Mods for gcc 4.4.x

plugins/amoeba/platforms/reference/tests/CMakeLists.txt

@@ -42,7 +42,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     #TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET} ${SHARED_AMOEBA_TINKER_PARAMETER_FILE_TARGET})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM__AMOEBA_TARGET} )
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
     # Link with static library

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

@@ -85,11 +85,12 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
     } 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;
@@ -128,12 +129,13 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex,  std::vector<Vec3>& p
     double quarticK       = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleQuartic();
     double penticK        = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAnglePentic();
     double sexticK        = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleSextic();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicAngleForce: 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;
@@ -157,10 +159,12 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex,  std::vector<Vec3>& p
     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;
@@ -214,6 +218,7 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
         computeAmoebaHarmonicAngleForce(ii, positions, amoebaHarmonicAngleForce, expectedForces, expectedEnergy, log );
     }
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -221,6 +226,7 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -235,6 +241,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicAngleFor
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -243,6 +250,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicAngleFor
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -299,8 +307,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //FILE* log = stderr;
 
         testOneAngle( log );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -100,7 +100,7 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
     for( int ii = 0; ii < amoebaHarmonicBondForce.getNumBonds(); ii++ ){
         computeAmoebaHarmonicBondForce(ii, positions, amoebaHarmonicBondForce, expectedForces, expectedEnergy );
     }
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -108,6 +108,7 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -120,7 +121,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicBondForc
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -129,6 +130,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicBondForc
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -209,9 +211,10 @@ int main( int numberOfArguments, char* argv[] ) {
 
         //testOneBond( log );
         testTwoBond( log );
-
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -87,11 +87,12 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
     } else {
         angle = RADIAN*acos(cosine);
     }
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "getPrefactorsGivenInPlaneAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealInPlaneAngle ); 
         (void) fflush( log );
     }
+#endif
 
     double deltaIdeal         = angle - idealInPlaneAngle;
     double deltaIdeal2        = deltaIdeal*deltaIdeal;
@@ -130,12 +131,13 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex,  std::vector<V
     double quarticK       = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleQuartic();
     double penticK        = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAnglePentic();
     double sexticK        = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleSextic();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n", 
                              bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
         (void) fflush( log );
     }
+#endif
 
     // T   = AD x CD
     // P   = B + T*delta
@@ -176,10 +178,12 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex,  std::vector<V
     double rAp2 = dotVector3( deltaR[AP],  deltaR[AP] );
     double rCp2 = dotVector3( deltaR[CP],  deltaR[CP] );
     if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
+#ifdef AMOEBA_DEBUG
         if( log ){
             (void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce:  rAp2 or rCp2 <= 0.0\n" );
             (void) fflush( log );
         }
+#endif
         return;
     }
 
@@ -290,7 +294,7 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
     for( int ii = 0; ii < amoebaHarmonicInPlaneAngleForce.getNumAngles(); ii++ ){
         computeAmoebaHarmonicInPlaneAngleForce(ii, positions, amoebaHarmonicInPlaneAngleForce, expectedForces, expectedEnergy, log );
     }
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -298,6 +302,7 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -311,7 +316,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneA
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -320,6 +325,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneA
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -377,8 +383,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //FILE* log = fopen( "AmoebaHarmonicInPlaneAngleForce.log", "w" );;
 
         testOneAngle( NULL );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -88,12 +88,14 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex,  std::vector<Vec3>&
     int particle1, particle2, particle3, particle4;
     double kAngleQuadratic;
     amoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters(bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic );
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bond %d [%d %d %d %d] k=[%10.3e %10.3e %10.3e %10.3e %10.3e]\n", 
                              bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic, kAngleCubic, kAngleQuartic, kAnglePentic, kAngleSextic );
         (void) fflush( log );
     }
+#endif
+
 
     enum { A, B, C, D, LastAtomIndex };
     enum { AB, CB, DB, AD, CD, LastDeltaIndex };
@@ -135,12 +137,13 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex,  std::vector<Vec3>&
     } else {
         angle = RADIAN*acos(cosine);
     }
- 
+#ifdef AMOEBA_DEBUG 
     if( log ){
         (void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bkk2=%14.7e rDB2=%14.7e cos=%14.7e dt=%14.7e]\n", 
                              bkk2, rDB2, cosine, angle );
         (void) fflush( log );
     }
+#endif
 
     // chain rule
  
@@ -256,6 +259,7 @@ static void computeAmoebaOutOfPlaneBendForces( Context& context, AmoebaOutOfPlan
         computeAmoebaOutOfPlaneBendForce(ii, positions, amoebaOutOfPlaneBendForce, expectedForces, expectedEnergy, log );
     }
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -263,6 +267,7 @@ static void computeAmoebaOutOfPlaneBendForces( Context& context, AmoebaOutOfPlan
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -276,7 +281,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaOutOfPlaneBendFo
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -285,6 +290,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaOutOfPlaneBendFo
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -412,16 +418,20 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
         particleIndices.push_back( 442 ); 
         kOutOfPlaneBend = 0.214755281E-01;
     } else {
+#ifdef AMOEBA_DEBUG
         if( log ){
             (void) fprintf( log, "Set id %d not recognized.\n", setId );
         }
-        char buffer[1024];
-        (void) sprintf( buffer, "Set id %d not recognized.", setId );
-        throw OpenMMException( buffer );
+#endif
+        std::stringstream buffer;
+        buffer << "Set id " << setId << " not recognized.";
+        throw OpenMMException( buffer.str() );
     }
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "Set id %d.\n", setId );
     }
+#endif
 
     amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
 
@@ -431,12 +441,14 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
 
     for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
         if( coordinates.find( particleIndices[ii] ) == coordinates.end() ){
+#ifdef AMOEBA_DEBUG
             if( log ){
                 (void) fprintf( log, "Coordinates %d not loaded.", particleIndices[ii] );
             }
-            char buffer[1024];
-            (void) sprintf( buffer, "Coordinates %d not loaded.", particleIndices[ii] );
-            throw OpenMMException( buffer );
+#endif
+            std::stringstream buffer;
+            buffer << "Coordinates " << particleIndices[ii] << " not loaded.";
+            throw OpenMMException( buffer.str() );
         }
         positions[ii] = coordinates[particleIndices[ii]];
     }
@@ -475,6 +487,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
     }
 
     if( iter == 6 ){
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: energy=%14.7e\n", totalEnergy);
         for( std::map<int,Vec3>::iterator ii = totalForces.begin(); ii != totalForces.end(); ii++ ){
@@ -485,6 +498,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
         }
         (void) fflush( log );
     }
+#endif
     }
 
 }
@@ -504,8 +518,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //for( int ii = 1; ii <= 6; ii++ ){
         //     testOneOutOfPlaneBend2( log, ii );
         //}
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -82,12 +82,13 @@ static void computeAmoebaPiTorsionForce(int bondIndex,  std::vector<Vec3>& posit
     double kTorsion;
 
     amoebaPiTorsionForce.getPiTorsionParameters(bondIndex, particle1, particle2, particle3, particle4,  particle5, particle6, kTorsion);
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaPiTorsionForce: bond %d [%d %d %d %d %d %d] k=%10.3e\n", 
                              bondIndex, particle1, particle2, particle3, particle4, particle5, particle6, kTorsion );
         (void) fflush( log );
     }
+#endif
 
     enum { AD, BD, EC, FC, P, Q, CP, DC, QD, T, U, TU, DP, QC, dT, dU, dP, dQ, dC1, dC2, dD1, dD2, LastDeltaIndex };
     double deltaR[LastDeltaIndex][3];
@@ -227,7 +228,7 @@ static void computeAmoebaPiTorsionForces( Context& context, AmoebaPiTorsionForce
     for( int ii = 0; ii < amoebaPiTorsionForce.getNumPiTorsions(); ii++ ){
         computeAmoebaPiTorsionForce(ii, positions, amoebaPiTorsionForce, expectedForces, expectedEnergy, log );
     }
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaPiTorsionForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -235,6 +236,7 @@ static void computeAmoebaPiTorsionForces( Context& context, AmoebaPiTorsionForce
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -248,7 +250,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaPiTorsionForce&
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaPiTorsionForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -257,6 +259,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaPiTorsionForce&
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -307,8 +310,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //FILE* log = fopen( "AmoebaPiTorsionForce1.log", "w" );;
 
         testOnePiTorsion( log );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -85,11 +85,13 @@ static void computeAmoebaStretchBendForce(int bondIndex,  std::vector<Vec3>& pos
 
     amoebaStretchBendForce.getStretchBendParameters(bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend);
     angleStretchBend *= RADIAN;
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaStretchBendForce: bond %d [%d %d %d] ab=%10.3e cb=%10.3e angle=%10.3e k=%10.3e\n", 
                              bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend );
         (void) fflush( log );
     }
+#endif
 
     enum { A, B, C, LastAtomIndex };
     enum { AB, CB, CBxAB, ABxP, CBxP, LastDeltaIndex };
@@ -182,11 +184,12 @@ static void computeAmoebaStretchBendForce(int bondIndex,  std::vector<Vec3>& pos
     forces[particle3][2]       -= subForce[2][2];
 
     *energy                    += term*dt*dr;
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaStretchBendForce: angle=%10.3e dt=%10.3e dr=%10.3e\n", angle, dt, dr ); 
         (void) fflush( log );
     }
+#endif
 
     return;
 }
@@ -210,7 +213,7 @@ static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendF
     for( int ii = 0; ii < amoebaStretchBendForce.getNumStretchBends(); ii++ ){
         computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy, log );
     }
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -218,6 +221,7 @@ static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendF
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -231,7 +235,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaStretchBendForce
    
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -240,6 +244,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaStretchBendForce
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -291,8 +296,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaStretchBendForce1.log", "w" );;
         testOneStretchBend( log );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -95,6 +95,7 @@ static void computeAmoebaTorsionForce(int bondIndex,  std::vector<Vec3>& positio
     torsions.push_back( torsion2 );
     torsions.push_back( torsion3 );
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaTorsionForce: bond %d [%d %d %d %d]\n", 
                              bondIndex, particle1, particle2, particle3, particle4 );
@@ -103,6 +104,7 @@ static void computeAmoebaTorsionForce(int bondIndex,  std::vector<Vec3>& positio
         }
         (void) fflush( log );
     }
+#endif
 
     enum { BA, CB, DC, CA, DB, LastDeltaIndex };
     double deltaR[LastDeltaIndex][3];
@@ -251,6 +253,7 @@ static void computeAmoebaTorsionForces( Context& context, AmoebaTorsionForce& am
         computeAmoebaTorsionForce(ii, positions, amoebaTorsionForce, expectedForces, expectedEnergy, log );
     }
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaTorsionForces: expected energy=%14.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -258,6 +261,8 @@ static void computeAmoebaTorsionForces( Context& context, AmoebaTorsionForce& am
         }
         (void) fflush( log );
     }
+#endif
+
     return;
 
 }
@@ -272,6 +277,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaTorsionForce& am
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaTorsionForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -280,6 +286,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaTorsionForce& am
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -336,8 +343,10 @@ int main( int numberOfArguments, char* argv[] ) {
         FILE* log = NULL;
         //FILE* log = fopen( "AmoebaTorsionForce.log", "w" );;
         testOneTorsion( log );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -102,6 +102,7 @@ static void computeAmoebaUreyBradleyForces( Context& context, AmoebaUreyBradleyF
         computeAmoebaUreyBradleyForce(ii, positions, amoebaUreyBradleyForce, expectedForces, expectedEnergy );
     }
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaUreyBradleyForces: expected energy=%15.7e\n", *expectedEnergy );
         for( unsigned int ii = 0; ii < positions.size(); ii++ ){
@@ -109,6 +110,7 @@ static void computeAmoebaUreyBradleyForces( Context& context, AmoebaUreyBradleyF
         }
         (void) fflush( log );
     }
+#endif
     return;
 
 }
@@ -122,6 +124,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaUreyBradleyForce
     State state                      = context.getState(State::Forces | State::Energy);
     const std::vector<Vec3> forces   = state.getForces();
 
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaUreyBradleyForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -130,6 +133,7 @@ void compareWithExpectedForceAndEnergy( Context& context, AmoebaUreyBradleyForce
         }
         (void) fflush( log );
     }
+#endif
 
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -211,8 +215,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //testOneBond( log );
         testTwoBond( log );
 
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {

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

@@ -133,7 +133,7 @@ void testVdw( FILE* log ) {
         forces[ii][1] *= conversion;
         forces[ii][2] *= conversion;
     }    
-
+#ifdef AMOEBA_DEBUG
     if( log ){
         (void) fprintf( log, "computeAmoebaVdwForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
         for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -142,6 +142,7 @@ void testVdw( FILE* log ) {
         }
         (void) fflush( log );
     }
+#endif
 
     double tolerance = 1.0e-03;
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
@@ -161,8 +162,10 @@ int main( int numberOfArguments, char* argv[] ) {
         //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaVdwForce1.log", "w" );;
         testVdw( log );
+#ifdef AMOEBA_DEBUG
         if( log && log != stderr )
             (void) fclose( log );
+#endif
 
     }
     catch(const std::exception& e) {