Correcting bug accessing ilegal memory in CC mat & tidying up

CMakeLists.txt

@@ -6,7 +6,7 @@ option (INCLUDE_CUDA "Build BioEM with CUDA support" ON)
 option (INCLUDE_OPENMP "Build BioEM with OpenMP support" ON)
 option (INCLUDE_MPI "Build BioEM with MPI support" ON)
 option (PRINT_CMAKE_VARIABLES "List all CMAKE Variables" OFF)
-option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" OFF)
+option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" ON)
 
 ###Set up general variables
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
@@ -18,9 +18,9 @@ set (BIOEM_ICC_FLAGS "-xHost -O3 -fno-alias -fno-fnalias -unroll -g0 -ipo")
 set (BIOEM_GCC_FLAGS "-O3 -march=native -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb")
 
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_ICC_FLAGS}")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_ICC_FLAGS}")
 else()
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
 endif()
 
 set (BIOEM_SOURCE_FILES "bioem.cpp" "main.cpp" "map.cpp" "model.cpp" "param.cpp" "cmodules/timer.cpp")
@@ -43,93 +43,94 @@ include_directories(${Boost_INCLUDE_DIRS})
 ###Find CUDA
 set (BIOEM_CUDA_STATUS "Disabled")
 if (INCLUDE_CUDA)
-	set (BIOEM_CUDA_STATUS "Not Found")
-	find_package(CUDA)
+        set (BIOEM_CUDA_STATUS "Not Found")
+        find_package(CUDA)
 endif()
 
 if (CUDA_FOUND)
-	if (CUDA_FORCE_GCC)
-		cmake_minimum_required(VERSION 2.8.10.1)
-		#Use GCC as host compiler for CUDA even though host compiler for other files is not GCC
-		set (CUDA_HOST_COMPILER gcc)
-	endif()
-	set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};--use_fast_math;-ftz=true;-O4;-Xptxas -O4")
-
-	list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_13,code=sm_13")
-	list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_20")
-	list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_21")
-	list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_30,code=sm_30")
-	list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_35,code=sm_35")
-
-	add_definitions(-DWITH_CUDA)
-	set (BIOEM_CUDA_STATUS "Found")
+        if (CUDA_FORCE_GCC)
+                cmake_minimum_required(VERSION 2.8.10.1)
+                #Use GCC as host compiler for CUDA even though host compiler for other files is not GCC
+                set (CUDA_HOST_COMPILER gcc)
+        endif()
+        set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};--use_fast_math;-ftz=true;-O4;-Xptxas -O4")
+
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_13,code=sm_13")
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_20")
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_21")
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_30,code=sm_30")
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_35,code=sm_35")
+        list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_52,code=sm_52")
+        add_definitions(-DWITH_CUDA)
+        set (BIOEM_CUDA_STATUS "Found")
 endif()
 
 ###Find OpenMP
 set (BIOEM_OPENMP_STATUS "Disabled")
 if (INCLUDE_OPENMP)
-	set (BIOEM_OPENMP_STATUS "Not Found")
-	find_package(OpenMP)
+        set (BIOEM_OPENMP_STATUS "Not Found")
+        find_package(OpenMP)
 endif()
 
 if(OPENMP_FOUND)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-	add_definitions(-DWITH_OPENMP)
-	set (BIOEM_OPENMP_STATUS "Found")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+        add_definitions(-DWITH_OPENMP)
+        set (BIOEM_OPENMP_STATUS "Found")
 endif()
 
 ###Find MPI
 set (BIOEM_MPI_STATUS "Disabled")
 if (INCLUDE_MPI)
-	set (BIOEM_MPI_STATUS "Not Found")
-	find_package(MPI)
+        set (BIOEM_MPI_STATUS "Not Found")
+        find_package(MPI)
 endif()
 
 if (MPI_FOUND)
-	include_directories(${MPI_INCLUDE_PATH})
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${MPI_LINK_FLAGS}")
-	add_definitions(-DWITH_MPI)
-	set (BIOEM_MPI_STATUS "Found")
+        include_directories(${MPI_INCLUDE_PATH})
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${MPI_LINK_FLAGS}")
+        add_definitions(-DWITH_MPI)
+        set (BIOEM_MPI_STATUS "Found")
 endif()
 
 ###Build Executable
 if (CUDA_FOUND)
-	set(BIOEM_TMP_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
-	if (CUDA_FORCE_GCC)
-		#Hack to use GCC flags for GCC host compiler during NVCC compilation, although host compiler is in fact not GCC for other files
-		set(CMAKE_CXX_FLAGS ${BIOEM_GCC_FLAGS})
-	endif()
-	cuda_add_executable(bioEM ${BIOEM_SOURCE_FILES} bioem_cuda.cu)
-	set(CMAKE_CXX_FLAGS ${BIOEM_TMP_CMAKE_CXX_FLAGS})
+        set(BIOEM_TMP_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+        if (CUDA_FORCE_GCC)
+                #Hack to use GCC flags for GCC host compiler during NVCC compilation, although host compiler is in fact not GCC for other files
+                set(CMAKE_CXX_FLAGS ${BIOEM_GCC_FLAGS})
+        endif()
+        cuda_add_executable(bioEM ${BIOEM_SOURCE_FILES} bioem_cuda.cu)
+        set(CMAKE_CXX_FLAGS ${BIOEM_TMP_CMAKE_CXX_FLAGS})
 else()
-	add_executable(bioEM ${BIOEM_SOURCE_FILES})
+        add_executable(bioEM ${BIOEM_SOURCE_FILES})
 endif()
 
+#Additional CXX Flags not used by CUDA compiler
 #Additional CXX Flags not used by CUDA compiler
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
 else()
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -Wno-vla -Wno-unused-result -Wno-unused-local-typedefs -pedantic")
-endif()
-if (NOT OPENMP_FOUND)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-vla -Wno-long-long  -Wall -pedantic")
 endif()
 
 ###Add Libraries
 if (CUDA_FOUND)
-	cuda_add_cufft_to_target(bioEM)
-	target_link_libraries(bioEM ${CUDA_CUDA_LIBRARY})
+        cuda_add_cufft_to_target(bioEM)
+#set(CUDA_LIBRARIES "/afs/ipp/.cs/cuda/6.5-gtx9/amd64_sles11/lib64/stubs/libcuda.so")
+#cuda_add_library() 
+        target_link_libraries(bioEM ${CUDA_CUDA_LIBRARY})
+#	  target_link_libraries(bioEM ${CUDA_LIBRARIES})
 endif()
 
 if (FFTWF_LIBRARIES)
-	target_link_libraries(bioEM ${FFTWF_LIBRARIES})
+        target_link_libraries(bioEM ${FFTWF_LIBRARIES})
 else()
-	target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
+        target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
 endif()
 target_link_libraries(bioEM -L${Boost_LIBRARY_DIRS} -lboost_program_options)
 
 if (MPI_FOUND)
-	target_link_libraries(bioEM ${MPI_LIBRARIES})
+        target_link_libraries(bioEM ${MPI_LIBRARIES})
 endif()
 
 ###Show Status
@@ -137,14 +138,16 @@ message(STATUS "Build Status")
 message(STATUS "FFTW library: ${FFTW_LIBDIR}")
 message(STATUS "Boost directory: ${Boost_LIBRARY_DIRS}")
 message(STATUS "FFTW includedir: ${FFTW_INCLUDEDIR}")
+message(STATUS "CUDA libraries:  ${CUDA_CUDA_LIBRARY}")
+message(STATUS "CUDA libraries:  ${CUDA_LIBRARIES}")
 message(STATUS "CUDA: ${BIOEM_CUDA_STATUS}")
 message(STATUS "OpenMP: ${BIOEM_OPENMP_STATUS}")
 message(STATUS "MPI: ${BIOEM_MPI_STATUS}")
 
 if (PRINT_CMAKE_VARIABLES)
-	get_cmake_property(_variableNames VARIABLES)
-	foreach (_variableName ${_variableNames})
-		message(STATUS "${_variableName}=${${_variableName}}")
-	endforeach()
+        get_cmake_property(_variableNames VARIABLES)
+        foreach (_variableName ${_variableNames})
+                message(STATUS "${_variableName}=${${_variableName}}")
+        endforeach()
 endif()
 

map.cpp

@@ -5,6 +5,12 @@
 
    See license statement for terms of distribution.
 
+   Note: This program contains subroutine "read_MRC" of the Situs 2.7.2 program. 
+   Ref: Willy Wriggers. Using Situs for the Integration of Multi-Resolution Structures. 
+   Biophysical Reviews, 2010, Vol. 2, pp. 21-27.
+   with a GPL lisences version XX.
+
+
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
 
 #include <fstream>
@@ -35,6 +41,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
   int allocsize = 0;
   if (param.loadMap)
     {
+      //************** Loading Map from Binary file *******
       FILE* fp = fopen("maps.dump", "rb");
       if (fp == NULL)
 	{
@@ -50,12 +57,14 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
     }
   else if(readMRC)
     {
+      //************** Reading MRC file *******
       ntotRefMap=0;
 
       if(readMultMRC)
 	{
 
-	cout << "Opening File with MRC list names: " << filemap << "\n"; 
+	  //************** Reading Multiple MRC files *************
+	  cout << "Opening File with MRC list names: " << filemap << "\n"; 
 	  ifstream input(filemap);
 
 	  if (!input.good())
@@ -74,9 +83,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 	      input.getline(line,511);
 	      char tmpVals[100]  = {0};
 
-		string strline(line);
+	      string strline(line);
 
- 	//	 cout << "MRC File name:" << strline << "\n";
+	      //	 cout << "MRC File name:" << strline << "\n";
 
 
 	      strncpy (tmpVals,line,99);
@@ -87,10 +96,10 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 
 	      if(strcmp(tmpm,"XXX")!=0)
 		{
-		indifile=strline.c_str();
+		  indifile=strline.c_str();
           
-                size_t foundpos= strline.find("mrc");
-                size_t endpos = strline.find_last_not_of(" \t");
+		  //   size_t foundpos= strline.find("mrc");
+		  //   size_t endpos = strline.find_last_not_of(" \t");
        
 
 		  //Reading Multiple MRC
@@ -106,15 +115,15 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
       else
 	{
 
-		 string strfilename(filemap);
+	  string strfilename(filemap);
 
-                size_t foundpos= strfilename.find("mrc");
-                size_t endpos = strfilename.find_last_not_of(" \t");
+	  size_t foundpos= strfilename.find("mrc");
+	  size_t endpos = strfilename.find_last_not_of(" \t");
 
-                if(foundpos > endpos){
-                cout << "Warining:::: mrc extension NOT dectected in file name::" << filemap <<" \n";
-                cout << "Warining::::  Are you sure you want to read an MRC? \n";
-                }
+	  if(foundpos > endpos){
+	    cout << "Warining:::: mrc extension NOT dectected in file name::" << filemap <<" \n";
+	    cout << "Warining::::  Are you sure you want to read an MRC? \n";
+	  }
 
 	  read_MRC(filemap,param);
 	  cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
@@ -123,6 +132,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
     }
   else
     {
+      //************** Reading Text file *************
       int nummap = -1;
       int lasti = 0;
       int lastj = 0;
@@ -201,7 +211,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 		  maps[nummap * refMapSize + i * numPixels + j] = (myfloat_t) z;
 		  lasti = i;
 		  lastj = j;
-	 //	 cout << countpix << " " << param.param_device.NumberPixels*param.param_device.NumberPixels << "\n";
+		  //	 cout << countpix << " " << param.param_device.NumberPixels*param.param_device.NumberPixels << "\n";
 		}
 	      else
 		{
@@ -221,20 +231,21 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
       cout << "Particle Maps read from Standard File: " << ntotRefMap << "\n";
     }
 
-//Dumping Maps
+  //************* If Dumping Maps *********************
   if (param.dumpMap)
-        {
-          FILE* fp = fopen("maps.dump", "w+b");
-          if (fp == NULL)
-            {
-              cout << "Error opening dump file\n";
-              exit(1);
-            }
-          fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
-          fwrite(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
-          fclose(fp);
-        }
+    {
+      FILE* fp = fopen("maps.dump", "w+b");
+      if (fp == NULL)
+	{
+	  cout << "Error opening dump file\n";
+	  exit(1);
+	}
+      fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
+      fwrite(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
+      fclose(fp);
+    }
 
+  //*********** To Debug with few Maps ********************
 
   if (getenv("BIOEM_DEBUG_NMAPS"))
     {
@@ -250,7 +261,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
 {
   // **************************************************************************************
-  // ********** Routine that pre-calculates Kernels for Convolution **********************
+  // ********** Routine that pre-calculates Reference maps FFT for Convolution/ Comparison **********************
   // ************************************************************************************
 
   RefMapsFFT = new mycomplex_t[ntotRefMap * param.FFTMapSize];
@@ -320,17 +331,19 @@ int bioem_RefMap::precalculate(bioem_param& param, bioem& bio)
 
 void bioem_Probability::init(size_t maps, size_t angles, size_t cc, bioem& bio)
 {
+  //********** Initializing pointers *******************
   nMaps = maps;
   nAngles = angles;
   nCC = cc;
   ptr = bio.malloc_device_host(get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC));
   cout << "Allocation #Maps " << maps << " #Angles " << angles << " #cross.cor " << cc << "\n";
-//<< " == " << get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC)<< "\n";
+  //<< " == " << get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC)<< "\n";
   set_pointers();
 }
 
 void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
 {
+
   bioem_Probability_map& pProbMap = getProbMap(0);
   bioem_Probability_map& pProbMapFrom = from->getProbMap(0);
   memcpy(&pProbMap, &pProbMapFrom, from->nMaps * sizeof(bioem_Probability_map));
@@ -358,6 +371,12 @@ void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
 
 int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 {
+
+  /* 	 subroutine "read_MRC" of the Situs 2.7.2 program. 
+	 Ref: Willy Wriggers. Using Situs for the Integration of Multi-Resolution Structures. 
+	 Biophysical Reviews, 2010, Vol. 2, pp. 21-27.*/
+
+
   myfloat_t st,st2;
   unsigned long count;
   FILE *fin;
@@ -453,7 +472,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
   if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
     {
       cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
-  	if(!param.notsqure)  exit(1);
+      if(!param.notsqure)  exit(1);
     }
 
   if (ntotRefMap == 0)
@@ -498,25 +517,25 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 		  }
 		else
 		  {
-		 if(!param.notsqure){
-		    maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = (myfloat_t) currfloat;
-		    st += currfloat;
-		    st2 += currfloat*currfloat;
-			} else {
-			if( i > 595 && i < 675 && j > 1250 && j< 1330 && nmap >230 && nmap <310)cout << "map1: " << i << " "<< j << " " << nmap << " " << currfloat <<"\n";
-			}
+		    if(!param.notsqure){
+		      maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = (myfloat_t) currfloat;
+		      st += currfloat;
+		      st2 += currfloat*currfloat;
+		    } else {
+		      if( i > 595 && i < 675 && j > 1250 && j< 1330 && nmap >230 && nmap <310)cout << "map1: " << i << " "<< j << " " << nmap << " " << currfloat <<"\n";
+		    }
 		  }
 	      }
-	if(param.notsqure)exit(1);
+	  if(param.notsqure)exit(1);
 	  //Normaling maps to zero mean and unit standard deviation
 	  if(!param.notnormmap){
-	  st /= float(nr*nc);
-	  st2 = sqrt(st2 / float(nr * nc) - st * st);
-	  for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
-	      maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] / st2 - st/st2;
-	      //cout <<"MAP:: " << i << " " << j << " " <<  maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j]  << "\n";
-	    }
-	}
+	    st /= float(nr*nc);
+	    st2 = sqrt(st2 / float(nr * nc) - st * st);
+	    for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
+		maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] / st2 - st/st2;
+		//cout <<"MAP:: " << i << " " << j << " " <<  maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j]  << "\n";
+	      }
+	  }
 	}
       ntotRefMap += ns ;
       //  cout << ntotRefMap << "\n";

model.cpp

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        < BioEM software for Bayesian inference of Electron Microscopy images>
-            Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
-            Max Planck Institute of Biophysics, Frankfurt, Germany.
+   < BioEM software for Bayesian inference of Electron Microscopy images>
+   Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
+   Max Planck Institute of Biophysics, Frankfurt, Germany.
 
-                See license statement for terms of distribution.
+   See license statement for terms of distribution.
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
 
@@ -20,289 +20,291 @@ using namespace std;
 
 bioem_model::bioem_model()
 {
-	points = NULL;
+  points = NULL;
 }
 
 bioem_model::~bioem_model()
 {
-	if (points) free(points);
+  if (points) free(points);
 }
 
 int bioem_model::readModel(bioem_param& param, const char* filemodel)
 {
-	// **************************************************************************************
-	// ***************Reading reference Models either PDB or x,y,z,r,d format****************
-	// **************************************************************************************
+  // **************************************************************************************
+  // ***************Reading reference Models either PDB or x,y,z,r,d format****************
+  // **************************************************************************************
 
-	ofstream exampleReadCoor;
-	exampleReadCoor.open ("COORDREAD");
+  ofstream exampleReadCoor;
+  exampleReadCoor.open ("COORDREAD");
 
-	exampleReadCoor << "Text --- Number ---- x ---- y ---- z ---- radius ---- density\n";
+  exampleReadCoor << "Text --- Number ---- x ---- y ---- z ---- radius ---- number of electron\n";
 	
-	int allocsize = 0;
+  int allocsize = 0;
 
-	std::ifstream input(filemodel);
-	if(readPDB)
-	{
-		ifstream input(filemodel);
-		if (!input.good())
-		{
-			cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
-			exit(0);
-		}
-
-		char line[512] = {0};
-		char tmpLine[512] = {0};
-		int numres = 0;
-		NormDen = 0.0;
-
-		string strfilename(filemodel);
+  std::ifstream input(filemodel);
+  if(readPDB)
+    {
+      //************** Reading PDB files **********************
 
-                size_t foundpos= strfilename.find(".pdb");
-                size_t endpos = strfilename.find_last_not_of(" \t");
+      ifstream input(filemodel);
+      if (!input.good())
+	{
+	  cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
+	  exit(0);
+	}
 
-                if(foundpos > endpos){
-                cout << "Warining:::: .pdb extension NOT dectected in file name \n";
-                cout << "Warining::::  Are you sure you want to read a PDB? \n";
-                }
+      char line[512] = {0};
+      char tmpLine[512] = {0};
+      int numres = 0;
+      NormDen = 0.0;
 
+      string strfilename(filemodel);
 
-		//  cout << " HERE	" << filemodel ;
-		// for eachline in the file
-		while (!input.eof())
-		{
-			input.getline(line, 511);
-
-			strncpy(tmpLine, line, strlen(line));
-			char *token = strtok(tmpLine, " ");
-
-			if (strcmp(token, "ATOM") == 0) // Optional,Mandatory if standard residues exist
-			{
-				/*
-				1-6 			"ATOM  "
-				7 - 11		 Integer		 serial		Atom serial number.
-				13 - 16		Atom			name		  Atom name.
-				17			 Character	   altLoc		Alternate location indicator.
-				18 - 20		Residue name	resName	   Residue name.
-				22			 Character	   chainID	   Chain identifier.
-				23 - 26		Integer		 resSeq		Residue sequence number.
-				27			 AChar		   iCode		 Code for insertion of residues.
-				31 - 38		Real(8.3)	   x			 Orthogonal coordinates for X in
-				39 - 46		Real(8.3)	   y			 Orthogonal coordinates for Y in
-				47 - 54		Real(8.3)	   z			 Orthogonal coordinates for Z in
-					 */
-
-				char name[5] = {0};
-				char resName[4] = {0};
-				float x = 0.0;
-				float y = 0.0;
-				float z = 0.0;
-				char tmp[6] = {0};
-
-				// parse name
-				strncpy(tmp, line + 12, 4);
-				sscanf (tmp, "%s", name);
-
-				// parse resName
-				strncpy(tmp, line + 17, 3);
-				sscanf (tmp, "%s", resName);
-
-				// parse x, y, z
-				char tmpVals[36]  = {0};
-
-				strncpy (tmpVals, line + 30, 8);
-				sscanf (tmpVals, "%f", &x);
-
-				strncpy (tmpVals, line + 38, 8);
-				sscanf (tmpVals, "%f", &y);
-
-				strncpy (tmpVals, line + 46, 8);
-				sscanf (tmpVals, "%f", &z);
-
-				if (strcmp(name, "CA") == 0)
-				{
-					if (allocsize == 0)
-					{
-						allocsize = 64;
-						points = (bioem_model_point*) mallocchk(sizeof(bioem_model_point) * allocsize);
-					}
-					else if (numres + 1 >= allocsize)
-					{
-						allocsize *= 2;
-						points = (bioem_model_point*) reallocchk(points, sizeof(bioem_model_point) * allocsize);
-					}
-					
-					//Getting residue Radius and electron density
-					points[numres].radius = getAminoAcidRad(resName);
-					points[numres].density = getAminoAcidDensity(resName);
-					NormDen += points[numres].density;
+      size_t foundpos= strfilename.find(".pdb");
+      size_t endpos = strfilename.find_last_not_of(" \t");
 
-					//Getting the coordinates
-					points[numres].point.pos[0] = (myfloat_t) x;
-					points[numres].point.pos[1] = (myfloat_t) y;
-					points[numres].point.pos[2] = (myfloat_t) z;
-					exampleReadCoor << "RESIDUE " << numres << " " << points[numres].point.pos[0] << " " <<  points[numres].point.pos[1] << " " << points[numres].point.pos[2] << " " << points[numres].radius  << " " << points[numres].density << "\n";
-					numres++;
-				}
-			}
+      if(foundpos > endpos){
+	cout << "Warining:::: .pdb extension NOT dectected in file name \n";
+	cout << "Warining::::  Are you sure you want to read a PDB? \n";
+      }
 
 
-		}
-		nPointsModel = numres;
-		cout << "Protein structure read from PDB\n";
-	}
-	else //Reading model from FILE FORMAT x,y,z,rad,density
+      //  cout << " HERE	" << filemodel ;
+      // for eachline in the file
+      while (!input.eof())
 	{
-
-
-		char line[128];
-		int numres = 0;
-		NormDen = 0.0;
-
-		string strfilename(filemodel);
-
-		size_t foundpos= strfilename.find(".pdb");
-		size_t endpos = strfilename.find_last_not_of(" \t");
-
-		if(foundpos < endpos){
-		cout << "Warining:::: .pdb dectected in file name whilst using text read \n";
-                cout << "Warining::::  Are you sure you do not need --ReadPDB? \n";
-		}
-		
-		FILE *file = fopen ( filemodel , "r" );
-		if (file == NULL)
-		{
-			cout << "Error opening file " << filemodel << "\n";
-			exit(1);
-		}
-		while ( fgets ( line, sizeof line, file ) != NULL )
+	  input.getline(line, 511);
+
+	  strncpy(tmpLine, line, strlen(line));
+	  char *token = strtok(tmpLine, " ");
+
+	  if (strcmp(token, "ATOM") == 0) // Optional,Mandatory if standard residues exist
+	    {
+	      /*
+		1-6 			"ATOM  "