Deleted lots of debugging code

openmmapi/include/openmm/GBVIForce.h

@@ -157,7 +157,7 @@ public:
      * 
      * @return number of bonds
      */
-    int getNumBonds( void ) const;
+    int getNumBonds() const;
 
     /**
      * Get the dielectric constant for the solvent.
@@ -208,7 +208,7 @@ public:
     /** 
      * Get Born radius scaling method
      */
-    BornRadiusScalingMethod getBornRadiusScalingMethod( void ) const;
+    BornRadiusScalingMethod getBornRadiusScalingMethod() const;
     /** 
      * Set Born radius scaling method
      */
@@ -216,7 +216,7 @@ public:
     /** 
      * Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
      */
-    double getQuinticLowerLimitFactor( void ) const;
+    double getQuinticLowerLimitFactor() const;
     /** 
      * Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
      */
@@ -224,7 +224,7 @@ public:
     /** 
      * Get the upper limit  used in the quintic spline scaling method, measured in nm (~5.0)
      */
-    double getQuinticUpperBornRadiusLimit( void ) const;
+    double getQuinticUpperBornRadiusLimit() const;
     /** 
      * Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
      */

openmmapi/src/GBVIForce.cpp

@@ -77,7 +77,7 @@ void GBVIForce::setCutoffDistance(double distance) {
     cutoffDistance = distance;
 }
 
-GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod( void ) const {
+GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod() const {
     return scalingMethod;
 }
 
@@ -85,7 +85,7 @@ void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
     scalingMethod = method;
 }
 
-double GBVIForce::getQuinticLowerLimitFactor( void ) const {
+double GBVIForce::getQuinticLowerLimitFactor() const {
     return quinticLowerLimitFactor;
 }
 
@@ -93,7 +93,7 @@ void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor )
     quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
 }
 
-double GBVIForce::getQuinticUpperBornRadiusLimit( void ) const {
+double GBVIForce::getQuinticUpperBornRadiusLimit() const {
     return quinticUpperBornRadiusLimit;
 }
 
@@ -113,7 +113,7 @@ void GBVIForce::setBondParameters( int index, int particle1, int particle2, doub
     bonds[index].bondLength = bondLength;
 }
 
-int GBVIForce::getNumBonds( void ) const {
+int GBVIForce::getNumBonds() const {
    return (int) bonds.size();
 }
 

openmmapi/src/GBVIForceImpl.cpp

@@ -145,8 +145,6 @@ int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
 }
 */
 
-#define GBVIDebug 0
-
 void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
                                      const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
 
@@ -219,26 +217,6 @@ void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<st
     if( errors ){
         throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
     }
-
-#if GBVIDebug
-    (void) fprintf( stderr, "                  R              q          gamma   scaled radii no. bnds\n" );
-    double totalQ = 0.0;
-    for( int i = 0; i < (int) scaledRadii.size(); i++ ){
-
-        double charge;
-        double gamma;
-        double radiusI;
-     
-        owner.getParticleParameters(i, charge, radiusI, gamma); 
-        totalQ += charge;
-        (void) fprintf( stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size() );
-    }
-    (void) fprintf( stderr, "Total charge=%e\n", totalQ );
-    (void) fflush( stderr );
-#endif
-
-#undef GBVIDebug
-
 }
 
 double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {

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

@@ -77,7 +77,7 @@ public:
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalAngleCubic( void ) const;
+    double getAmoebaGlobalAngleCubic() const;
 
     /**
      * Set the global quartic term
@@ -91,7 +91,7 @@ public:
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalAngleQuartic( void ) const;
+    double getAmoebaGlobalAngleQuartic() const;
 
     /**
      * Set the global pentic term
@@ -105,7 +105,7 @@ public:
      * 
      * @return global penticK term
      */
-    double getAmoebaGlobalAnglePentic( void ) const;
+    double getAmoebaGlobalAnglePentic() const;
 
     /**
      * Set the global sextic term
@@ -119,7 +119,7 @@ public:
      * 
      * @return global sextic term
      */
-    double getAmoebaGlobalAngleSextic( void ) const;
+    double getAmoebaGlobalAngleSextic() const;
 
     /**
      * Add an angle term to the force field.

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

@@ -78,7 +78,7 @@ public:
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalBondCubic( void ) const;
+    double getAmoebaGlobalBondCubic() const;
 
     /**
      * Set the global quartic term
@@ -92,7 +92,7 @@ public:
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalBondQuartic( void ) const;
+    double getAmoebaGlobalBondQuartic() const;
 
     /**
      * Add a bond term to the force field.

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

@@ -127,7 +127,7 @@ public:
     /**
      * Get the flag signaling whether the cavity term should be included
      */
-    int getIncludeCavityTerm( ) const;
+    int getIncludeCavityTerm() const;
 
     /**
      * Set the flag signaling whether the cavity term should be included

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

@@ -77,7 +77,7 @@ public:
      * 
      * @return global cubicK term
      */
-    double getAmoebaGlobalInPlaneAngleCubic( void ) const;
+    double getAmoebaGlobalInPlaneAngleCubic() const;
 
     /**
      * Set the global quartic term
@@ -91,7 +91,7 @@ public:
      * 
      * @return global  quartic term
      */
-    double getAmoebaGlobalInPlaneAngleQuartic( void ) const;
+    double getAmoebaGlobalInPlaneAngleQuartic() const;
 
     /**
      * Set the global pentic term
@@ -105,7 +105,7 @@ public:
      * 
      * @return global penticK term
      */
-    double getAmoebaGlobalInPlaneAnglePentic( void ) const;
+    double getAmoebaGlobalInPlaneAnglePentic() const;
 
     /**
      * Set the global sextic term
@@ -119,7 +119,7 @@ public:
      * 
      * @return global  sextic term
      */
-    double getAmoebaGlobalInPlaneAngleSextic( void ) const;
+    double getAmoebaGlobalInPlaneAngleSextic() const;
 
     /**
      * Add an angle term to the force field.

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h

@@ -97,7 +97,7 @@ private:
 
     static int CovalentDegrees[AmoebaMultipoleForce::CovalentEnd];
     static bool initializedCovalentDegrees;
-    static const int* getCovalentDegrees( void );
+    static const int* getCovalentDegrees();
 };
 
 } // namespace OpenMM

plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp

@@ -63,7 +63,7 @@ void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle
     angles[index].quadraticK = quadraticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleCubic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleCubic() const {
     return _globalCubicK;
 }
 
@@ -71,7 +71,7 @@ void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
     _globalCubicK           = cubicK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleQuartic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleQuartic() const {
     return _globalQuarticK;
 }
 
@@ -79,7 +79,7 @@ void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAnglePentic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAnglePentic() const {
     return _globalPenticK;
 }
 
@@ -87,7 +87,7 @@ void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
     _globalPenticK           = penticK;
 }
 
-double AmoebaAngleForce::getAmoebaGlobalAngleSextic( void ) const {
+double AmoebaAngleForce::getAmoebaGlobalAngleSextic() const {
     return _globalSexticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp

@@ -67,11 +67,11 @@ void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) {
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaBondForce::getAmoebaGlobalBondCubic( void ) const {
+double AmoebaBondForce::getAmoebaGlobalBondCubic() const {
     return _globalCubicK;
 }
 
-double AmoebaBondForce::getAmoebaGlobalBondQuartic( void ) const {
+double AmoebaBondForce::getAmoebaGlobalBondQuartic() const {
     return _globalQuarticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp

@@ -73,11 +73,11 @@ void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic() const {
     return _globalCubicK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic() const {
     return _globalQuarticK;
 }
 
@@ -89,11 +89,11 @@ void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK
     _globalSexticK         = quarticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic() const {
     return _globalPenticK;
 }
 
-double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic( void ) const {
+double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic() const {
     return _globalSexticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -45,7 +45,7 @@ AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polari
     pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
 }
 
-AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod( void ) const {
+AmoebaMultipoleForce::NonbondedMethod AmoebaMultipoleForce::getNonbondedMethod() const {
     return nonbondedMethod;
 }
 
@@ -53,7 +53,7 @@ void AmoebaMultipoleForce::setNonbondedMethod( AmoebaMultipoleForce::NonbondedMe
     nonbondedMethod = method;
 }
 
-AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType( void ) const {
+AmoebaMultipoleForce::PolarizationType AmoebaMultipoleForce::getPolarizationType() const {
     return polarizationType;
 }
 
@@ -77,7 +77,7 @@ void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
     aewald = inputAewald; 
 } 
  
-int AmoebaMultipoleForce::getPmeBSplineOrder( void ) const { 
+int AmoebaMultipoleForce::getPmeBSplineOrder() const { 
     return pmeBSplineOrder; 
 } 
  
@@ -103,7 +103,7 @@ void AmoebaMultipoleForce::setPmeGridDimensions( const std::vector<int>& gridDim
     return;
 } 
 
-int AmoebaMultipoleForce::getMutualInducedMaxIterations( void ) const {
+int AmoebaMultipoleForce::getMutualInducedMaxIterations() const {
     return mutualInducedMaxIterations;
 }
 
@@ -111,7 +111,7 @@ void AmoebaMultipoleForce::setMutualInducedMaxIterations( int inputMutualInduced
     mutualInducedMaxIterations = inputMutualInducedMaxIterations;
 }
 
-double AmoebaMultipoleForce::getMutualInducedTargetEpsilon( void ) const {
+double AmoebaMultipoleForce::getMutualInducedTargetEpsilon() const {
     return mutualInducedTargetEpsilon;
 }
 

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -138,7 +138,7 @@ std::vector<std::string> AmoebaMultipoleForceImpl::getKernelNames() {
     return names;
 }
 
-const int* AmoebaMultipoleForceImpl::getCovalentDegrees( void ) {
+const int* AmoebaMultipoleForceImpl::getCovalentDegrees() {
     if( !initializedCovalentDegrees ){
         initializedCovalentDegrees                                      = true;
         CovalentDegrees[AmoebaMultipoleForce::Covalent12]               = 1;

plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp

@@ -44,7 +44,7 @@ AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
 
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendCubic() const {
     return _globalCubicK;
 }
 
@@ -52,7 +52,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendCubic(double cubicK
     _globalCubicK           = cubicK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendQuartic() const {
     return _globalQuarticK;
 }
 
@@ -60,7 +60,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendQuartic(double quar
     _globalQuarticK         = quarticK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendPentic() const {
     return _globalPenticK;
 }
 
@@ -68,7 +68,7 @@ void AmoebaOutOfPlaneBendForce::setAmoebaGlobalOutOfPlaneBendPentic(double penti
     _globalPenticK           = penticK;
 }
 
-double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic( void ) const {
+double AmoebaOutOfPlaneBendForce::getAmoebaGlobalOutOfPlaneBendSextic() const {
     return _globalSexticK;
 }
 

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -66,7 +66,7 @@ void AmoebaVdwForce::setSigmaCombiningRule( const std::string& inputSigmaCombini
     sigmaCombiningRule = inputSigmaCombiningRule;
 }
 
-const std::string& AmoebaVdwForce::getSigmaCombiningRule( void ) const {
+const std::string& AmoebaVdwForce::getSigmaCombiningRule() const {
     return sigmaCombiningRule;
 }
 
@@ -74,7 +74,7 @@ void AmoebaVdwForce::setEpsilonCombiningRule( const std::string& inputEpsilonCom
     epsilonCombiningRule = inputEpsilonCombiningRule;
 }
 
-const std::string& AmoebaVdwForce::getEpsilonCombiningRule( void ) const {
+const std::string& AmoebaVdwForce::getEpsilonCombiningRule() const {
     return epsilonCombiningRule;
 }
 

plugins/amoeba/openmmapi/src/AmoebaWcaDispersionForce.cpp

@@ -63,35 +63,35 @@ void AmoebaWcaDispersionForce::setParticleParameters(int particleIndex, double r
     parameters[particleIndex].epsilon         = epsilon;
 }
 
-double AmoebaWcaDispersionForce::getEpso( void ) const {
+double AmoebaWcaDispersionForce::getEpso() const {
     return epso;
 }
 
-double AmoebaWcaDispersionForce::getEpsh( void ) const {
+double AmoebaWcaDispersionForce::getEpsh() const {
     return epsh;
 }
 
-double AmoebaWcaDispersionForce::getRmino( void ) const {
+double AmoebaWcaDispersionForce::getRmino() const {
     return rmino;
 }
 
-double AmoebaWcaDispersionForce::getRminh( void ) const {
+double AmoebaWcaDispersionForce::getRminh() const {
     return rminh;
 }
 
-double AmoebaWcaDispersionForce::getAwater( void ) const {
+double AmoebaWcaDispersionForce::getAwater() const {
     return awater;
 }
 
-double AmoebaWcaDispersionForce::getShctd( void ) const {
+double AmoebaWcaDispersionForce::getShctd() const {
     return shctd;
 }
 
-double AmoebaWcaDispersionForce::getDispoff( void ) const {
+double AmoebaWcaDispersionForce::getDispoff() const {
     return dispoff;
 }
 
-double AmoebaWcaDispersionForce::getSlevy( void ) const {
+double AmoebaWcaDispersionForce::getSlevy() const {
     return slevy;
 }
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp

@@ -33,8 +33,6 @@
 using std::vector;
 using namespace OpenMM;
 
-#undef AMOEBA_DEBUG
-
 AmoebaReferenceMultipoleForce::AmoebaReferenceMultipoleForce() :
                                                    _nonbondedMethod(NoCutoff),
                                                    _numParticles(0), 
@@ -233,33 +231,6 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps(const vector< vector< vector<
             }
         }
     }
-
-    //showScaleMapForParticle(2, stderr);
-    //showScaleMapForParticle(10, stderr);
-
-    return;
-}
-
-void AmoebaReferenceMultipoleForce::showScaleMapForParticle(unsigned int particleI, FILE* log) const 
-{
-
-#ifdef AMOEBA_DEBUG
-    (void) fprintf(log, "Scale map particle %5u maxIndex=%u\n", particleI, _maxScaleIndex[particleI]);
-
-    std::string scaleNames[LAST_SCALE_TYPE_INDEX] = { "D", "P", "M" }; 
-    for (unsigned int ii = 0; ii < _scaleMaps[particleI].size(); ii++) {
-        MapIntRealOpenMM scaleMap = _scaleMaps[particleI][ii];
-        (void) fprintf(log, "  %s scale ", scaleNames[ii].c_str());
-        for (MapIntRealOpenMMCI jj = scaleMap.begin(); jj != scaleMap.end(); jj++) {
-            //if (jj->first > particleI && jj->second < 1.0)
-            if (jj->second < 1.0)
-            (void) fprintf(log, "%4d=%5.2f ", jj->first, jj->second);
-        }    
-        (void) fprintf(log, "\n");
-    }    
-    (void) fprintf(log, "\n");
-    (void) fflush(log);
-#endif
 }
 
 RealOpenMM AmoebaReferenceMultipoleForce::getMultipoleScaleFactor(unsigned int particleI, unsigned int particleJ, ScaleType scaleType) const 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h

@@ -712,15 +712,6 @@ protected:
      */
     void setupScaleMaps(const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo);
 
-    /**
-     * Show scaling factor map
-     *
-     * @param particleI index of particle whose scale map is to be shown
-     * @param log       output destination 
-     * 
-     */
-    void showScaleMapForParticle(unsigned int particleI, FILE* log) const;
-
     /**
      * Get multipole scale factor for particleI & particleJ
      * 

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp

@@ -77,7 +77,7 @@ static void crossProductVector3(double* vectorX, double* vectorY, double* vector
 
 static void getPrefactorsGivenAngleCosine(double cosine, double idealAngle, double quadraticK, double cubicK,
                                           double quarticK, double penticK, double sexticK,
-                                          double* dEdR, double* energyTerm, FILE* log) {
+                                          double* dEdR, double* energyTerm) {
 
     double angle;
     if (cosine >= 1.0) {
@@ -89,12 +89,6 @@ static void getPrefactorsGivenAngleCosine(double cosine, double idealAngle, doub
     else {
         angle = RADIAN*acos(cosine);
     }
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "getPrefactorsGivenAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealAngle); 
-        (void) fflush(log);
-    }
-#endif
 
     double deltaIdeal         = angle - idealAngle;
     double deltaIdeal2        = deltaIdeal*deltaIdeal;
@@ -122,7 +116,7 @@ static void getPrefactorsGivenAngleCosine(double cosine, double idealAngle, doub
 }
 
 static void computeAmoebaAngleForce(int bondIndex,  std::vector<Vec3>& positions, AmoebaAngleForce& AmoebaAngleForce,
-                                             std::vector<Vec3>& forces, double* energy, FILE* log) {
+                                             std::vector<Vec3>& forces, double* energy) {
 
     int particle1, particle2, particle3;
     double idealAngle;
@@ -133,13 +127,6 @@ static void computeAmoebaAngleForce(int bondIndex,  std::vector<Vec3>& positions
     double quarticK       = AmoebaAngleForce.getAmoebaGlobalAngleQuartic();
     double penticK        = AmoebaAngleForce.getAmoebaGlobalAnglePentic();
     double sexticK        = AmoebaAngleForce.getAmoebaGlobalAngleSextic();
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n", 
-                             bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK);
-        (void) fflush(log);
-    }
-#endif
 
     double deltaR[2][3];
     double r2_0 = 0.0;
@@ -163,17 +150,10 @@ static void computeAmoebaAngleForce(int bondIndex,  std::vector<Vec3>& positions
     double dot    = deltaR[0][0]*deltaR[1][0] + deltaR[0][1]*deltaR[1][1] + deltaR[0][2]*deltaR[1][2];
     double cosine = dot/sqrt(r2_0*r2_1);
 
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "dot=%10.3e r2_0=%10.3e r2_1=%10.3e\n", dot, r2_0, r2_1); 
-        (void) fflush(log);
-    }
-#endif
-
     double dEdR;
     double energyTerm;
     getPrefactorsGivenAngleCosine(cosine, idealAngle, quadraticK, cubicK,
-                                  quarticK, penticK, sexticK, &dEdR, &energyTerm, log);
+                                  quarticK, penticK, sexticK, &dEdR, &energyTerm);
 
     double termA  = -dEdR/(r2_0*rp);
     double termC  =  dEdR/(r2_1*rp);
@@ -203,7 +183,7 @@ static void computeAmoebaAngleForce(int bondIndex,  std::vector<Vec3>& positions
 }
 
 static void computeAmoebaAngleForces(Context& context, AmoebaAngleForce& AmoebaAngleForce,
-                                             std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log) {
+                                             std::vector<Vec3>& expectedForces, double* expectedEnergy) {
 
     // get positions and zero forces
 
@@ -219,50 +199,27 @@ static void computeAmoebaAngleForces(Context& context, AmoebaAngleForce& AmoebaA
 
     *expectedEnergy = 0.0;
     for (int ii = 0; ii < AmoebaAngleForce.getNumAngles(); ii++) {
-        computeAmoebaAngleForce(ii, positions, AmoebaAngleForce, expectedForces, expectedEnergy, log);
-    }
-
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy);
-        for (unsigned int ii = 0; ii < positions.size(); ii++) {
-            (void) fprintf(log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2]);
-        }
-        (void) fflush(log);
+        computeAmoebaAngleForce(ii, positions, AmoebaAngleForce, expectedForces, expectedEnergy);
     }
-#endif
-    return;
-
 }
 
 void compareWithExpectedForceAndEnergy(Context& context, AmoebaAngleForce& AmoebaAngleForce,
-                                       double tolerance, const std::string& idString, FILE* log) {
+                                       double tolerance, const std::string& idString) {
 
     std::vector<Vec3> expectedForces;
     double expectedEnergy;
-    computeAmoebaAngleForces(context, AmoebaAngleForce, expectedForces, &expectedEnergy, log);
+    computeAmoebaAngleForces(context, AmoebaAngleForce, expectedForces, &expectedEnergy);
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
 
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy());
-        for (unsigned int ii = 0; ii < forces.size(); ii++) {
-            (void) fprintf(log, "%6u [%14.7e %14.7e %14.7e]   [%14.7e %14.7e %14.7e]\n", ii,
-                            expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2]);
-        }
-        (void) fflush(log);
-    }
-#endif
-
     for (unsigned int ii = 0; ii < forces.size(); ii++) {
         ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
     }
     ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
 }
 
-void testOneAngle(FILE* log) {
+void testOneAngle() {
 
     System system;
     int numberOfParticles = 3;
@@ -299,7 +256,7 @@ void testOneAngle(FILE* log) {
     positions[2] = Vec3(0, 0, 1);
 
     context.setPositions(positions);
-    compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
+    compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle");
     
     // Try changing the angle parameters and make sure it's still correct.
     
@@ -307,14 +264,14 @@ void testOneAngle(FILE* log) {
     bool exceptionThrown = false;
     try {
         // This should throw an exception.
-        compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
+        compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle");
     }
     catch (std::exception ex) {
         exceptionThrown = true;
     }
     ASSERT(exceptionThrown);
     amoebaAngleForce->updateParametersInContext(context);
-    compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
+    compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle");
 }
 
 int main(int numberOfArguments, char* argv[]) {
@@ -322,16 +279,7 @@ int main(int numberOfArguments, char* argv[]) {
     try {
         std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
-        //FILE* log = fopen("AmoebaAngleForce.log", "w");;
-        FILE* log = NULL;
-        //FILE* log = stderr;
-
-        testOneAngle(log);
-#ifdef AMOEBA_DEBUG
-        if (log && log != stderr)
-            (void) fclose(log);
-#endif
-
+        testOneAngle();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp

@@ -85,7 +85,7 @@ static void computeAmoebaBondForce(int bondIndex,  std::vector<Vec3>& positions,
 }
 
 static void computeAmoebaBondForces(Context& context, AmoebaBondForce& AmoebaBondForce,
-                                             std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log) {
+                                             std::vector<Vec3>& expectedForces, double* expectedEnergy) {
 
     // get positions and zero forces
 
@@ -103,37 +103,16 @@ static void computeAmoebaBondForces(Context& context, AmoebaBondForce& AmoebaBon
     for (int ii = 0; ii < AmoebaBondForce.getNumBonds(); ii++) {
         computeAmoebaBondForce(ii, positions, AmoebaBondForce, expectedForces, expectedEnergy);
     }
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy);
-        for (unsigned int ii = 0; ii < positions.size(); ii++) {
-            (void) fprintf(log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2]);
-        }
-        (void) fflush(log);
-    }
-#endif
-    return;
-
 }
 
-void compareWithExpectedForceAndEnergy(Context& context, AmoebaBondForce& AmoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
+void compareWithExpectedForceAndEnergy(Context& context, AmoebaBondForce& AmoebaBondForce, double tolerance, const std::string& idString) {
 
     std::vector<Vec3> expectedForces;
     double expectedEnergy;
-    computeAmoebaBondForces(context, AmoebaBondForce, expectedForces, &expectedEnergy, NULL);
+    computeAmoebaBondForces(context, AmoebaBondForce, expectedForces, &expectedEnergy);
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-#ifdef AMOEBA_DEBUG
-    if (log) {
-        (void) fprintf(log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy());
-        for (unsigned int ii = 0; ii < forces.size(); ii++) {
-            (void) fprintf(log, "%6u [%15.7e %15.7e %15.7e]   [%15.7e %15.7e %15.7e]\n", ii,
-                            expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2]);
-        }
-        (void) fflush(log);
-    }
-#endif
 
     for (unsigned int ii = 0; ii < forces.size(); ii++) {
         ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
@@ -141,7 +120,7 @@ void compareWithExpectedForceAndEnergy(Context& context, AmoebaBondForce& Amoeba
     ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
 }
 
-void testOneBond(FILE* log) {
+void testOneBond() {
 
     System system;
 
@@ -168,10 +147,10 @@ void testOneBond(FILE* log) {
     positions[1] = Vec3(0, 0, 0);
 
     context.setPositions(positions);
-    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testOneBond", log);
+    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testOneBond");
 }
 
-void testTwoBond(FILE* log) {
+void testTwoBond() {
 
     System system;
 
@@ -203,7 +182,7 @@ void testTwoBond(FILE* log) {
     positions[2] = Vec3(1, 0, 1);
 
     context.setPositions(positions);
-    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
+    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond");
     
     // Try changing the bond parameters and make sure it's still correct.
     
@@ -212,14 +191,14 @@ void testTwoBond(FILE* log) {
     bool exceptionThrown = false;
     try {
         // This should throw an exception.
-        compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
+        compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond");
     }
     catch (std::exception ex) {
         exceptionThrown = true;
     }
     ASSERT(exceptionThrown);
     amoebaBondForce->updateParametersInContext(context);
-    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
+    compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond");
 }
 
 int main(int numberOfArguments, char* argv[]) {
@@ -227,16 +206,8 @@ int main(int numberOfArguments, char* argv[]) {
     try {
         std::cout << "TestReferenceAmoebaBondForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
-        FILE* log = NULL;
-        //FILE* log = stderr;
-
-        //testOneBond(log);
-        testTwoBond(log);
-#ifdef AMOEBA_DEBUG
-        if (log && log != stderr)
-            (void) fclose(log);
-#endif
-
+        //testOneBond();
+        testTwoBond();
     }
     catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;