Merge pull request #6 from Marxan-source-code/marzone4

Marzone4

analysis.hpp

@@ -43,7 +43,8 @@ class Analysis {
       myfile << "\n";
     }
 
-    for (int i = 0; i < pu.puno; i++)
+    // Pu must be printed in reverse order for compatibility with zonae cogito
+    for (int i = pu.puno-1; i >= 0; i--)
     {
       if (imode > 1)
       {

marzone.bat

@@ -1,3 +1,3 @@
 @echo off
-marzone.exe
+MarZone_x64.exe
 pause 

marzone.cpp

@@ -239,7 +239,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
     if (fnames.savetotalareas)
     {
         tempname = fnames.savename + "_totalareas" + getFileSuffix(fnames.savetotalareas);
-        CalcTotalAreas(pu, spec, tempname, true);
+        CalcTotalAreas(pu, spec, tempname);
     }
 
     // finalise zone and non-zone targets now that matrix has been loaded
@@ -382,6 +382,10 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
     omp_lock_t bestR_write_lock;
     omp_init_lock(&bestR_write_lock);
 
+    // lock for solutions matrix
+    omp_lock_t matrix_write_lock;
+    omp_init_lock(&matrix_write_lock);
+
     //create seeds for local rng engines
     vector<unsigned int> seeds(runoptions.repeats);
     for (int run_id = 1; run_id <= runoptions.repeats; run_id++)
@@ -459,6 +463,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
                 if (runoptions.verbose > 1)
                 {
                     progbuffer << "  ThermalAnnealing:";
+                    reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
                     PrintResVal(reserveThread, spec, zones, runoptions.misslevel, progbuffer);
                 }
 
@@ -475,6 +480,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
                 if (runoptions.verbose > 1)
                 {
                     progbuffer << "  PopAnnealing:";
+                    reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
                     PrintResVal(reserveThread, spec, zones, runoptions.misslevel, progbuffer);
                 }
             }
@@ -488,6 +494,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
                 if (runoptions.verbose > 1 && (runoptions.runopts == 2 || runoptions.runopts == 5))
                 {
                     progbuffer << "\n  Heuristic:";
+                    reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
                     PrintResVal(reserveThread, spec, zones, runoptions.misslevel, progbuffer);
                 }
 
@@ -504,6 +511,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
                 if (runoptions.verbose > 1)
                 {
                     progbuffer << "  Iterative Improvement:";
+                    reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
                     PrintResVal(reserveThread, spec, zones, runoptions.misslevel, progbuffer);
                 }
             } // Activate Iterative Improvement
@@ -521,6 +529,9 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
 
             debugbuffer << "WriteSolution ran " << irun << "\n";
 
+            // re-evaluate entire system in case of any floating point/evaluation errors.
+            reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
+
             if (fnames.savespecies && fnames.saverun)
             {
                 // output species distribution for a run (specific reserve)
@@ -540,8 +551,6 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
             // Saving the best from all the runs
             if (fnames.savebest)
             {
-                // re-evaluate entire system in case of any floating point/evaluation errors.
-                reserveThread.EvaluateObjectiveValue(pu, spec, zones, runoptions.blm);
                 if (reserveThread.objective.total < bestR.objective.total)
                 {
                     omp_set_lock(&bestR_write_lock);
@@ -564,6 +573,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
 
             if (fnames.savesolutionsmatrix)
             {
+                omp_set_lock(&matrix_write_lock);
                 string solutionsMatrixName = fnames.savename + "_solutionsmatrix" + getFileSuffix(fnames.savesolutionsmatrix);
                 reserveThread.AppendSolutionsMatrix(solutionsMatrixName, zones.zoneCount, fnames.savesolutionsmatrix, fnames.solutionsmatrixheaders);
 
@@ -573,6 +583,7 @@ int MarZone(string sInputFileName, int marxanIsSecondary)
                     // append solutions matrix for each zone separately
                     reserveThread.AppendSolutionsMatrixZone(solutionsMatrixZoneName, i, fnames.savesolutionsmatrix, fnames.solutionsmatrixheaders);
                 }
+                omp_unset_lock(&matrix_write_lock);
             }
 
             if (fnames.savezoneconnectivitysum)
@@ -976,14 +987,17 @@ void ShowPauseExit(void)
 
 void WriteSecondarySyncFileRun(int iSyncRun)
 {
-     FILE* fsync;
-     char sSyncFileName[80];
+    FILE *fsync;
+    char sSyncFileName[80];
 
-     sprintf(sSyncFileName,"sync%i",iSyncRun);
+    if (iSyncRun)
+        sprintf(sSyncFileName, "sync%i", iSyncRun);
+    else
+        sprintf(sSyncFileName, "sync");
 
-     fsync = fopen(sSyncFileName,"w");
-     fprintf(fsync,"%s",sSyncFileName);
-     fclose(fsync);
+    fsync = fopen(sSyncFileName, "w");
+    fprintf(fsync, "%s", sSyncFileName);
+    fclose(fsync);
 }
 
 /* SecondaryExit does not deliver a message prior to exiting, but creates a file so C-Plan knows marxan has exited */
@@ -1160,7 +1174,7 @@ void ApplySpecProp(Species& spec, Pu& pu)
     spec.SetSpeciesProportionTarget(speciesSums);
 }
 
-void CalcTotalAreas(Pu& pu, Species& spec, string filename /*= "MarZoneTotalAreas.csv"*/, bool save /*= false*/)
+void CalcTotalAreas(Pu& pu, Species& spec, string filename /*= "MarZoneTotalAreas.csv"*/, bool save /*= true*/)
 {
     int ipu, i, ism, isp;
     vector<int> TotalOccurrences, TO_2, TO_3;
@@ -1347,15 +1361,16 @@ int main(int argc,char *argv[])
                 marzone::SecondaryExit();
             return 1;
         } // Abnormal Exit
-        if (marxanIsSecondary == 1)
-            marzone::SecondaryExit();
     } 
     catch (const std::exception& e)
     {
         marzone::logger.ShowErrorMessage("Error occurred in execution: " + std::string(e.what()));
         exit(EXIT_FAILURE);
     }
 
+    if (marxanIsSecondary == 1)
+        marzone::SecondaryExit();
+
     return 0;
 }
 

marzone.hpp

@@ -22,7 +22,7 @@ namespace marzone
     /* Protytpe function Headers */
     void SetRunOptions(srunoptions &runoptions);
     int CalcPenalties(Pu &pu, Species &spec, Zones &zones, Reserve &r, int clumptype);
-    void CalcTotalAreas(Pu& pu, Species& spec, string filename = "MarZoneTotalAreas.csv", bool save = false);
+    void CalcTotalAreas(Pu& pu, Species& spec, string filename = "MarZoneTotalAreas.csv", bool save = true);
     double ReturnPuZoneCost(int ipu,int iZone, Pu& pu, Zones& zones);
 
     void ApplySpecProp(Species& spec, Pu& pu);

reserve.hpp

@@ -135,6 +135,14 @@ namespace marzone
         // Clear map clumps for this species
         if (spec.specList[isp].target2)
           ClearClumps(isp); // for target2 species, clear existing pu.
+
+        // Reset zone species if specified
+        int zoneBase = isp * zones.zoneCount;
+        for (int i = 0; i < zones.zoneCount; i++) {
+          iZoneSpecIndex = zoneBase + i;
+          zoneSpec[iZoneSpecIndex].amount = 0;
+          zoneSpec[iZoneSpecIndex].occurrence = 0;
+        }
       }
 
       for (int ipu = 0; ipu < solution.size(); ipu++)
@@ -927,7 +935,7 @@ namespace marzone
             rOccurrenceTarget = zones.zoneTarget[isp][i].occurrence;
             rOccurrencesHeld = zoneSpec[iZoneArrayIndex].occurrence;
 
-            myfile << d << rTarget << d << rAmountHeld << d << zones.zoneContribValues[iZoneArrayIndex] << d << rOccurrenceTarget << d << rOccurrencesHeld;
+            myfile << d << rTarget << d << rAmountHeld << d << zones.zoneContribValues[iZoneArrayIndex]*rAmountHeld << d << rOccurrenceTarget << d << rOccurrencesHeld;
 
             temp = ReturnStringIfTargetMet(rTarget, rAmountHeld, rOccurrenceTarget, rOccurrencesHeld, rMPM, misslevel);
             myfile << d << temp;
@@ -1157,6 +1165,10 @@ namespace marzone
         if (rTestMPM < rMPM)
           rMPM = rTestMPM;
       }
+
+      if (!targetArea && !targetOcc) 
+        temp = "";
+
       return temp;
     }
 

zones.hpp

@@ -657,7 +657,9 @@ class Zones {
             {
                 if (i == 0) // the "available" zone.
                 {
-                    zoneContribValues[(j*zoneCount)+i] = 0;
+                    // zoneContribValues[(j*zoneCount)+i] = 0;
+                    // It is unclear what the original code was doing with the "availableZoneInput", so we will keep consistent w/ manual and default all to 1.
+                    zoneContribValues[(j*zoneCount)+i] = 1;
                 } else {
                     zoneContribValues[(j*zoneCount)+i] = 1;
                 }