Start of cleanup of all ModuleEngines related code that was hurriedly changed for KSP 1.0
Start of cleanup of all ModuleEngines related code that was hurriedly changed for KSP 1.0

--- a/KerbalEngineer/Extensions/PartExtensions.cs
+++ b/KerbalEngineer/Extensions/PartExtensions.cs
@@ -55,6 +55,7 @@
         /// <summary>
         ///     Gets whether the part has fuel.
         /// </summary>
+        /* not used
         public static bool EngineHasFuel(this Part part)
         {
             PartModule cachePartModule = GetModule<ModuleEngines>(part);
@@ -71,7 +72,7 @@
 
             return false;
         }
-
+        */
         /// <summary>
         ///     Gets the cost of the part excluding resources.
         /// </summary>
@@ -123,6 +124,7 @@
         /// <summary>
         ///     Gets the maximum thrust of the part if it's an engine.
         /// </summary>
+        /* not used
         public static double GetMaxThrust(this Part part)
         {
             PartModule cachePartModule = GetModule<ModuleEngines>(part);
@@ -139,6 +141,7 @@
 
             return 0.0;
         }
+        */
 
         /// <summary>
         ///     Gets the first typed PartModule in the part's module list.
@@ -221,13 +224,17 @@
         public static ModuleEnginesFX GetModuleMultiModeEngine(this Part part)
         {
             ModuleEnginesFX moduleEngineFx;
-            string mode = GetModule<MultiModeEngine>(part).mode;
-            for (int i = 0; i < part.Modules.Count; ++i)
-            {
-                moduleEngineFx = part.Modules[i] as ModuleEnginesFX;
-                if (moduleEngineFx != null && moduleEngineFx.engineID == mode)
-                {
-                    return moduleEngineFx;
+            MultiModeEngine multiMod = GetModule<MultiModeEngine>(part);
+            if (multiMod != null)
+            {
+                string mode = multiMod.mode;
+                for (int i = 0; i < part.Modules.Count; ++i)
+                {
+                    moduleEngineFx = part.Modules[i] as ModuleEnginesFX;
+                    if (moduleEngineFx != null && moduleEngineFx.engineID == mode)
+                    {
+                        return moduleEngineFx;
+                    }
                 }
             }
             return null;
@@ -343,6 +350,7 @@
         /// <summary>
         ///     Gets the current specific impulse for the engine.
         /// </summary>
+        /* not used
         public static double GetSpecificImpulse(this Part part, float atmosphere)
         {
             PartModule cachePartModule = GetModule<ModuleEngines>(part);
@@ -359,6 +367,7 @@
 
             return 0.0;
         }
+        */
 
         /// <summary>
         ///     Gets the total mass of the part including resources.
@@ -588,6 +597,12 @@
             }
         }
 
+        // This needs updating to handle multi-mode engines and engines with multiple ModuleEngines correctly.
+        // It currently just shows the stats of the currently active module for multi-mode engines and just 
+        // the first ModuleEngines for engines with multiple modules.
+        // It should really show all the modes for multi-mode engines as separate sections.
+        // For other engines with multiple ModuleEngines it should combine the separate modules into a single set of data
+        // The constructor should be changed to take the Part itself.  It can be called if HasModule<ModuleEngines>() is true.
         public class ProtoModuleEngine
         {
             private readonly PartModule module;
@@ -627,19 +642,6 @@
                 MinimumThrust = engine.minThrust;
                 Propellants = engine.propellants;
             }
-
-            private void SetModuleEnginesFx()
-            {
-                ModuleEnginesFX engine = module as ModuleEnginesFX;
-                if (engine == null)
-                {
-                    return;
-                }
-
-                MaximumThrust = engine.maxThrust * (engine.thrustPercentage * 0.01);
-                MinimumThrust = engine.minThrust;
-                Propellants = engine.propellants;
-            }
         }
     }
 }

--- a/KerbalEngineer/Flight/Readouts/Rendezvous/RendezvousProcessor.cs
+++ b/KerbalEngineer/Flight/Readouts/Rendezvous/RendezvousProcessor.cs
@@ -1,7 +1,7 @@
 // 
 //     Kerbal Engineer Redux
 // 
-//     Copyright (C) 2014 CYBUTEK
+//     Copyright (C) 2015 CYBUTEK
 // 
 //     This program is free software: you can redistribute it and/or modify
 //     it under the terms of the GNU General Public License as published by
@@ -17,30 +17,19 @@
 //     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 // 
 
-#region Using Directives
-
-using System;
-
-using KerbalEngineer.Extensions;
-using KerbalEngineer.Helpers;
-
-#endregion
-
 namespace KerbalEngineer.Flight.Readouts.Rendezvous
 {
+    using System;
+    using Extensions;
+    using Helpers;
+
     public class RendezvousProcessor : IUpdatable, IUpdateRequest
     {
-        #region Fields
-
         private static readonly RendezvousProcessor instance = new RendezvousProcessor();
 
         private Orbit originOrbit;
         private Orbit targetOrbit;
 
-        #endregion
-
-        #region Properties
-
         /// <summary>
         ///     Gets the target's altitude above its reference body.
         /// </summary>
@@ -71,7 +60,10 @@
         /// </summary>
         public static RendezvousProcessor Instance
         {
-            get { return instance; }
+            get
+            {
+                return instance;
+            }
         }
 
         /// <summary>
@@ -149,10 +141,6 @@
         /// </summary>
         public bool UpdateRequested { get; set; }
 
-        #endregion
-
-        #region Methods: public
-
         /// <summary>
         ///     Request and update to calculate the details.
         /// </summary>
@@ -166,7 +154,13 @@
         /// </summary>
         public void Update()
         {
-            if (FlightGlobals.fetch.VesselTarget == null)
+            if (FlightGlobals.fetch == null ||
+                FlightGlobals.fetch.VesselTarget == null ||
+                FlightGlobals.ActiveVessel == null ||
+                FlightGlobals.ActiveVessel.targetObject == null ||
+                FlightGlobals.ActiveVessel.targetObject.GetOrbit() == null ||
+                FlightGlobals.ship_orbit == null ||
+                FlightGlobals.ship_orbit.referenceBody == null)
             {
                 ShowDetails = false;
                 return;
@@ -174,55 +168,50 @@
 
             ShowDetails = true;
 
-            this.targetOrbit = FlightGlobals.fetch.VesselTarget.GetOrbit();
-            this.originOrbit = (FlightGlobals.ship_orbit.referenceBody == Planetarium.fetch.Sun || FlightGlobals.ship_orbit.referenceBody == FlightGlobals.ActiveVessel.targetObject.GetOrbit().referenceBody)
+            targetOrbit = FlightGlobals.fetch.VesselTarget.GetOrbit();
+            originOrbit = (FlightGlobals.ship_orbit.referenceBody == Planetarium.fetch.Sun ||
+                           FlightGlobals.ship_orbit.referenceBody == FlightGlobals.ActiveVessel.targetObject.GetOrbit().referenceBody)
                 ? FlightGlobals.ship_orbit
                 : FlightGlobals.ship_orbit.referenceBody.orbit;
 
-            RelativeInclination = this.originOrbit.GetRelativeInclination(this.targetOrbit);
+            RelativeInclination = originOrbit.GetRelativeInclination(targetOrbit);
             RelativeVelocity = FlightGlobals.ship_tgtSpeed;
-            RelativeSpeed = FlightGlobals.ship_obtSpeed - this.targetOrbit.orbitalSpeed;
-            PhaseAngle = this.originOrbit.GetPhaseAngle(this.targetOrbit);
-            InterceptAngle = this.CalcInterceptAngle();
-            TimeToAscendingNode = this.originOrbit.GetTimeToVector(this.GetAscendingNode());
-            TimeToDescendingNode = this.originOrbit.GetTimeToVector(this.GetDescendingNode());
-            AngleToAscendingNode = this.originOrbit.GetAngleToVector(this.GetAscendingNode());
-            AngleToDescendingNode = this.originOrbit.GetAngleToVector(this.GetDescendingNode());
-            AltitudeSeaLevel = this.targetOrbit.altitude;
-            ApoapsisHeight = this.targetOrbit.ApA;
-            PeriapsisHeight = this.targetOrbit.PeA;
-            TimeToApoapsis = this.targetOrbit.timeToAp;
-            TimeToPeriapsis = this.targetOrbit.timeToPe;
-            SemiMajorAxis = this.targetOrbit.semiMajorAxis;
-            SemiMinorAxis = this.targetOrbit.semiMinorAxis;
-
-            Distance = Vector3d.Distance(this.targetOrbit.pos, this.originOrbit.pos);
-            OrbitalPeriod = this.targetOrbit.period;
-        }
-
-        #endregion
-
-        #region Methods: private
+            RelativeSpeed = FlightGlobals.ship_obtSpeed - targetOrbit.orbitalSpeed;
+            PhaseAngle = originOrbit.GetPhaseAngle(targetOrbit);
+            InterceptAngle = CalcInterceptAngle();
+            TimeToAscendingNode = originOrbit.GetTimeToVector(GetAscendingNode());
+            TimeToDescendingNode = originOrbit.GetTimeToVector(GetDescendingNode());
+            AngleToAscendingNode = originOrbit.GetAngleToVector(GetAscendingNode());
+            AngleToDescendingNode = originOrbit.GetAngleToVector(GetDescendingNode());
+            AltitudeSeaLevel = targetOrbit.altitude;
+            ApoapsisHeight = targetOrbit.ApA;
+            PeriapsisHeight = targetOrbit.PeA;
+            TimeToApoapsis = targetOrbit.timeToAp;
+            TimeToPeriapsis = targetOrbit.timeToPe;
+            SemiMajorAxis = targetOrbit.semiMajorAxis;
+            SemiMinorAxis = targetOrbit.semiMinorAxis;
+
+            Distance = Vector3d.Distance(targetOrbit.pos, originOrbit.pos);
+            OrbitalPeriod = targetOrbit.period;
+        }
 
         private double CalcInterceptAngle()
         {
-            var originRadius = (this.originOrbit.semiMinorAxis + this.originOrbit.semiMajorAxis) * 0.5;
-            var targetRadius = (this.targetOrbit.semiMinorAxis + this.targetOrbit.semiMajorAxis) * 0.5;
-            var angle = 180.0 * (1.0 - Math.Pow((originRadius + targetRadius) / (2.0 * targetRadius), 1.5));
+            double originRadius = (originOrbit.semiMinorAxis + originOrbit.semiMajorAxis) * 0.5;
+            double targetRadius = (targetOrbit.semiMinorAxis + targetOrbit.semiMajorAxis) * 0.5;
+            double angle = 180.0 * (1.0 - Math.Pow((originRadius + targetRadius) / (2.0 * targetRadius), 1.5));
             angle = PhaseAngle - angle;
             return RelativeInclination < 90.0 ? AngleHelper.Clamp360(angle) : AngleHelper.Clamp360(360.0 - (180.0 - angle));
         }
 
         private Vector3d GetAscendingNode()
         {
-            return Vector3d.Cross(this.targetOrbit.GetOrbitNormal(), this.originOrbit.GetOrbitNormal());
+            return Vector3d.Cross(targetOrbit.GetOrbitNormal(), originOrbit.GetOrbitNormal());
         }
 
         private Vector3d GetDescendingNode()
         {
-            return Vector3d.Cross(this.originOrbit.GetOrbitNormal(), this.targetOrbit.GetOrbitNormal());
-        }
-
-        #endregion
+            return Vector3d.Cross(originOrbit.GetOrbitNormal(), targetOrbit.GetOrbitNormal());
+        }
     }
 }

--- a/KerbalEngineer/VesselSimulator/EngineSim.cs
+++ b/KerbalEngineer/VesselSimulator/EngineSim.cs
@@ -31,6 +31,7 @@
         private static readonly Pool<EngineSim> pool = new Pool<EngineSim>(Create, Reset);
 
         private readonly ResourceContainer resourceConsumptions = new ResourceContainer();
+        private readonly ResourceContainer resourceFlowModes = new ResourceContainer();
 
         public double actualThrust = 0;
         public bool isActive = false;
@@ -52,6 +53,7 @@
         private static void Reset(EngineSim engineSim)
         {
             engineSim.resourceConsumptions.Reset();
+            engineSim.resourceFlowModes.Reset();
             engineSim.actualThrust = 0;
             engineSim.isActive = false;
             engineSim.isp = 0;
@@ -98,51 +100,72 @@
             engineSim.isActive = active;
             engineSim.thrustVec = vecThrust;
             engineSim.resourceConsumptions.Reset();
+            engineSim.resourceFlowModes.Reset();
             engineSim.appliedForces.Clear();
 
             double flowRate = 0.0;
             if (engineSim.partSim.hasVessel)
             {
+                if (log != null) log.buf.AppendLine("hasVessel is true"); 
+
                 float flowModifier = GetFlowModifier(atmChangeFlow, atmCurve, engineSim.partSim.part.atmDensity, velCurve, machNumber, ref engineSim.maxMach);
                 engineSim.isp = atmosphereCurve.Evaluate((float)atmosphere);
                 engineSim.thrust = GetThrust(Mathf.Lerp(minFuelFlow, maxFuelFlow, GetThrustPercent(thrustPercentage)) * flowModifier, engineSim.isp);
                 engineSim.actualThrust = engineSim.isActive ? resultingThrust : 0.0;
+                if (log != null)
+                {
+                    log.buf.AppendFormat("flowMod = {0:g6}\n", flowModifier);
+                    log.buf.AppendFormat("isp     = {0:g6}\n", engineSim.isp);
+                    log.buf.AppendFormat("thrust  = {0:g6}\n", engineSim.thrust);
+                    log.buf.AppendFormat("actual  = {0:g6}\n", engineSim.actualThrust);
+                }
 
                 if (throttleLocked)
                 {
+                    if (log != null) log.buf.AppendLine("throttleLocked is true, using thrust for flowRate");
                     flowRate = GetFlowRate(engineSim.thrust, engineSim.isp);
                 }
                 else
                 {
                     if (currentThrottle > 0.0f && engineSim.partSim.isLanded == false)
                     {
+                        if (log != null) log.buf.AppendLine("throttled up and not landed, using actualThrust for flowRate");
                         flowRate = GetFlowRate(engineSim.actualThrust, engineSim.isp);
                     }
                     else
                     {
+                        if (log != null) log.buf.AppendLine("throttled down or landed, using thrust for flowRate");
                         flowRate = GetFlowRate(engineSim.thrust, engineSim.isp);
                     }
                 }
             }
             else
             {
+                if (log != null) log.buf.AppendLine("hasVessel is false");
                 float flowModifier = GetFlowModifier(atmChangeFlow, atmCurve, CelestialBodies.SelectedBody.GetDensity(BuildAdvanced.Altitude), velCurve, machNumber, ref engineSim.maxMach);
                 engineSim.isp = atmosphereCurve.Evaluate((float)atmosphere);
                 engineSim.thrust = GetThrust(Mathf.Lerp(minFuelFlow, maxFuelFlow, GetThrustPercent(thrustPercentage)) * flowModifier, engineSim.isp);
+                engineSim.actualThrust = 0d;
+                if (log != null)
+                {
+                    log.buf.AppendFormat("flowMod = {0:g6}\n", flowModifier);
+                    log.buf.AppendFormat("isp     = {0:g6}\n", engineSim.isp);
+                    log.buf.AppendFormat("thrust  = {0:g6}\n", engineSim.thrust);
+                    log.buf.AppendFormat("actual  = {0:g6}\n", engineSim.actualThrust);
+                }
+
+                if (log != null) log.buf.AppendLine("no vessel, using thrust for flowRate");
                 flowRate = GetFlowRate(engineSim.thrust, engineSim.isp);
             }
 
             if (log != null) log.buf.AppendFormat("flowRate = {0:g6}\n", flowRate);
-
-            engineSim.thrust = flowRate * (engineSim.isp * IspG);
-            // I did not look into the diff between those 2 so I made them equal...
-            engineSim.actualThrust = engineSim.thrust;
 
             float flowMass = 0f;
             for (int i = 0; i < propellants.Count; ++i)
             {
                 Propellant propellant = propellants[i];
-                flowMass += propellant.ratio * ResourceContainer.GetResourceDensity(propellant.id);
+                if (!propellant.ignoreForIsp)
+                    flowMass += propellant.ratio * ResourceContainer.GetResourceDensity(propellant.id);
             }
 
             if (log != null) log.buf.AppendFormat("flowMass = {0:g6}\n", flowMass);
@@ -164,6 +187,7 @@
                         theEngine.partId,
                         consumptionRate);
                 engineSim.resourceConsumptions.Add(propellant.id, consumptionRate);
+                engineSim.resourceFlowModes.Add(propellant.id, (double)propellant.GetFlowMode());
             }
 
             double thrustPerThrustTransform = engineSim.thrust / thrustTransforms.Count;
@@ -269,7 +293,7 @@
                     sourcePartSets.Add(type, sourcePartSet);
                 }
 
-                switch (ResourceContainer.GetResourceFlowMode(type))
+                switch ((ResourceFlowMode)this.resourceFlowModes[type])
                 {
                     case ResourceFlowMode.NO_FLOW:
                         if (partSim.resources[type] > SimManager.RESOURCE_MIN && partSim.resourceFlowStates[type] != 0)

--- a/KerbalEngineer/VesselSimulator/Simulation.cs
+++ b/KerbalEngineer/VesselSimulator/Simulation.cs
@@ -139,6 +139,7 @@
                 log.buf.AppendLine("PrepareSimulation started");
                 dumpTree = true;
             }
+            this._timer.Reset();
             this._timer.Start();
 
             // Store the parameters in members for ease of access in other functions
@@ -299,6 +300,7 @@
                 MonoBehaviour.print("RunSimulation started");
             }
 
+            this._timer.Reset();
             this._timer.Start();
 
             LogMsg log = null;