Time-averaged quadratic switches missing in biology and sediment input scripts

[arango]

• Added the time-averaged switches (Aout) for biological and sediment quadratic tracers in their respective input scripts:

In bio_fennel.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1:NBT,Ngrids].

Aout(idTvar) == 12*T    ! ..., NO3, ...           biological tracer

Aout(idTTav) == 12*F    ! ..., NO3_2, ...         quadratic <t*t> tracer terms
Aout(idUTav) == 12*F    ! ..., u_NO3, ...         quadratic <u*t> tracer terms
Aout(idVTav) == 12*F    ! ..., v_NO3, ...         quadratic <v*t> tracer terms
Aout(iHUTav) == 12*F    ! ..., Huon_NO3, ...      tracer volume flux, <Huon*t>
Aout(iHVTav) == 12*F    ! ..., Hvom_NO3, ...      tracer volume flux, <Hvom*t>

In ecosim.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file, [NBT,Ngrids] values are expected.

  Aout(idTvar) == 61*T   ! ..., DIC, ...           biological tracer

  Aout(idTTav) == 61*F   ! ..., DIC_2, ...         quadratic <t*t> tracer terms
  Aout(idUTav) == 61*F   ! ..., u_DIC, ...         quadratic <u*t> tracer terms
  Aout(idVTav) == 61*F   ! ..., v_DIC, ...         quadratic <v*t> tracer terms
  Aout(iHUTav) == 61*F   ! ..., Huon_DIC, ...      tracer volume flux, <Huon*t>
  Aout(iHVTav) == 61*F   ! ..., Hvom_DIC, ...      tracer volume flux, <Hvom*t>

In nemuro.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1;NBT,Ngrids].

Aout(idTvar) == 11*T    ! ..., NO3, ...          biological tracer

Aout(idTTav) == 11*F    ! ..., NO3_2, ...        quadratic <t*t> tracer terms
Aout(idUTav) == 11*F    ! ..., u_NO3, ...        quadratic <u*t> tracer terms
Aout(idVTav) == 11*F    ! ..., v_NO3, ...        quadratic <v*t> tracer terms
Aout(iHUTav) == 11*F    ! ..., Huon_NO3, ...     tracer volume flux, <Huon*t>
Aout(iHVTav) == 11*F    ! ..., Hvom_NO3, ...     tracer volume flux, <Hvom*t>

In npzd_Franks.in and npzd_Powell.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1:NBT,Ngrids].

Aout(idTvar) == 4*T     ! ..., NO3, ...           biological tracer

Aout(idTTav) == 4*F     ! ..., NO3_2, ...         quadratic <t*t> tracer terms
Aout(idUTav) == 4*F     ! ..., u_NO3, ...         quadratic <u*t> tracer terms
Aout(idVTav) == 4*F     ! ..., v_NO3, ...         quadratic <v*t> tracer terms
Aout(iHUTav) == 4*F     ! ..., Huon_NO3, ...      tracer volume flux, <Huon*t>
Aout(iHVTav) == 4*F     ! ..., Hvom_NO3, ...      tracer volume flux, <Hvom*t>

In npzd_iron.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1:NBT,Ngrids].

Aout(idTvar) == 6*T     ! ..., NO3, ...           biological tracer

Aout(idTTav) == 6*F     ! ..., NO3_2, ...         quadratic <t*t> tracer terms
Aout(idUTav) == 6*F     ! ..., u_NO3, ...         quadratic <u*t> tracer terms
Aout(idVTav) == 6*F     ! ..., v_NO3, ...         quadratic <v*t> tracer terms
Aout(iHUTav) == 6*F     ! ..., Huon_NO3, ...      tracer volume flux, <Huon*t>
Aout(iHVTav) == 6*F     ! ..., Hvom_NO3, ...      tracer volume flux, <Hvom*t>

In sediment.in we now have:

! Logical switches (TRUE/FALSE) to activate writing of time-averaged
! cohesive sediment fields into AVERAGE output file.

Aout(idmud)  == T       ! mud_01, ...             suspended concentration

Aout(iMTTav) == F       ! mud_01_2, ...           quadratic <t*t> tracer terms
Aout(iMUTav) == F       ! u_mud_01, ...           quadratic <u*t> tracer terms
Aout(iMVTav) == F       ! v_mud_01, ...           quadratic <v*t> tracer terms
Aout(MHUTav) == F       ! Huon_mud_01, ...        tracer volume flux, <Huon*t>
Aout(MHVTav) == F       ! Hvom_mud_01, ...        tracer volume flux, <Hvom*t>

Aout(iMUbld) == T       ! bedload_Umud_01, ...    bed load at U-points
Aout(iMVbld) == T       ! bedload_Vmud_01, ...    bed load at V-points

...

! Logical switches (TRUE/FALSE) to activate writing of time-averaged
! non-cohesive sediment fields into AVERAGE output file.

Aout(idsand) == T       ! sand_01, ...            suspended concentration

Aout(iSTTav) == F       ! sand_01_2, ...          quadratic <t*t> tracer terms
Aout(iSUTav) == F       ! u_sand_01, ...          quadratic <u*t> tracer terms
Aout(iSVTav) == F       ! v_sand_01, ...          quadratic <v*t> tracer terms
Aout(SHUTav) == F       ! Huon_sand_01, ...       tracer volume flux, <Huon*t>
Aout(SHVTav) == F       ! Hvom_sand_01, ...       tracer volume flux, <Hvom*t>

Aout(iSUbld) == T       ! bedload_Usand_01, ...   bed load at U-points
Aout(iSVbld) == T       ! bedload_Vsand_01, ...   bed load at V-points

WARNING: The name of all tracers quadratic variables were renamed for clarity. And underscore was added to the basic variable. For example, the quadratic values for temperature are:

Aout(idTTav) == F F     ! temp_2, ...        quadratic <t*t> tracer terms
Aout(idUTav) == F F     ! u_temp, ...        quadratic <u*t> tracer terms
Aout(idVTav) == F F     ! v_temp, ...        quadratic <v*t> tracer terms
Aout(iHUTav) == F F     ! Huon_temp, ...     tracer volume flux, <Huon*t>
Aout(iHVTav) == F F     ! Hvom_temp, ...     tracer volume flux, <Hvom*t>

Examples of the variable names for biology and sediment are shown above.

Many thanks to Aboozar Tabatabai for bringing this to my attention.

• Corrected the printing out the diagnostics labels in diag.F when using shared-memory. Many thanks to Mark Hadfield for {​https://www.myroms.org/forum/viewtopic.php?f=19&t=3166 bringing] this to my attention.

WARNING: Notice that all the input scripts for physics (ocean.in) in addition to the ones for biology and sediment were updated. The changes to the ocean.in are only done in the documentation for Aout. The test cases repository is also updated accordingly.