Cleanup

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -43,12 +43,13 @@ namespace OpenMM {
  * <p>
  * To use this class, create a AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the
  * System to define its parameters.  The number of particles for which you define GBSA parameters must
- * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * be equal to the number of particles in the System, or else an exception will be thrown when you
  * try to create a Context.  After a particle has been added, you can modify its force field parameters
  * by calling setParticleParameters().
  */
 
 class OPENMM_EXPORT AmoebaGeneralizedKirkwoodForce : public Force {
+
 public:
 
     /*

plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicAngleForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -44,8 +44,10 @@ namespace OpenMM {
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
- class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
+class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba HarmonicAngleForce.
      */
@@ -124,8 +126,7 @@ public:
      * @param quadratic k   the quadratic 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 length, 
-                 double quadraticK );
+    int addAngle(int particle1, int particle2, int particle3, double length, double quadraticK );
 
     /**
      * Get the force field parameters for a angle term.
@@ -137,8 +138,7 @@ public:
      * @param length        the equilibrium angle, measured in radians
      * @param quadratic k   the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
-    void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length,
-                            double& quadraticK ) const;
+    void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK ) const;
 
     /**
      * Set the force field parameters for a angle term.

plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicBondForce.h

@@ -34,9 +34,9 @@
 
 #include "openmm/Force.h"
 #include "openmm/Vec3.h"
+#include "openmm/internal/windowsExport.h"
 #include <map>
 #include <vector>
-#include "openmm/internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -46,8 +46,10 @@ namespace OpenMM {
  * a bond has been added, you can modify its force field parameters by calling setBondParameters().
  */
 
- class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
+class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba HarmonicBondForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicInPlaneAngleForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -45,8 +45,10 @@ namespace OpenMM {
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
- class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
+class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba HarmonicAngleForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -48,14 +48,17 @@ namespace OpenMM {
  */
 
 class OPENMM_EXPORT AmoebaMultipoleForce : public Force {
+
 public:
  
     enum AmoebaNonbondedMethod {
+
         /** 
          * No cutoff is applied to nonbonded interactions.  The full set of N^2 interactions is computed exactly.
          * This necessarily means that periodic boundary conditions cannot be used.  This is the default.
          */
         NoCutoff = 0,
+
         /**
          * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
          * with all periodic copies of every other particle.
@@ -88,12 +91,12 @@ public:
     }
 
     /**
-     * Get the method used for handling long range nonbonded interactions.
+     * Get the method used for handling long-range nonbonded interactions.
      */
     AmoebaNonbondedMethod getNonbondedMethod( void ) const;
 
     /**
-     * Set the method used for handling long range nonbonded interactions.
+     * Set the method used for handling long-range nonbonded interactions.
      */
     void setNonbondedMethod(AmoebaNonbondedMethod method);
 

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -45,7 +45,9 @@ namespace OpenMM {
  */
 
 class OPENMM_EXPORT AmoebaOutOfPlaneBendForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba OutOfPlaneBendForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -44,8 +44,10 @@ namespace OpenMM {
  * a torsion has been added, you can modify its force field parameters by calling setPiTorsionParameters().
  */
 
- class OPENMM_EXPORT AmoebaPiTorsionForce : public Force {
+class OPENMM_EXPORT AmoebaPiTorsionForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba PiTorsionForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -44,8 +44,10 @@ namespace OpenMM {
  * a stretchBend has been added, you can modify its force field parameters by calling setStretchBendParameters().
  */
 
- class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
+class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba StretchBendForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionForce.h

@@ -47,6 +47,7 @@ namespace OpenMM {
  */
 
 class OPENMM_EXPORT AmoebaTorsionForce : public Force {
+
 public:
 
     static const unsigned int ParametersPerTorsion  = 2;

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -33,9 +33,10 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
+#include "openmm/internal/windowsExport.h"
+
 #include <vector>
 #include <cmath>
-#include "openmm/internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -158,7 +159,9 @@ private:
 };
 
 class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
+
 public:
+
     int particle1, particle2, particle3, particle4, particle5;
     int chiralCheckAtomIndex;
     int gridIndex;

plugins/amoeba/openmmapi/include/openmm/AmoebaUreyBradleyForce.h

@@ -34,9 +34,10 @@
 
 #include "openmm/Force.h"
 #include "openmm/Vec3.h"
+#include "openmm/internal/windowsExport.h"
+
 #include <map>
 #include <vector>
-#include "openmm/internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -46,8 +47,10 @@ namespace OpenMM {
  * a bond has been added, you can modify its force field parameters by calling setUreyBradleyParameters().
  */
 
- class OPENMM_EXPORT AmoebaUreyBradleyForce : public Force {
+class OPENMM_EXPORT AmoebaUreyBradleyForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba UreyBradleyForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -44,8 +44,10 @@ namespace OpenMM {
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
- class OPENMM_EXPORT AmoebaVdwForce : public Force {
+class OPENMM_EXPORT AmoebaVdwForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba VdwForce.
      */

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -33,8 +33,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/Force.h"
-#include <vector>
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -44,8 +44,10 @@ namespace OpenMM {
  * a angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
- class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
+class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
+
 public:
+
     /**
      * Create a Amoeba WcaDispersionForce.
      */

plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h

@@ -47,12 +47,16 @@ namespace OpenMM {
  * This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaHarmonicBondForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaHarmonicBondForce";
     }
+
     CalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -60,6 +64,7 @@ public:
      * @param force      the AmoebaHarmonicBondForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaHarmonicBondForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -69,16 +74,20 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+
 };
 
 class CalcAmoebaUreyBradleyForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaUreyBradleyForce";
     }
 
     CalcAmoebaUreyBradleyForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -86,6 +95,7 @@ public:
      * @param force      the AmoebaUreyBradleyForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaUreyBradleyForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -95,18 +105,23 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+
 };
 
 /**
  * This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaHarmonicAngleForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaHarmonicAngleForce";
     }
+
     CalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -114,6 +129,7 @@ public:
      * @param force      the HarmonicAngleForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaHarmonicAngleForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -129,12 +145,16 @@ public:
  * This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaHarmonicInPlaneAngleForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaHarmonicInPlaneAngleForce";
     }
+
     CalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -142,6 +162,7 @@ public:
      * @param force      the HarmonicInPlaneAngleForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -157,12 +178,16 @@ public:
  * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaTorsionForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaTorsionForce";
     }
+
     CalcAmoebaTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -170,6 +195,7 @@ public:
      * @param force      the TorsionForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaTorsionForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -185,12 +211,16 @@ public:
  * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaPiTorsionForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaPiTorsionForce";
     }
+
     CalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -198,6 +228,7 @@ public:
      * @param force      the PiTorsionForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaPiTorsionForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -213,12 +244,16 @@ public:
  * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaStretchBendForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaStretchBendForce";
     }
+
     CalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -226,6 +261,7 @@ public:
      * @param force      the StretchBendForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaStretchBendForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -241,12 +277,16 @@ public:
  * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaOutOfPlaneBendForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaOutOfPlaneBendForce";
     }
+
     CalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -254,6 +294,7 @@ public:
      * @param force      the OutOfPlaneBendForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaOutOfPlaneBendForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -269,12 +310,16 @@ public:
  * This kernel is invoked by AmoebaTorsionTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaTorsionTorsionForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaTorsionTorsionForce";
     }
+
     CalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -282,6 +327,7 @@ public:
      * @param force      the TorsionTorsionForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaTorsionTorsionForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -297,12 +343,16 @@ public:
  * This kernel is invoked by AmoebaMultipoleForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaMultipoleForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaMultipoleForce";
     }
+
     CalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
+
     /**
      * Initialize the kernel.
      * 
@@ -310,6 +360,7 @@ public:
      * @param force      the MultipoleForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaMultipoleForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -325,10 +376,13 @@ public:
  * This kernel is invoked by AmoebaGeneralizedKirkwoodForce to calculate the forces acting on the system and the energy of the system.
  */
 class CalcAmoebaGeneralizedKirkwoodForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaGeneralizedKirkwoodForce";
     }
+
     CalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
 
@@ -339,6 +393,7 @@ public:
      * @param force      the GBSAOBCForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -356,9 +411,11 @@ public:
  */
 class CalcAmoebaVdwForceKernel : public KernelImpl {
 public:
+
     static std::string Name() {
         return "CalcAmoebaVdwForce";
     }
+
     CalcAmoebaVdwForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
 
@@ -369,6 +426,7 @@ public:
      * @param force      the GBSAOBCForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaVdwForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *
@@ -384,10 +442,13 @@ public:
  * This kernel is invoked by AmoebaWcaDispersionForce to calculate the WCA dispersion forces acting on the system and the WCA dispersion energy of the system.
  */
 class CalcAmoebaWcaDispersionForceKernel : public KernelImpl {
+
 public:
+
     static std::string Name() {
         return "CalcAmoebaWcaDispersionForce";
     }
+
     CalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
 
@@ -398,6 +459,7 @@ public:
      * @param force      the GBSAOBCForce this kernel will be used for
      */
     virtual void initialize(const System& system, const AmoebaWcaDispersionForce& force) = 0;
+
     /**
      * Execute the kernel to calculate the forces and/or energy.
      *