Index: firmware/App/Modes/ModeGenPermeate.c
===================================================================
diff -u -r5ad3da2cfc5014e6beebf3b67ef394a3a65426a0 -r764e0e8c7a889f72a9b6bdced9ef08a09d72b36e
--- firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision 5ad3da2cfc5014e6beebf3b67ef394a3a65426a0)
+++ firmware/App/Modes/ModeGenPermeate.c	(.../ModeGenPermeate.c)	(revision 764e0e8c7a889f72a9b6bdced9ef08a09d72b36e)
@@ -16,6 +16,7 @@
 ***************************************************************************/
 
 #include "BoostPump.h"
+#include "Conductivity.h"
 #include "DDInterface.h"
 #include "FPModeStandby.h"
 #include "FPOperationModes.h"
@@ -41,7 +42,9 @@
 #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 )
+#define PUMP_REST_TIMEOUT_MS                       ( 3 * MS_PER_SECOND )                        ///< Verify Water timer ( in ms )
+#define RO_REJECTION_WAIT_TIME_MS                  ( 8 * MS_PER_SECOND )                        ///< Verify Water timer ( in ms )
+#define MIN_RO_REJECTION_RATIO_PCT                 90.0F                                        ///< Minimum RO rejection ration in percentage
 
 // ********** private data **********
 
@@ -56,8 +59,8 @@
 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;                                                                  ///<
+static U32 timeInState;                                                                         ///< Time to wait after reset before starting close loop control (temporary)
+static BOOL stateTransitioned;                                                                  ///< Flag to check if permeate tank state transitioned
 
 // ********** private function prototypes **********
 
@@ -92,7 +95,7 @@
     fullDutyCount                               = 0;
     prevFullAvgDutyCycle                        = 0.0F;
     isFullAvgValid                              = FALSE;
-    waitTimeAfterReset                          = 0;
+    timeInState                                 = 0;
     stateTransitioned                           = FALSE;
 
 }
@@ -176,9 +179,9 @@
     switch( state )
     {
         case FP_GENP_TANK_FILL_STATE:
-            initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : 0.70F;
+            initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
             setROPumpTargetDutyCycle( initDutyCycle, TRUE );
-            waitTimeAfterReset = getMSTimerCount();
+            timeInState = getMSTimerCount();
             if ( TRUE == isBoostPumpInstalled() )
             {
                 setBoostPumpTargetPressure( GEN_PERMEATE_BOOST_PUMP_TGT_PSI );
@@ -188,7 +191,7 @@
         case FP_GENP_TANK_FULL_STATE:
             initDutyCycle = isFullAvgValid ? prevFullAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
             setROPumpTargetDutyCycle( initDutyCycle, TRUE );
-            waitTimeAfterReset = getMSTimerCount();
+            timeInState = getMSTimerCount();
             if ( TRUE == isBoostPumpInstalled() )
             {
                 signalBoostPumpHardStop();
@@ -212,13 +215,23 @@
 {
     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 )
+    F32 initDutyCycle = isFillAvgValid ? prevFillAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
+    if ( TRUE == didTimeout( timeInState, 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 );
     }
+    // Wait for RO rejection to stabilize after transition from full to fill + RO Rejection moving average duration
+    if ( TRUE == didTimeout( timeInState, RO_REJECTION_WAIT_TIME_MS ) )
+    {
+        F32 avgRORR = getRORRAverage();
+        // Alarm if the filtered average is less than allowed RO rejection limit
+        if ( avgRORR < MIN_RO_REJECTION_RATIO_PCT )
+        {
+            SET_ALARM_WITH_2_U32_DATA( ALARM_ID_FP_REJECTION_RATIO_LOW_RANGE, avgRORR, MIN_RO_REJECTION_RATIO_PCT)
+        }
+    }
     if ( permemeateTankState == PERMEATE_TANK_FULL_STATE )
     {
         state = FP_GENP_TANK_FULL_STATE;
@@ -238,7 +251,7 @@
 {
     FP_GENP_MODE_STATE_T state = FP_GENP_TANK_FULL_STATE;
     F32 initDutyCycle = isFullAvgValid ? prevFullAvgDutyCycle : getCurrentROPumpDutyCyclePCT();
-    if ( TRUE == didTimeout( waitTimeAfterReset, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
+    if ( TRUE == didTimeout( timeInState, PUMP_REST_TIMEOUT_MS ) && stateTransitioned == TRUE )
     {
         stateTransitioned = FALSE;
         resetPIController( PI_CONTROLLER_ID_RO_PUMP_FLOW, initDutyCycle, 0.0F );