Merge pull request #1413 from virtualcell/dan-ss-random-seed2

Dan ss random seed2

vcell-core/src/main/java/org/vcell/solver/langevin/LangevinLngvWriter.java

@@ -1,5 +1,6 @@
 package org.vcell.solver.langevin;
 
+import java.math.BigInteger;
 import java.util.*;
 
 import cbit.vcell.geometry.AnalyticSubVolume;
@@ -73,6 +74,7 @@ public class LangevinLngvWriter {
 	public final static String SYSTEM_ANNOTATION = "SYSTEM ANNOTATIONS";
 	public final static String MOLECULE_ANNOTATIONS = "MOLECULE ANNOTATIONS";
 	public final static String REACTION_ANNOTATIONS = "REACTION ANNOTATIONS";
+	public final static String SIMULATION_OPTIONS = "SIMULATION OPTIONS";
 
 	public final static String DEFAULT_FOLDER = "Default Folder";
 	private String systemName;		// The system name (same as the file name, usually)
@@ -244,11 +246,16 @@ public static String writeLangevinLngv(Simulation simulation, long randomSeed) t
 //		writeReactionAnnotations(sb);
 		sb.append("\n");
 
-		/*
-		TODO: The following are being produced when the simulation is created, and are being updated as simulations run (I think)
-		 from C:\TEMP\springsalad-new\spring3reactions\spring3reactions_SIMULATIONS\Simulation0_SIM_FOLDER\Simulation0_SIM.txt
 
-		*** SIMULATION STATE ***
+		/* ****** WRITE THE SIMULATION OPTIONS *********************/
+		sb.append("*** " + SIMULATION_OPTIONS + " ***");
+		sb.append("\n");
+		sb.append("\n");
+		writeSimulationOptions(simulation, sb);
+		sb.append("\n");
+
+/*
+		// TODO: SIMULATION STATE produced by the solver, will be used in ClusterAnalyzer to postprocess run results
 
 		Runs: 6
 		Parallel: true
@@ -258,6 +265,9 @@ public static String writeLangevinLngv(Simulation simulation, long randomSeed) t
 		HasResults: false
 		RunOnCluster: false
 
+		TODO: The following are being produced when the simulation is created, and are being updated as simulations run (I think)
+		 from C:\TEMP\springsalad-new\spring3reactions\spring3reactions_SIMULATIONS\Simulation0_SIM_FOLDER\Simulation0_SIM.txt
+
 		*** PROCESSOR FILES ***
 
 		MoleculeAverages: 'null'
@@ -959,6 +969,41 @@ private static void writeSpeciesInfo(StringBuilder sb) {
 		return;
 	}
 
+	/*
+	 * We provide the SIMULATION OPTIONS block as part of the input to the solver
+	 * The only important field really is the RandomSeed, which is optional, the rest are not needed by the
+	 * current solver implementation
+	 *
+	 * There is a related SIMULATION STATE block which is generated by the solver when it finishes running
+	 * Then the SpringSaLaD client is parsing it and will use the Runs field in the ClusterAnalyzer module
+	 * for analyzing the results (of one or multiple runs). We'll probably do something similar server-side in
+	 * the postprocessing module
+	 */
+	public static void writeSimulationOptions(Simulation simulation, StringBuilder sb) {
+		SolverTaskDescription std = simulation.getSolverTaskDescription();
+		LangevinSimulationOptions lso = std.getLangevinSimulationOptions();
+
+		int numTrials = std.getNumTrials();
+		BigInteger randomSeed = lso.getRandomSeed();
+		int simultaneousRuns = lso.getNumOfParallelLocalRuns();
+
+		// TODO: do not delete this, until we decide on how much info the solver needs
+		// These are not needed but may be nice to have in the future, makes the solver instance more aware
+//		sb.append("Runs: " + numTrials);	// the SpringSaLaD client parser expects this to be the first line in block
+//		sb.append("\n");
+//		sb.append("Parallel: " + (simultaneousRuns == 1 ? "true" : "false"));
+//		sb.append("\n");
+//		sb.append("SimultaneousRuns: " + simultaneousRuns);		// this is always 1 on local and quota dependent on server
+//		sb.append("\n");
+
+		// if we don't specify a random seed the solver will do its thing like in the past (use system time in ms)
+		if(randomSeed != null) {
+			sb.append("RandomSeed: " + randomSeed);
+			sb.append("\n");
+		}
+
+	}
+
 	public static void writeSpatialInformation(GeometrySpec geometrySpec, Simulation simulation, StringBuilder sb) {    // SpringSaLaD exporting the time information
         if (geometrySpec.getDimension() != 3) {
             throw new RuntimeException("SpringSaLaD requires 3D geometry");