Index: firmware/App/Modes/ModeGenPermeate.c
===================================================================
diff -u -r6a318f2db61c3567fceea2c1963e0b02d90c8aee -r3475e61837973cd54b99c24fce8e6085d340aad2
--- firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision 6a318f2db61c3567fceea2c1963e0b02d90c8aee)
+++ firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision 3475e61837973cd54b99c24fce8e6085d340aad2)
@@ -25,6 +25,7 @@
 #include "ModeGenPermeate.h"
 #include "ModePreGenPermeate.h"
 #include "PermeateTank.h"
+#include "PIControllers.h"
 #include "ROPump.h"
 #include "TaskGeneral.h"
 #include "Timers.h"
@@ -40,12 +41,23 @@
 #define PRE_GEN_PERMEATE_DATA_PUBLISH_INTERVAL     ( MS_PER_SECOND / TASK_GENERAL_INTERVAL )    ///< Interval (ms/task time) at which the gen permeate mode data published.
 #define GEN_PERMEATE_BOOST_PUMP_TGT_PSI            25.0F                                        ///< Pressure target in PSI for the boost pump during generate permeate mode.
 #define GEN_PERMEATE_RO_PUMP_TGT_ML                750                                          ///< Flow target in ml/min for the ro pump during generate permeate mode.
+#define PUMP_REST_TIMEOUT_MS                       ( 3 * MS_PER_SECOND )                       ///< Verify Water timer ( in ms )
 
 // ********** private data **********
 
 static FP_GENP_MODE_STATE_T genPermeateState;                                                   ///< Currently active generate Permeate state.
 static U32 genPermeateDataPublicationTimerCounter;                                              ///< Used to schedule generate Permeate data publication to CAN bus.
 static OVERRIDE_U32_T genPermeateDataPublishInterval;                                           ///< Generate permeate mode data publish interval.
+static F32 fillDutySum;                                                                         ///< Sum of duty cycle values for one fill cycle.
+static U32 fillDutyCount;                                                                       ///< Sample counts for one fill cycle.
+static F32 prevFillAvgDutyCycle;                                                                ///< Average vale of duty cycle during previous fill state.
+static BOOL isFillAvgValid;                                                                     ///< Flag to check if the average fill duty cycle value is valid or not.
+static F32 fullDutySum;                                                                         ///< Sum of duty cycle values for one full cycle.
+static U32 fullDutyCount;                                                                       ///< Sample counts for one full cycle.
+static F32 prevFullAvgDutyCycle;                                                                ///< Average vale of duty cycle during previous full state.
+static BOOL isFullAvgValid;                                                                     ///< Flag to check if the average full duty cycle value is valid or not.
+static U32 waitTimeAfterReset;                                                                  ///< Time to wait after reset before starting close loop control (temporary)
+static BOOL stateTransitioned;                                                                  ///<
 
 // ********** private function prototypes **********
 
@@ -54,6 +66,10 @@
 static FP_GENP_MODE_STATE_T handleGenPTankFillState( void );
 static void setModeGenPTransition( FP_GENP_MODE_STATE_T state );
 static U32 getGenPermeateDataPublishInterval( void );
+//static void startTankFillState( void );
+//static void startTankFullState( void );
+static void updateDutyCycleAvg( FP_GENP_MODE_STATE_T state );
+static void calculateDutyCycleAvg( FP_GENP_MODE_STATE_T state );
 
 /*********************************************************************//**
  * @brief
@@ -70,6 +86,17 @@
     genPermeateDataPublishInterval.ovInitData   = 0;
     genPermeateDataPublishInterval.override     = OVERRIDE_RESET;
     genPermeateDataPublicationTimerCounter      = 0;
+    fillDutySum                                 = 0.0F;
+    fillDutyCount                               = 0;
+    prevFillAvgDutyCycle                        = 0.0F;
+    isFillAvgValid                              = FALSE;
+    fullDutySum                                 = 0.0F;
+    fullDutyCount                               = 0;
+    prevFullAvgDutyCycle                        = 0.0F;
+    isFullAvgValid                              = FALSE;
+    waitTimeAfterReset                          = 0;
+    stateTransitioned                           = FALSE;
+
 }
 
 /*********************************************************************//**
@@ -107,10 +134,12 @@
     switch ( genPermeateState )
     {
         case FP_GENP_TANK_FILL_STATE:
+            updateDutyCycleAvg( FP_GENP_TANK_FILL_STATE );
             genPermeateState = handleGenPTankFillState();
             break;
 
         case FP_GENP_TANK_FULL_STATE:
+            updateDutyCycleAvg( FP_GENP_TANK_FULL_STATE );
             genPermeateState = handleGenPTankFullState();
             break;
 
@@ -122,6 +151,8 @@
 
     if ( prevState != genPermeateState )
     {
+        stateTransitioned = TRUE;
+        calculateDutyCycleAvg( prevState );
         setModeGenPTransition( genPermeateState );
         SEND_EVENT_WITH_2_U32_DATA( FP_EVENT_GENP_CHANGE, genPermeateState, prevState )
     }
@@ -142,17 +173,24 @@
  *************************************************************************/
 static void setModeGenPTransition( FP_GENP_MODE_STATE_T state )
 {
+    F32 initDutyCycle = 0.0F;
     // Execute on running state
     switch( state )
     {
         case FP_GENP_TANK_FILL_STATE:
+            initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : 0.70F;
+            setROPumpTargetDutyCycle( initDutyCycle, TRUE );
+            waitTimeAfterReset = getMSTimerCount();
             if ( TRUE == isBoostPumpInstalled() )
             {
                 setBoostPumpTargetPressure( GEN_PERMEATE_BOOST_PUMP_TGT_PSI );
             }
             break;
 
         case FP_GENP_TANK_FULL_STATE:
+            initDutyCycle = isFullAvgValid ? prevFullAvgDutyCycle : getTargetROPumpDutyCyclePCT();
+            setROPumpTargetDutyCycle( initDutyCycle, TRUE );
+            waitTimeAfterReset = getMSTimerCount();
             if ( TRUE == isBoostPumpInstalled() )
             {
                 signalBoostPumpHardStop();
@@ -176,7 +214,13 @@
 {
     FP_GENP_MODE_STATE_T state = FP_GENP_TANK_FILL_STATE;
     PERMEATE_TANK_STATE_T permemeateTankState = getPermeateTankState();
-
+    F32 initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : 0.70F; // TODO - what value to start in initial cycle
+    if ( TRUE == didTimeout( waitTimeAfterReset, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
+    {
+        stateTransitioned = FALSE;
+        resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, initDutyCycle, 0.0F );
+        setROPumpTargetFlowRateMLPM( GEN_PERMEATE_RO_PUMP_TGT_ML, TRUE );
+    }
     if ( permemeateTankState == PERMEATE_TANK_FULL_STATE )
     {
         state = FP_GENP_TANK_FULL_STATE;
@@ -195,6 +239,13 @@
 static FP_GENP_MODE_STATE_T handleGenPTankFullState( void )
 {
     FP_GENP_MODE_STATE_T state = FP_GENP_TANK_FULL_STATE;
+    F32 initDutyCycle = isFullAvgValid ? prevFullAvgDutyCycle : getTargetROPumpDutyCyclePCT();
+    if ( TRUE == didTimeout( waitTimeAfterReset, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
+    {
+        stateTransitioned = FALSE;
+        resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, initDutyCycle, 0.0F );
+        setROPumpTargetFlowRateMLPM( GEN_PERMEATE_RO_PUMP_TGT_ML, TRUE );
+    }
     PERMEATE_TANK_STATE_T permemeateTankState = getPermeateTankState();
 
     if ( permemeateTankState == PERMEATE_TANK_FILL_STATE )
@@ -207,6 +258,59 @@
 
 /*********************************************************************//**
  * @brief
+ * The updateDutyCycleAvg function accumulates duty cycle samples for
+ * states in generate permeate mode.
+ * @details \b Inputs: none
+ * @details \b Outputs: none
+ * @param state genPermeateState enum
+ * @return none
+ *************************************************************************/
+static void updateDutyCycleAvg( FP_GENP_MODE_STATE_T state )
+{
+    F32 duty = getCurrentROPumpDutyCyclePCT();
+    if ( state == FP_GENP_TANK_FILL_STATE )
+    {
+        fillDutySum += duty;
+        fillDutyCount++;
+    }
+    else if ( state == FP_GENP_TANK_FULL_STATE )
+    {
+        fullDutySum += duty;
+        fullDutyCount++;
+    }
+
+}
+
+/*********************************************************************//**
+ * @brief
+ * The calculateDutyCycleAvg function computes the average duty cycle
+ * from the accumulated samples collected using updateDutyCyle.
+ * @details \b Inputs: none
+ * @details \b Outputs: none
+ * @param state genPermeateState enum
+ * @return none
+ *************************************************************************/
+static void calculateDutyCycleAvg( FP_GENP_MODE_STATE_T state )
+{
+    if ( state == FP_GENP_TANK_FILL_STATE && fillDutyCount > 0)
+    {
+        prevFillAvgDutyCycle = fillDutySum / (F32)fillDutyCount;
+        isFillAvgValid       = TRUE;
+        fillDutySum          = 0.0F;
+        fillDutyCount        = 0;
+    }
+    else if ( state == FP_GENP_TANK_FULL_STATE && fullDutyCount > 0 )
+    {
+        prevFullAvgDutyCycle = fullDutySum / (F32)fullDutyCount;
+        isFullAvgValid       = TRUE;
+        fullDutySum          = 0.0F;
+        fullDutyCount        = 0;
+    }
+
+}
+
+/*********************************************************************//**
+ * @brief
  * The getCurrentGenPermeateState function returns the current state of the
  * gen permeate mode.
  * @details \b Inputs: genPermeateState