Turned off logging

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp

@@ -34,7 +34,6 @@
 using namespace OpenMM;
 
 extern "C" void OPENMM_AMOEBA_REFERENCE_EXPORT registerKernelFactories() {
-fprintf( stderr,"In registerKernelFactories AmoebaReferenceKernelFactory\n" ); fflush( stderr );
     for( int ii = 0; ii < Platform::getNumPlatforms(); ii++ ){
         Platform& platform = Platform::getPlatform(ii);
         if( platform.getName() == "Reference" ){

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

@@ -296,8 +296,8 @@ int main( int numberOfArguments, char* argv[] ) {
         std::cout << "TestCudaAmoebaHarmonicAngleForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
         //FILE* log = fopen( "AmoebaHarmonicAngleForce.log", "w" );;
-        //FILE* log = NULL;
-        FILE* log = stderr;
+        FILE* log = NULL;
+        //FILE* log = stderr;
 
         testOneAngle( log );
         if( log && log != stderr )

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

@@ -204,8 +204,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaHarmonicBondForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
-        //FILE* log = NULL;
-        FILE* log = stderr;
+        FILE* log = NULL;
+        //FILE* log = stderr;
 
         //testOneBond( log );
         testTwoBond( log );

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

@@ -372,8 +372,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaHarmonicInPlaneAngleForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
-        //FILE* log = NULL;
-        FILE* log = stderr;
+        FILE* log = NULL;
+        //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaHarmonicInPlaneAngleForce.log", "w" );;
 
         testOneAngle( NULL );

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

@@ -495,8 +495,8 @@ int main( int numberOfArguments, char* argv[] ) {
         std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
 
-        FILE* log = stderr;
-        //FILE* log = NULL;
+        //FILE* log = stderr;
+        FILE* log = NULL;
         //FILE* log = fopen( "AmoebaOutOfPlaneBendForce.log", "w" );;
 
         testOneOutOfPlaneBend( log );

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

@@ -303,8 +303,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaPiTorsionForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
-        //FILE* log = NULL;
-        FILE* log = stderr;
+        FILE* log = NULL;
+        //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaPiTorsionForce1.log", "w" );;
 
         testOnePiTorsion( log );

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

@@ -287,8 +287,8 @@ int main( int numberOfArguments, char* argv[] ) {
         std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
 
-        //FILE* log = NULL;
-        FILE* log = stderr;
+        FILE* log = NULL;
+        //FILE* log = stderr;
         //FILE* log = fopen( "AmoebaStretchBendForce1.log", "w" );;
         testOneStretchBend( log );
         if( log && log != stderr )

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

@@ -156,7 +156,6 @@ static void computeAmoebaTorsionForce(int bondIndex,  std::vector<Vec3>& positio
     for( int ii = 0; ii < 3; ii++ ){
         dEdPhi += torsions[ii][0]*((double) (ii+1))*( cosine[ii]*sin( torsions[ii][1] ) - sine[ii]*cos( torsions[ii][1] ) );
     }
-fprintf( stderr,"Tst: dEdPhi=%15.7e\n", dEdPhi ); fflush( stderr );
  
     // ---------------------------------------------------------------------------------------
   
@@ -333,8 +332,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaTorsionForce running test..." << std::endl;
         Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
-        FILE* log = stderr;
-        //FILE* log = NULL;
+        //FILE* log = stderr;
+        FILE* log = NULL;
         //FILE* log = fopen( "AmoebaTorsionForce.log", "w" );;
         testOneTorsion( log );
         if( log && log != stderr )