Merge branch 'master' into BioEM-1.0

* master:
  Corrections David: remove deprecated FFT_COMPATIBILITY_NATIVE, and use FFTW padding, fix non-zero error code & compiler warnings

bioem_cuda.cu

@@ -509,7 +509,7 @@ int bioem_cuda::deviceStartRun()
 					cout << "Error planning CUFFT\n";
 					exit(1);
 				}
-				if (cufftSetCompatibilityMode(plan[i][j], CUFFT_COMPATIBILITY_NATIVE) != CUFFT_SUCCESS)
+			        if (cufftSetCompatibilityMode(plan[i][j], CUFFT_COMPATIBILITY_FFTW_PADDING) != CUFFT_SUCCESS)
 				{
 					cout << "Error planning CUFFT compatibility\n";
 					exit(1);

map.cpp

@@ -52,9 +52,21 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 	  cout << "Error opening dump file\n";
 	  exit(1);
 	}
-      fread(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
+      size_t elements_read;
+      elements_read = fread(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
+      if (elements_read != 1)
+      {
+        cout << "Error reading file\n";
+        exit(1);
+      }
       maps = (myfloat_t*) mallocchk(ntotRefMap * refMapSize * sizeof(myfloat_t));
-      fread(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
+      elements_read = fread(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
+      if (elements_read != (size_t) ntotRefMap)
+      {
+        cout << "Error reading file\n";
+        exit(1);
+      }
+
       fclose(fp);
 
       cout << "Particle Maps read from Map Dump\n";
@@ -74,7 +86,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 	  if (!input.good())
 	    {
 	      cout << "Failed to open file contaning MRC names: " << filemap << "\n";
-	      exit(0);
+	      exit(1);
 	    }
 
 	  char line[512] = {0};

model.cpp

@@ -54,7 +54,7 @@ int bioem_model::readModel(bioem_param& param, const char* filemodel)
       if (!input.good())
 	{
 	  cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
-	  exit(0);
+	  exit(1);
 	}
 
       char line[512] = {0};
@@ -275,7 +275,7 @@ myfloat_t bioem_model::getAminoAcidRad(char *name)
   if(iaa == 0)
     {
       cout << "PROBLEM WITH AMINO ACID " << name << endl;
-      exit(0);
+      exit(1);
     }
   return iaa;
 
@@ -310,7 +310,7 @@ myfloat_t bioem_model::getAminoAcidDensity(char *name)
   if(iaa == 0.0)
     {
       cout << "PROBLEM WITH AMINO ACID " << name << endl;
-      exit(0);
+      exit(1);
     }
   return iaa;
 }

param.cpp

@@ -70,7 +70,6 @@ int bioem_param::readParameters(const char* fileinput)
   bool yesGPal = false;
   bool yesGPbe = false;
   bool yesMDC = false ;
-  bool notsquare =false;	
   bool yesBFact=false; 
   bool yesDefocus=false;
   bool yesAMP=false;
@@ -111,7 +110,7 @@ int bioem_param::readParameters(const char* fileinput)
   if (!input.good())
     {
       cout << "Failed to open file: " << fileinput << "\n";
-      exit(0);
+      exit(1);
     }
 
   char line[512] = {0};
@@ -520,7 +519,7 @@ int bioem_param::forprintBest(const char* fileinput)
   if (!input.good())
     {
       cout << "Failed to open Best Parameter file: " << fileinput << "\n";
-      exit(0);
+      exit(1);
     }
 
   delete[] angles;