diff --git a/python/test/launch-SpatialKappa/launch-SpatialKappa.py b/python/test/launch-SpatialKappa/launch-SpatialKappa.py
index a3a14e5..55f3693 100644
--- a/python/test/launch-SpatialKappa/launch-SpatialKappa.py
+++ b/python/test/launch-SpatialKappa/launch-SpatialKappa.py
@@ -8,8 +8,22 @@
 sim.runForTime(0.01)
 print('Time: %4.3f. %5.0f molecules of P %5.0f molecules of Ca' % (sim.getTime(), sim.getObservation("P"), sim.getObservation("ca")))
 
+## Add an integer number of Ca ions (but given as a float
+sim.addAgent('ca', 11.0) 
+print('Time: %4.3f. %5.0f molecules of P %5.0f molecules of Ca, 11 more than before' % (sim.getTime(), sim.getObservation("P"), sim.getObservation("ca")))
+
+## Adding a non-integer number of ions should throw an error:
+try:
+    sim.addAgent('ca', 11.5) 
+except:
+    print "Error was raised correctly"
+
 sim.runUntilTime(0.1)
 print('Time: %4.3f. %5.0f molecules of P %5.0f molecules of Ca' % (sim.getTime(), sim.getObservation("P"), sim.getObservation("ca")))
 
+## Add an integer number of Ca ions specified as an integer
+sim.addAgent('ca', 10)
+
 sim.runForTime(0.01)
 print('Time: %4.3f. %5.0f molecules of P %5.0f molecules of Ca' % (sim.getTime(), sim.getObservation("P"), sim.getObservation("ca")))
+
diff --git a/src/java/org/demonsoft/spatialkappa/api/SpatialKappaSim.java b/src/java/org/demonsoft/spatialkappa/api/SpatialKappaSim.java
index 90cb42b..f558259 100644
--- a/src/java/org/demonsoft/spatialkappa/api/SpatialKappaSim.java
+++ b/src/java/org/demonsoft/spatialkappa/api/SpatialKappaSim.java
@@ -53,16 +53,11 @@ public void loadFile(String kappaFile) throws Exception {
     }
 
     private void initialiseSim() {
-        try {
-            System.out.println("initialiseSim()");
-            simulation = new TransitionMatchingSimulation(kappaModel);
-        } catch (Exception e) {
-            System.out.println("Error in initialiseSim()");
-        }
+        simulation = new TransitionMatchingSimulation(kappaModel);
     }
 
-    public void runUntilTime(float stepEndTime) {
-        simulation.runByTime2(stepEndTime*(float)timeMult);
+    public void runUntilTime(float stepEndTime, boolean progress) {
+        simulation.runByTime2(stepEndTime*(float)timeMult, progress);
         if (verbose) {
             // This allows us to get the value of a particular observable
             Observation observation = simulation.getCurrentObservation();
@@ -70,9 +65,9 @@ public void runUntilTime(float stepEndTime) {
         }
     }
 
-    public void runForTime(float dt) {
+    public void runForTime(float dt, boolean progress) {
         float stepEndTime = getTime() + dt;
-        runUntilTime(stepEndTime);
+        runUntilTime(stepEndTime, progress);
     }
 
     public Map<String, Variable> getVariables() {
@@ -98,7 +93,7 @@ public double getObservation(String key) {
     }
     
     // value can be negative
-    public void addAgent(String key, double value) {
+    public void addAgent(String key, int value) {
         List<Agent> agents = new ArrayList<Agent>();
         SimulationState state = (SimulationState) simulation;                
         for (Complex complex : kappaModel.getFixedLocatedInitialValuesMap().keySet()) {
@@ -107,14 +102,23 @@ public void addAgent(String key, double value) {
                 if (key.equals(currentAgent.name)) {
                     // if (verbose) { System.out.println("ADD STUFF"); }
                     agents.add(currentAgent);
-                    state.addComplexInstances(agents, (int)value);
+                    state.addComplexInstances(agents, value);
                     agents.clear();
                 }
             }
         }
     }
 
-    public void setAgentInitialValue(String key, double value) {
+    public void addAgent(String key, double value) {
+        int ivalue = (int)value;
+        if (ivalue != value) {
+            String error = "Trying to add non-integer number (" + value + ") of \'" + key +  "\' agents";
+            throw(new IllegalArgumentException(error));
+        }
+        addAgent(key, (int)value);
+    }
+
+    public void setAgentInitialValue(String key, int value) {
         List<Agent> agents = new ArrayList<Agent>();
         for (Complex complex : kappaModel.getFixedLocatedInitialValuesMap().keySet()) {
             for (Agent currentAgent : complex.agents) {
@@ -123,13 +127,16 @@ public void setAgentInitialValue(String key, double value) {
                         System.out.println("Set number of " + currentAgent.name + " to " + value);
                     }
                     agents.add(currentAgent);
-                    kappaModel.overrideInitialValue(agents, Integer.toString((int)value), NOT_LOCATED);
+                    kappaModel.overrideInitialValue(agents, Integer.toString(value), NOT_LOCATED);
                     agents.clear();
                 }
             }
         }
         initialiseSim();
-        System.out.println("Number of " + key + " is " +  getObservation(key));
+        if (verbose) { System.out.println("Number of " + key + " is " +  getObservation(key)); }
+    }
+    public void setAgentInitialValue(String key, double value) {
+        setAgentInitialValue(key, (int)value);
     }
     
     private void getFixedLocatedInitialValuesMap() {
diff --git a/src/java/org/demonsoft/spatialkappa/tools/TransitionMatchingSimulation.java b/src/java/org/demonsoft/spatialkappa/tools/TransitionMatchingSimulation.java
index 84620f9..99525e9 100644
--- a/src/java/org/demonsoft/spatialkappa/tools/TransitionMatchingSimulation.java
+++ b/src/java/org/demonsoft/spatialkappa/tools/TransitionMatchingSimulation.java
@@ -201,10 +201,13 @@ public void runByTime(float totalTime, float timePerStep) {
         while (!noTransitionsPossible && !stop && time < totalTime);
         notifyObservationListeners(true, 1);
     }
-    
     public void runByTime2(float stepEndTime) {
+        runByTime2(stepEndTime, true);
+    }
+
+    public void runByTime2(float stepEndTime, boolean progress) {
         if (verbose) {
-            System.out.println("runByTime2. time = " + time + " ; stepEndTime = " + stepEndTime);
+            System.out.println("\rTime = " + time + " / " + stepEndTime + " [" + time/stepEndTime*100 + "%]");
         }
     	  startTime = Calendar.getInstance().getTimeInMillis();
         stop = false;
@@ -217,6 +220,9 @@ public void runByTime2(float stepEndTime) {
             }
             resetTransitionsFiredCount();
             while (time < stepEndTime && !noTransitionsPossible && !stop) {
+                if (progress) {
+                    System.out.format("\rTime = %12.5f/%5.5f [%3.3f%%]", time, stepEndTime, time/stepEndTime*100);
+                }
                 float nextEventTime = time + getTimeDelta();
                 if (verbose) {
                     System.out.println("runByTime2: nextEventTime = " + nextEventTime);
@@ -224,6 +230,10 @@ public void runByTime2(float stepEndTime) {
                 if (nextEventTime > stepEndTime) {
                     time = stepEndTime;
                     notifyObservationListeners(true, 1);
+                    if (progress) {
+                        System.out.format("\rTime = %12.5f/%5.5f [%3.3f%%]\n", time, stepEndTime, 100.0);
+                        System.out.flush();
+                    }
                     return;
                 }
                 int clashes = 0;