--- trunk/gadget/gadget.cc	2017/05/08 07:59:53	26
+++ trunk/gadget/gadget.cc	2017/05/08 11:58:23	27
@@ -13,6 +13,7 @@
 Ecosystem* EcoSystem;
 StochasticData* data = 0;
 Ecosystem** EcoSystems;
+MainInfo _main;
 
 volatile int interrupted = 0;
 volatile int interrupted_print = 0;
@@ -20,7 +21,7 @@
 
 int main(int aNumber, char* const aVector[]) {
 
-  MainInfo main;
+
 
 //  omp_set_num_threads(4);
 
@@ -53,42 +54,42 @@
   if (chdir(workingdir) != 0) //JMB change back to where we were ...
     handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
 
-  main.read(aNumber, aVector);
-  main.checkUsage(inputdir, workingdir);
+  _main.read(aNumber, aVector);
+  _main.checkUsage(inputdir, workingdir);
 
   if (chdir(inputdir) != 0)
     handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
-  EcoSystem = new Ecosystem(main);
+  EcoSystem = new Ecosystem(_main);
 
 #ifdef INTERRUPT_HANDLER
   //JMB dont register interrupt if doing a network run
-  if (!(main.runNetwork()))
+  if (!(_main.runNetwork()))
     registerInterrupts(&interrupted);
 #endif
 
   if (chdir(workingdir) != 0)
     handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
-  if ((main.getPI()).getPrint())
-    EcoSystem->writeInitialInformation((main.getPI()).getOutputFile());
+  if ((_main.getPI()).getPrint())
+    EcoSystem->writeInitialInformation((_main.getPI()).getOutputFile());
 
-  if (main.runStochastic()) {
-    if (main.runNetwork()) {
+  if (_main.runStochastic()) {
+    if (_main.runNetwork()) {
 #ifdef GADGET_NETWORK //to help compiling when pvm libraries are unavailable
       EcoSystem->Initialise();
       data = new StochasticData();
       while (data->getDataFromNetwork()) {
         EcoSystem->Update(data);
-        EcoSystem->Simulate(main.runPrint());
+        EcoSystem->Simulate(_main.runPrint());
         data->sendDataToNetwork(EcoSystem->getLikelihood());
         data->readNextLineFromNetwork();
       }
       delete data;
 #endif
 
-    } else if (main.getInitialParamGiven()) {
+    } else if (_main.getInitialParamGiven()) {
       if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file
         handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
-      data = new StochasticData(main.getInitialParamFile());
+      data = new StochasticData(_main.getInitialParamFile());
       if (chdir(workingdir) != 0)
         handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
 
@@ -96,21 +97,21 @@
       EcoSystem->checkBounds();
 
       EcoSystem->Initialise();
-      if (main.printInitial()) {
+      if (_main.printInitial()) {
         EcoSystem->Reset();  //JMB only need to call reset() before the print commands
-        EcoSystem->writeStatus(main.getPrintInitialFile());
+        EcoSystem->writeStatus(_main.getPrintInitialFile());
       }
 
-      EcoSystem->Simulate(main.runPrint());
-      if ((main.getPI()).getPrint())
+      EcoSystem->Simulate(_main.runPrint());
+      if ((_main.getPI()).getPrint())
         EcoSystem->writeValues();
 
       while (data->isDataLeft()) {
         data->readNextLine();
         EcoSystem->Update(data);
         EcoSystem->checkBounds();
-        EcoSystem->Simulate(main.runPrint());
-        if ((main.getPI()).getPrint())
+        EcoSystem->Simulate(_main.runPrint());
+        if ((_main.getPI()).getPrint())
           EcoSystem->writeValues();
       }
       delete data;
@@ -120,24 +121,24 @@
         handle.logMessage(LOGWARN, "Warning - no parameter input file given, using default values");
 
       EcoSystem->Initialise();
-      if (main.printInitial()) {
+      if (_main.printInitial()) {
         EcoSystem->Reset();  //JMB only need to call reset() before the print commands
-        EcoSystem->writeStatus(main.getPrintInitialFile());
+        EcoSystem->writeStatus(_main.getPrintInitialFile());
       }
 
-      EcoSystem->Simulate(main.runPrint());
-      if ((main.getPI()).getPrint())
+      EcoSystem->Simulate(_main.runPrint());
+      if ((_main.getPI()).getPrint())
         EcoSystem->writeValues();
     }
 
-  } else if (main.runOptimise()) {
+  } else if (_main.runOptimise()) {
 	  if (EcoSystem->numVariables() == 0)
 		  handle.logMessage(LOGFAIL, "Error - no parameters can be optimised");
 
-	  if (main.getInitialParamGiven()) {
+	  if (_main.getInitialParamGiven()) {
 		  if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file
 			handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
-		  data = new StochasticData(main.getInitialParamFile());
+		  data = new StochasticData(_main.getInitialParamFile());
 		  if (chdir(workingdir) != 0)
 			handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
 
@@ -147,23 +148,23 @@
 		  handle.logMessage(LOGFAIL, "Error - no parameter input file specified");
 
 	  EcoSystem->Initialise();
-	  if (main.printInitial()) {
+	  if (_main.printInitial()) {
 		  EcoSystem->Reset();  //JMB only need to call reset() before the print commands
-		  EcoSystem->writeStatus(main.getPrintInitialFile());
+		  EcoSystem->writeStatus(_main.getPrintInitialFile());
 	  	  }
 
 #ifdef _OPENMP
-          if (main.runParallel()){
+          if (_main.runParallel()){
 	  	int numThr = omp_get_max_threads ( );
 		handle.logMessage(LOGINFO, "Info - initialise ", numThr," EcoSystems ");
 	  	EcoSystems = new Ecosystem*[numThr];
 	  	int i;
-#pragma omp parallel for shared(EcoSystems,main,data,handle)
+#pragma omp parallel for shared(EcoSystems,_main,data,handle)
 	  	for (i=0; i<numThr; i++)
 	  	{
 		        handle.logMessage(LOGINFO, "Info - Ecosystem ", i);
-	                if (main.getInitialParamGiven()) {
-		  	    EcoSystems[i] = new Ecosystem(main);
+	                if (_main.getInitialParamGiven()) {
+		  	    EcoSystems[i] = new Ecosystem(_main);
 		  	    EcoSystems[i]->Update(data);
 		            EcoSystems[i]->checkBounds();
 			}
@@ -173,17 +174,17 @@
 #endif
 	  EcoSystem->Optimise();
 	  delete data;
-	  if (main.getForcePrint())
-		  EcoSystem->Simulate(main.getForcePrint());
+	  if (_main.getForcePrint())
+		  EcoSystem->Simulate(_main.getForcePrint());
   }
 
   handle.logMessage(LOGMESSAGE, "");  //write blank line to log file
-  if (main.printFinal() && !(main.runNetwork()))
-    EcoSystem->writeStatus(main.getPrintFinalFile());
+  if (_main.printFinal() && !(_main.runNetwork()))
+    EcoSystem->writeStatus(_main.getPrintFinalFile());
 
   //JMB print final values of parameters
-  if (!(main.runNetwork()))
-    EcoSystem->writeParams((main.getPI()).getParamOutFile(), (main.getPI()).getPrecision());
+  if (!(_main.runNetwork()))
+    EcoSystem->writeParams((_main.getPI()).getParamOutFile(), (_main.getPI()).getPrecision());
 
   if (check)
     free(workingdir);