Elimininated obsolete SimTKOpenMMCommon files

platforms/cpu/src/CpuCustomGBForce.cpp

@@ -25,7 +25,6 @@
 #include <string.h>
 #include <sstream>
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomGBForce.h"

platforms/cpu/src/CpuCustomManyParticleForce.cpp

@@ -26,7 +26,6 @@
 #include <sstream>
 #include <utility>
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomManyParticleForce.h"

platforms/cpu/src/CpuCustomNonbondedForce.cpp

@@ -25,7 +25,6 @@
 #include <string.h>
 #include <sstream>
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomNonbondedForce.h"

platforms/cpu/src/CpuLangevinDynamics.cpp

@@ -23,7 +23,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuLangevinDynamics.h"
 

platforms/cpu/src/CpuNonbondedForce.cpp

@@ -24,7 +24,6 @@
 
 #include <complex>
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForce.h"
 #include "ReferenceForce.h"

platforms/cpu/src/CpuNonbondedForceVec4.cpp

@@ -22,7 +22,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForceVec4.h"
 

platforms/cpu/src/CpuNonbondedForceVec8.cpp

@@ -22,7 +22,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForceVec8.h"
 #include "openmm/OpenMMException.h"

platforms/reference/include/CpuGBVI.h

@@ -39,7 +39,7 @@ class CpuGBVI {
       // GB/VI parameters
 
       GBVIParameters* _gbviParameters;
-      RealOpenMMVector _switchDeriviative;
+      std::vector<RealOpenMM> _switchDeriviative;
 
    public:
 
@@ -93,7 +93,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
+      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
       
       /**---------------------------------------------------------------------------------------
       
@@ -174,7 +174,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges);
+      RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges);
       
       /**---------------------------------------------------------------------------------------
       
@@ -187,7 +187,7 @@ class CpuGBVI {
          --------------------------------------------------------------------------------------- */
       
       void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
-                             const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
+                             const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
       
       /**---------------------------------------------------------------------------------------
       
@@ -254,7 +254,7 @@ class CpuGBVI {
     
        --------------------------------------------------------------------------------------- */
     
-      RealOpenMMVector& getSwitchDeriviative();
+      std::vector<RealOpenMM>& getSwitchDeriviative();
     
     /**---------------------------------------------------------------------------------------
     
@@ -303,9 +303,9 @@ class CpuGBVI {
     
         --------------------------------------------------------------------------------------- */
     
-    void printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
-                   const RealOpenMMVector& bornRadii,
-                   const RealOpenMMVector& bornForces,
+    void printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges,
+                   const std::vector<RealOpenMM>& bornRadii,
+                   const std::vector<RealOpenMM>& bornForces,
                    const std::vector<OpenMM::RealVec>& forces,
                    const std::string& idString, FILE* log);
 

platforms/reference/include/CpuObc.h

@@ -39,7 +39,7 @@ class CpuObc {
 
       // arrays containing OBC chain derivative 
 
-      RealOpenMMVector _obcChain;
+      std::vector<RealOpenMM> _obcChain;
 
       // flag to signal whether ACE approximation
       // is to be included
@@ -117,7 +117,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMMVector& getObcChain();
+      std::vector<RealOpenMM>& getObcChain();
       
       /**---------------------------------------------------------------------------------------
       
@@ -128,7 +128,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
+      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
       
       /**---------------------------------------------------------------------------------------
         
@@ -142,8 +142,8 @@ class CpuObc {
         
             --------------------------------------------------------------------------------------- */
         
-      void computeAceNonPolarForce(const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii, 
-                                   RealOpenMM* energy, RealOpenMMVector& forces) const;
+      void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<RealOpenMM>& bornRadii,
+                                   RealOpenMM* energy, std::vector<RealOpenMM>& forces) const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -156,7 +156,7 @@ class CpuObc {
          --------------------------------------------------------------------------------------- */
       
       RealOpenMM computeBornEnergyForces(const std::vector<OpenMM::RealVec>& atomCoordinates,
-                                         const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces);
+                                         const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& forces);
       
     /**---------------------------------------------------------------------------------------
     
@@ -173,9 +173,9 @@ class CpuObc {
         --------------------------------------------------------------------------------------- */
     
     void printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
-                  const RealOpenMMVector& partialCharges,
-                  const RealOpenMMVector& bornRadii,
-                  const RealOpenMMVector& bornForces,
+                  const std::vector<RealOpenMM>& partialCharges,
+                  const std::vector<RealOpenMM>& bornRadii,
+                  const std::vector<RealOpenMM>& bornForces,
                   const std::vector<OpenMM::RealVec>& forces,
                   const std::string& idString, FILE* log);
     

platforms/reference/include/GBVIParameters.h

@@ -25,7 +25,8 @@
 #ifndef __GBVIParameters_H__
 #define __GBVIParameters_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -57,9 +58,9 @@ class GBVIParameters {
 
       // parameter vectors
 
-      RealOpenMMVector _atomicRadii;
-      RealOpenMMVector _scaledRadii;
-      RealOpenMMVector _gammaParameters;
+      std::vector<RealOpenMM> _atomicRadii;
+      std::vector<RealOpenMM> _scaledRadii;
+      std::vector<RealOpenMM> _gammaParameters;
 
       // cutoff and periodic boundary conditions
       
@@ -160,7 +161,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      const RealOpenMMVector& getScaledRadii() const;
+      const std::vector<RealOpenMM>& getScaledRadii() const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -170,7 +171,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      void setScaledRadii(const RealOpenMMVector& scaledRadii);
+      void setScaledRadii(const std::vector<RealOpenMM>& scaledRadii);
         
       /**---------------------------------------------------------------------------------------
       
@@ -180,7 +181,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getAtomicRadii() const;
+      const std::vector<RealOpenMM>& getAtomicRadii() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -190,7 +191,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setAtomicRadii(const RealOpenMMVector& atomicRadii);
+      void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
 
       /**---------------------------------------------------------------------------------------
       
@@ -200,7 +201,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getGammaParameters() const;
+      const std::vector<RealOpenMM>& getGammaParameters() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -210,7 +211,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setGammaParameters(const RealOpenMMVector& gammaParameters);
+      void setGammaParameters(const std::vector<RealOpenMM>& gammaParameters);
 
       /**---------------------------------------------------------------------------------------
 

platforms/reference/include/ObcParameters.h

@@ -25,7 +25,8 @@
 #ifndef __ObcParameters_H__
 #define __ObcParameters_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
+#include <vector>
 
 namespace OpenMM {
 
@@ -57,8 +58,8 @@ class ObcParameters {
 
       // scaled radius factors (S_kk in HCT paper)
 
-      RealOpenMMVector _atomicRadii;
-      RealOpenMMVector _scaledRadiusFactors;
+      std::vector<RealOpenMM> _atomicRadii;
+      std::vector<RealOpenMM> _scaledRadiusFactors;
 
       // cutoff and periodic boundary conditions
       
@@ -264,7 +265,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      const RealOpenMMVector& getScaledRadiusFactors() const;
+      const std::vector<RealOpenMM>& getScaledRadiusFactors() const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -274,7 +275,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      void setScaledRadiusFactors(const RealOpenMMVector& scaledRadiusFactors);
+      void setScaledRadiusFactors(const std::vector<RealOpenMM>& scaledRadiusFactors);
         
       /**---------------------------------------------------------------------------------------
       
@@ -284,7 +285,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getAtomicRadii() const;
+      const std::vector<RealOpenMM>& getAtomicRadii() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -294,7 +295,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setAtomicRadii(const RealOpenMMVector& atomicRadii);
+      void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
 
 
       /**---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceAndersenThermostat.h

@@ -25,7 +25,6 @@
 #ifndef __ReferenceAndersenThermostat_H__
 #define __ReferenceAndersenThermostat_H__
 
-#include "SimTKOpenMMCommon.h"
 #include <vector>
 
 namespace OpenMM {

platforms/reference/include/ReferenceCMAPTorsionIxn.h

@@ -25,7 +25,6 @@
 #ifndef __ReferenceCMAPTorsionIxn_H__
 #define __ReferenceCMAPTorsionIxn_H__
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceBondIxn.h"
 #include <vector>

platforms/reference/include/ReferenceConstraintAlgorithm.h

@@ -25,8 +25,9 @@
 #ifndef __ReferenceConstraintAlgorithm_H__
 #define __ReferenceConstraintAlgorithm_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 

platforms/reference/include/ReferenceDynamics.h

@@ -26,7 +26,6 @@
 #define __ReferenceDynamics_H__
 
 #include "ReferenceConstraintAlgorithm.h"
-#include "SimTKOpenMMCommon.h"
 #include "openmm/System.h"
 #include <cstddef>
 #include <vector>

platforms/reference/include/ReferenceLincsAlgorithm.h

@@ -131,12 +131,9 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
          @param atomCoordinatesP atom coordinates prime
          @param inverseMasses    1/mass
 
-         @return SimTKOpenMMCommon::DefaultReturn if converge; else
-          return SimTKOpenMMCommon::ErrorReturn
-
          --------------------------------------------------------------------------------------- */
 
-      int apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+      void apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                        std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
 
       /**---------------------------------------------------------------------------------------
@@ -148,12 +145,9 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
          @param velocities       atom velocities
          @param inverseMasses    1/mass
 
-         @return SimTKOpenMMCommon::DefaultReturn if converge; else
-          return SimTKOpenMMCommon::ErrorReturn
-
          --------------------------------------------------------------------------------------- */
 
-      int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+      void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                      std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
 };
 

platforms/reference/include/ReferenceMonteCarloBarostat.h

@@ -25,7 +25,6 @@
 #ifndef __ReferenceMonteCarloBarostat_H__
 #define __ReferenceMonteCarloBarostat_H__
 
-#include "SimTKOpenMMCommon.h"
 #include <utility>
 #include <vector>
 

platforms/reference/include/ReferencePME.h

@@ -32,7 +32,7 @@
 #ifndef __ReferencePME_H__
 #define __ReferencePME_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
 #include <vector>
 

platforms/reference/include/ReferencePairIxn.h

@@ -27,6 +27,7 @@
 
 #include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
 namespace OpenMM {
 

platforms/reference/include/SimTKOpenMMCommon.h

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#ifndef __SimTKOpenMMCommon_H__
-#define __SimTKOpenMMCommon_H__
-
-#include <vector>
-#include <string>
-#include "RealVec.h"
-
-namespace OpenMM {
-
-typedef std::vector<RealOpenMM> RealOpenMMVector;
-typedef RealOpenMMVector::iterator RealOpenMMVectorI;
-typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI;
-
-// ---------------------------------------------------------------------------------------
-
-class SimTKOpenMMCommon {
-
-   public:
-
-      static const std::string NotSet;
-      static const RealOpenMM BigCutoffValue;
-      static const std::string Comment;
-      static const std::string Tab;
-      static const std::string YesU;
-      static const std::string YesUl;
-      static const std::string YesL;
-
-      // subroutine returns
-
-      static const int DefaultReturn;
-      static const int ErrorReturn;
-};
-
-} // namespace OpenMM
-
-#endif // __SimTKOpenMMCommon_H__