WIP save mko files during simulations and create avg PSD file at the end

src/basic/io/Restart.java

@@ -238,6 +238,11 @@ public void writeSurfaceBinary(int dimensions, int[] sizes, float[][] data, int
     String fileName = format("%ssurface%03d.mko", folder, simulationNumber);
     RestartLow.writeLowBinary(dimensions, sizes, data, fileName);
   }
+
+  public void writeSurfaceBinary(int dimensions, int[] sizes, float[][] data, int simulationNumber, int coverage) {
+    String fileName = format("%ssurface%d0%02d.mko", folder, simulationNumber, coverage);
+    RestartLow.writeLowBinary(dimensions, sizes, data, fileName);
+  }
 
   public void writeSurfaceBinary2D(float[][] data, int simulationNumber) {
     int sizes[] = new int[2];

src/kineticMonteCarlo/kmcCore/growth/AbstractGrowthKmc.java

@@ -22,6 +22,7 @@
 import basic.Parser;
 import basic.io.OutputType;
 import basic.io.Restart;
+import basic.io.OutputType.formatFlag;
 import kineticMonteCarlo.site.AbstractGrowthSite;
 import kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaAccelerator;
 import kineticMonteCarlo.site.ModifiedBuffer;
@@ -34,6 +35,7 @@
 import javafx.geometry.Point3D;
 import static kineticMonteCarlo.site.AbstractSite.TERRACE;
 import kineticMonteCarlo.unitCell.AbstractGrowthUc;
+import utils.MathUtils;
 import utils.StaticRandom;
 import utils.list.LinearList;
 
@@ -93,9 +95,11 @@ public abstract class AbstractGrowthKmc extends AbstractSurfaceKmc {
   private long simulatedSteps;
   private double sumProbabilities;
   private Restart restart;
+  private Parser parser;
 
   public AbstractGrowthKmc(Parser parser) {
     super(parser);
+    this.parser = parser;
     simulationNumber = 0;
     justCentralFlake = parser.justCentralFlake();
     periodicSingleFlake = parser.isPeriodicSingleFlake();
@@ -475,8 +479,24 @@ private void printData(Integer coverage) {
       printCoverage = getCoverage();
     }
     if (printCoverage > 0.01 && (int) (printCoverage * 100) % 5 == 0) { //only write when is bigger than 1% and multiple of %5
-      int surfaceNumber = 1000 * simulationNumber + (int) (getCoverage() * 100);
-      restart.writeSvg(surfaceNumber, getLattice(), true);
+      int surfaceNumber = 1000 * simulationNumber + (int) (getCoverage() * 100);  
+      if (parser.getOutputFormats().contains(formatFlag.SVG)) {
+        restart.writeSvg(surfaceNumber, getLattice(), true);
+      }
+      if (parser.getOutputFormats().contains(formatFlag.MKO) && parser.doPsd()) {
+
+        int[] surfaceSizes = new int[2];
+        // More precise (more points) the PSD better precision we get
+        surfaceSizes[0] = (int) (parser.getCartSizeX() * parser.getPsdScale());
+        surfaceSizes[1] = (int) (parser.getCartSizeY() * parser.getPsdScale());
+        int[] extentSizes = new int[2];
+        extentSizes[0] = (int) (surfaceSizes[0] * parser.getPsdExtend());
+        extentSizes[1] = (int) (surfaceSizes[1] * parser.getPsdExtend());
+        float[][] sampledSurface = getSampledSurface(surfaceSizes[0], surfaceSizes[1]);
+        float[][] extentSurface = MathUtils.increaseEmptyArea(sampledSurface, parser.getPsdExtend());
+        restart.writeSurfaceBinary(2, extentSizes, extentSurface, simulationNumber, (int) (printCoverage * 100));
+      }
+
     }
     restart.writeExtraOutput(lattice, printCoverage, nucleations, getTime(), 
             (double) (depositionRatePerSite * freeArea), getList().getDiffusionProbability(), simulatedSteps, sumProbabilities);

src/kineticMonteCarlo/simulation/AbstractSimulation.java

@@ -32,6 +32,7 @@
 import java.util.logging.Logger;
 import kineticMonteCarlo.kmcCore.AbstractKmc;
 import kineticMonteCarlo.kmcCore.catalysis.AbstractCatalysisKmc;
+import main.PsdFromSurfaces;
 import ratesLibrary.IRates;
 import utils.MathUtils;
 import utils.StaticRandom;
@@ -175,13 +176,12 @@ public void doSimulation() {
       } else { // simulate until a given coverage or size (single flake)
         kmc.simulate();
       }
-
       printOutput();
       totalTime += kmc.getTime();
       islands += countIslands();
       gyradius += getGyradius();
     }
-
+    PsdFromSurfaces pfs = new PsdFromSurfaces(parser, restart.getFolder());
     printFooter();
     doPsd();
   }
@@ -300,7 +300,7 @@ void printOutput() {
           restart.writeCatalysisAdsorptionDataText(simulations, data);
         }
         if (parser.getOutputFormats().contains(formatFlag.MKO)) {
-          restart.writeSurfaceBinary(2, extentSizes, extentSurface, simulations);
+          restart.writeSurfaceBinary(2, extentSizes, extentSurface, simulations,(int) (coverage[0] * 100));
         }
         if (parser.getOutputFormats().contains(formatFlag.TXT)) {
           restart.writeSurfaceText2D(2, extentSizes, extentSurface, simulations);

src/main/PsdFromSurfaces.java

@@ -33,7 +33,7 @@
  */
 public class PsdFromSurfaces {
 
-  public PsdFromSurfaces(Parser parser) {
+  public PsdFromSurfaces(Parser parser, String restartFolderName) {
     System.out.println("This is a utility of morphokinetics program");
     String surfaceFileName;
     boolean showGui;
@@ -47,7 +47,7 @@ public PsdFromSurfaces(Parser parser) {
     showGui = parser.withGui() && parser.visualise();
     doTent = !parser.getSurfaceType().equals("plane");
 
-    Restart restart = new Restart("./");
+    Restart restart = new Restart(restartFolderName);
     int[] sizes = null;
     float[][] surface = null;
     PsdSignature2D psd = null;