Updated Doxygen comments to specify units in a more consistent way

openmmapi/include/openmm/AndersenThermostat.h

@@ -68,12 +68,16 @@ public:
     AndersenThermostat(double defaultTemperature, double defaultCollisionFrequency);
     /**
      * Get the default temperature of the heat bath (in Kelvin).
+     *
+     * @return the default temperature of the heat bath, measured in Kelvin.
      */
     double getDefaultTemperature() const {
         return defaultTemp;
     }
     /**
      * Get the default collision frequency (in 1/ps).
+     *
+     * @return the default collision frequency, measured in 1/ps.
      */
     double getDefaultCollisionFrequency() const {
         return defaultFreq;

openmmapi/include/openmm/BrownianIntegrator.h

@@ -54,12 +54,16 @@ public:
     BrownianIntegrator(double temperature, double frictionCoeff, double stepSize);
     /**
      * Get the temperature of the heat bath (in Kelvin).
+     *
+     * @return the temperature of the heat bath (in Kelvin).
      */
     double getTemperature() const {
         return temperature;
     }
     /**
      * Set the temperature of the heat bath (in Kelvin).
+     *
+     * @param temp    the temperature of the heat bath, measured in Kelvin.
      */
     void setTemperature(double temp) {
         temperature = temp;
@@ -67,6 +71,8 @@ public:
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @return the friction coefficient, measured in 1/ps
      */
     double getFriction() const {
         return friction;
@@ -74,6 +80,8 @@ public:
     /**
      * Set the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @param coeff    the friction coefficient, measured in 1/ps
      */
     void setFriction(double coeff) {
         friction = coeff;

openmmapi/include/openmm/CustomGBForce.h

@@ -233,11 +233,15 @@ public:
     /**
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @return the cutoff distance, measured in nm
      */
     double getCutoffDistance() const;
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @param distance    the cutoff distance, measured in nm
      */
     void setCutoffDistance(double distance);
     /**

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -161,11 +161,15 @@ public:
     /**
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @return the cutoff distance, measured in nm
      */
     double getCutoffDistance() const;
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @param distance    the cutoff distance, measured in nm
      */
     void setCutoffDistance(double distance);
     /**

openmmapi/include/openmm/GBSAOBCForce.h

@@ -142,11 +142,15 @@ public:
     /**
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @return the cutoff distance, measured in nm
      */
     double getCutoffDistance() const;
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @param distance    the cutoff distance, measured in nm
      */
     void setCutoffDistance(double distance);
 protected:

openmmapi/include/openmm/GBVIForce.h

@@ -177,11 +177,15 @@ public:
     /** 
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @return the cutoff distance, measured in nm
      */
     double getCutoffDistance() const;
     /** 
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @param distance    the cutoff distance, measured in nm
      */
     void setCutoffDistance(double distance);
 protected:

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -65,7 +65,7 @@ public:
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
      * @param angle     the equilibrium angle, measured in radians
-     * @param k         the harmonic force constant for the angle
+     * @param k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
      * @return the index of the angle that was added
      */
     int addAngle(int particle1, int particle2, int particle3, double angle, double k);
@@ -77,7 +77,7 @@ public:
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
      * @param angle     the equilibrium angle, measured in radians
-     * @param k         the harmonic force constant for the angle
+     * @param k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
     /**
@@ -88,7 +88,7 @@ public:
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
      * @param angle     the equilibrium angle, measured in radians
-     * @param k         the harmonic force constant for the angle
+     * @param k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k);
 protected:

openmmapi/include/openmm/HarmonicBondForce.h

@@ -64,7 +64,7 @@ public:
      * @param particle1 the index of the first particle connected by the bond
      * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
-     * @param k         the harmonic force constant for the bond
+     * @param k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
      * @return the index of the bond that was added
      */
     int addBond(int particle1, int particle2, double length, double k);
@@ -75,7 +75,7 @@ public:
      * @param particle1 the index of the first particle connected by the bond
      * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
-     * @param k         the harmonic force constant for the bond
+     * @param k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
      */
     void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
     /**
@@ -85,7 +85,7 @@ public:
      * @param particle1 the index of the first particle connected by the bond
      * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
-     * @param k         the harmonic force constant for the bond
+     * @param k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
      */
     void setBondParameters(int index, int particle1, int particle2, double length, double k);
 protected:

openmmapi/include/openmm/Integrator.h

@@ -57,6 +57,8 @@ public:
     /**
      * Get the size of each time step, in picoseconds.  If this integrator uses variable time steps,
      * the size of the most recent step is returned.
+     *
+     * @return the step size, measured in ps
      */
     double getStepSize() const {
         return stepSize;
@@ -64,6 +66,8 @@ public:
     /**
      * Set the size of each time step, in picoseconds.  If this integrator uses variable time steps,
      * the effect of calling this method is undefined, and it may simply be ignored.
+     *
+     * @param size    the step size, measured in ps
      */
     void setStepSize(double size) {
         stepSize = size;

openmmapi/include/openmm/LangevinIntegrator.h

@@ -54,12 +54,16 @@ public:
     LangevinIntegrator(double temperature, double frictionCoeff, double stepSize);
     /**
      * Get the temperature of the heat bath (in Kelvin).
+     *
+     * @return the temperature of the heat bath, measured in Kelvin
      */
     double getTemperature() const {
         return temperature;
     }
     /**
      * Set the temperature of the heat bath (in Kelvin).
+     *
+     * @param temp    the temperature of the heat bath, measured in Kelvin
      */
     void setTemperature(double temp) {
         temperature = temp;
@@ -67,6 +71,8 @@ public:
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @return the friction coefficient, measured in 1/ps
      */
     double getFriction() const {
         return friction;
@@ -74,6 +80,8 @@ public:
     /**
      * Set the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @param coeff    the friction coefficient, measured in 1/ps
      */
     void setFriction(double coeff) {
         friction = coeff;

openmmapi/include/openmm/NonbondedForce.h

@@ -125,11 +125,15 @@ public:
     /**
      * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @return the cutoff distance, measured in nm
      */
     double getCutoffDistance() const;
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
      * is NoCutoff, this value will have no effect.
+     *
+     * @param distance    the cutoff distance, measured in nm
      */
     void setCutoffDistance(double distance);
     /**

openmmapi/include/openmm/RBTorsionForce.h

@@ -65,12 +65,12 @@ public:
      * @param particle2    the index of the second particle forming the torsion
      * @param particle3    the index of the third particle forming the torsion
      * @param particle3    the index of the fourth particle forming the torsion
-     * @param c0           the coefficient of the constant term
-     * @param c1           the coefficient of the 1st order term
-     * @param c2           the coefficient of the 2nd order term
-     * @param c3           the coefficient of the 3rd order term
-     * @param c4           the coefficient of the 4th order term
-     * @param c5           the coefficient of the 5th order term
+     * @param c0           the coefficient of the constant term, measured in kJ/mol
+     * @param c1           the coefficient of the 1st order term, measured in kJ/mol
+     * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
+     * @param c3           the coefficient of the 3rd order term, measured in kJ/mol
+     * @param c4           the coefficient of the 4th order term, measured in kJ/mol
+     * @param c5           the coefficient of the 5th order term, measured in kJ/mol
      * @return the index of the torsion that was added
      */
     int addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
@@ -82,12 +82,12 @@ public:
      * @param particle2    the index of the second particle forming the torsion
      * @param particle3    the index of the third particle forming the torsion
      * @param particle3    the index of the fourth particle forming the torsion
-     * @param c0           the coefficient of the constant term
-     * @param c1           the coefficient of the 1st order term
-     * @param c2           the coefficient of the 2nd order term
-     * @param c3           the coefficient of the 3rd order term
-     * @param c4           the coefficient of the 4th order term
-     * @param c5           the coefficient of the 5th order term
+     * @param c0           the coefficient of the constant term, measured in kJ/mol
+     * @param c1           the coefficient of the 1st order term, measured in kJ/mol
+     * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
+     * @param c3           the coefficient of the 3rd order term, measured in kJ/mol
+     * @param c4           the coefficient of the 4th order term, measured in kJ/mol
+     * @param c5           the coefficient of the 5th order term, measured in kJ/mol
      */
     void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const;
     /**
@@ -98,12 +98,12 @@ public:
      * @param particle2    the index of the second particle forming the torsion
      * @param particle3    the index of the third particle forming the torsion
      * @param particle3    the index of the fourth particle forming the torsion
-     * @param c0           the coefficient of the constant term
-     * @param c1           the coefficient of the 1st order term
-     * @param c2           the coefficient of the 2nd order term
-     * @param c3           the coefficient of the 3rd order term
-     * @param c4           the coefficient of the 4th order term
-     * @param c5           the coefficient of the 5th order term
+     * @param c0           the coefficient of the constant term, measured in kJ/mol
+     * @param c1           the coefficient of the 1st order term, measured in kJ/mol
+     * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
+     * @param c3           the coefficient of the 3rd order term, measured in kJ/mol
+     * @param c4           the coefficient of the 4th order term, measured in kJ/mol
+     * @param c5           the coefficient of the 5th order term, measured in kJ/mol
      */
     void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
 protected:

openmmapi/include/openmm/VariableLangevinIntegrator.h

@@ -64,12 +64,16 @@ public:
     VariableLangevinIntegrator(double temperature, double frictionCoeff, double errorTol);
     /**
      * Get the temperature of the heat bath (in Kelvin).
+     *
+     * @return the temperature of the heat bath, measured in Kelvin
      */
     double getTemperature() const {
         return temperature;
     }
     /**
      * Set the temperature of the heat bath (in Kelvin).
+     *
+     * @param temp    the temperature of the heat bath, measured in Kelvin
      */
     void setTemperature(double temp) {
         temperature = temp;
@@ -77,6 +81,8 @@ public:
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @return the friction coefficient, measured in 1/ps
      */
     double getFriction() const {
         return friction;
@@ -84,6 +90,8 @@ public:
     /**
      * Set the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
+     *
+     * @param coeff    the friction coefficient, measured in 1/ps
      */
     void setFriction(double coeff) {
         friction = coeff;