @@ void testIllegalVariable() {
     System system;
     system.addParticle(1.0);
     CustomNonbondedForce* force = new CustomNonbondedForce("r+none");
-    vector<double> params;
-    force->addParticle(params);
+    force->addParticle();
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;

tests/TestCustomTorsionForce.h

@@ -173,8 +173,7 @@ void testIllegalVariable() {
     system.addParticle(1.0);
     system.addParticle(1.0);
     CustomTorsionForce* force = new CustomTorsionForce("theta+none");
-    vector<double> params;
-    force->addTorsion(0, 1, 2, 3, params);
+    force->addTorsion(0, 1, 2, 3);
     system.addForce(force);
     VerletIntegrator integrator(0.001);
     bool threwException = false;