#839 closed upgrade (Done)
VERY IMPORTANT: Tracer Advection Revisited — at Version 3
| Reported by: | arango | Owned by: | |
|---|---|---|---|
| Priority: | major | Milestone: | Release ROMS/TOMS 3.9 |
| Component: | Nonlinear | Version: | 3.9 |
| Keywords: | Cc: |
Description (last modified by )
All the tracer advection CPP options were removed and replaced with logical switches to facilitate applying a desired horizontal and vertical scheme to each tracer. One may have a particular scheme for temperature and a different for salinity, inert, biological, or sediment tracer. It is usually desirable to have a positive-definite or monotonic algorithm for salinity and passive tracers.
- WARNING: ROMS standard input files for physics, biology, and sediment were modified to include the tracer advection switches. In roms.in we have:
! Set horizontal and vertical advection schemes for active and inert ! tracers. A different advection scheme is allowed for each tracer. ! For example, a positive-definite (monotonic) algorithm can be activated ! for salinity and inert tracers, while a different one is set for ! temperature. [1:NAT+NPT,Ngrids] values are expected. ! ! Keyword Advection Algorithm ! ! A4 4th-order Akima (horizontal/vertical) ! C2 2nd-order centered differences (horizontal/vertical) ! C4 4th-order centered differences (horizontal/vertical) ! HSIMT 3th-order HSIMT-TVD (horizontal/vertical) ! MPDATA recursive flux corrected MPDATA (horizontal/vertical) ! SPLINES parabolic splines (only vertical) ! SU3 split third-order upstream (horizontal/vertical) ! U3 3rd-order upstream-biased (only horizontal) ! ! The user has the option of specifying the full Keyword or the first ! two letters, regardless if using uppercase or lowercase. If nested ! grids, specify values for each grid (see glossary below). Hadvection == U3 \ ! temperature MPDATA ! salinity Vadvection == C4 \ ! temperature MPDATA ! salinity ! Adjoint-based algorithms can have different horizontal and schemes ! for active and inert tracers. ad_Hadvection == U3 \ ! temperature U3 ! salinity ad_Vadvection == C4 \ ! temperature C4 ! salinity
Notice that similar switches are defined for the adjoint-based algorithms.
For the Fennel biological model, we specify the tracer advection switches in bio_fennel.in :
! Set horizontal and vertical advection schemes for biological tracers. ! A different advection scheme is allowed for each tracer. For example, ! a positive-definite (monotonic) algorithm can be activated for ! salinity and biological tracers, while a different one is set for ! temperature. [1:NAT+NPT,Ngrids] values are expected. ! ! Keyword Advection Algorithm ! ! A4 4th-order Akima (horizontal/vertical) ! C2 2nd-order centered differences (horizontal/vertical) ! C4 4th-order centered differences (horizontal/vertical) ! HSIMT 3th-order HSIMT-TVD (horizontal/vertical) ! MPDATA recursive flux corrected MPDATA (horizontal/vertical) ! SPLINES parabolic splines (only vertical) ! SU3 split third-order upstream (horizontal/vertical) ! U3 3rd-order upstream-biased (only horizontal) ! ! The user has the option of specifying the full Keyword or the first ! two letters, regardless if using uppercase or lowercase. If nested ! grids, specify values for each grid. Hadvection == HSIMT \ ! idbio( 1), NO3 HSIMT \ ! idbio( 2), NH4 HSIMT \ ! idbio( 3), chlorophyll HSIMT \ ! idbio( 4), phytoplankton HSIMT \ ! idbio( 5), zooplankton HSIMT \ ! idbio( 6), LdetritusN HSIMT \ ! idbio( 7), SdetritusN HSIMT \ ! idbio( 8), LdetritusC HSIMT \ ! idbio( 9), SdetritusC HSIMT \ ! idbio(10), TIC HSIMT \ ! idbio(11), alkalinity HSIMT ! idbio(12), oxygen Vadvection == HSIMT \ ! idbio( 1), NO3 HSIMT \ ! idbio( 2), NH4 HSIMT \ ! idbio( 3), chlorophyll HSIMT \ ! idbio( 4), phytoplankton HSIMT \ ! idbio( 5), zooplankton HSIMT \ ! idbio( 6), LdetritusN HSIMT \ ! idbio( 7), SdetritusN HSIMT \ ! idbio( 8), LdetritusC HSIMT \ ! idbio( 9), SdetritusC HSIMT \ ! idbio(10), TIC HSIMT \ ! idbio(11), alkalinity HSIMT ! idbio(12), oxygen
Alternatively, it advantageous to specify the tracer advection switches in a compact form. For example, in ecosim.in we have:
Hadvection == HSIMT ! idbio(:), compact Vadvection == HSIMT ! idbio(:), compact ! Adjoint-based algorithms can have different horizontal and schemes ! for active and inert tracers. ad_Hadvection == U3 ! idbio(:), compact ad_Vadvection == C4That is all EcoSim tracers have the same tracer advection algorithm. A similar strategy can be used for the sediment tracers in sediment.in.
In a nested application, the syntax is as follows:
Hadvection == A4 \ ! temperature, Grid 1 A4 \ ! temperature, Grid 2 A4 \ ! temperature, Grid 3 HSIMT \ ! salinity, Grid 1 HSIMT \ ! salinity, Grid 2 HSIMT ! salinity, Grid 3 Vadvection == A4 \ ! temperature, Grid 1 A4 \ ! temperature, Grid 2 A4 \ ! temperature, Grid 3 HSIMT \ ! salinity, Grid 1 HSIMT \ ! salinity, Grid 2 HSIMT ! salinity, Grid 3
- A new tracer scheme HSIMT (Wu and Zhu, 2010) that uses a Total Variation Diminishing (TVD) limiter is included. It is adapted from Hui Wu code and implemented in COAWST by Tarandeep Kalra and John Warner. The HSIMT algorithm can be used for salinity and passive tracer to achieve monotonicity. For more information, check the following publication:
Hui Wu and Jianrong Zhu, 2010: Advection scheme with 3rd high-order spatial interpolation at the middle temporal level and its application to saltwater intrusion in Changjiang Estuary, Ocean Modelling 33, 33-51, doi:10.1016/j.ocemod.2009.12.001The HSIMT algorithm is inlined into ROMS code in step3d_t.F instead of calling a subroutine inside of DO-loops to avoid computational inefficiency and facilitate the tangent linear and adjoint transformation.
It is recommended to use HSIMT or MPDATA for passive tracers since the have a positive-definite dynamical range. The HSIMT is more modern and efficient than the recursive MPDATA algorithm. When using HSIMT or MPDATA, the user needs to specify the same scheme for both horizontal and vertical tracer advection.
- All the tracer advection algorithms are available at run time. For example, in the step3d_t.F the horizontal advective fluxes are computed as:
HADV_FLUX : IF (Hadvection(itrc,ng)%CENTERED2) THEN FX(i,j) = ... FE(i,j) = ... ELSE IF (Hadvection(itrc,ng)%MPDATA) THEN FX(i,j) = ... FE(i,j) = ... ELSE IF (Hadvection(itrc,ng)%HSIMT) THEN FX(i,j) = ... FE(i,j) = ... ELSE IF ((Hadvection(itrc,ng)%AKIMA4).or. & & (Hadvection(itrc,ng)%CENTERED4).or. & & (Hadvection(itrc,ng)%SPLIT_U3).or. & & (Hadvection(itrc,ng)%UPSTREAM3)) THEN FX(i,j) = ... FE(i,j) = ... END IF HADV_FLUXand for vertical advective fluxVADV_FLUX : IF (Vadvection(itrc,ng)%SPLINES) THEN FC(i,k) = .. ELSE IF (Vadvection(itrc,ng)%AKIMA4) THEN FC(i,k) = .. ELSE IF (Vadvection(itrc,ng)%CENTERED2) THEN FC(i,k) = .. ELSE IF (Vadvection(itrc,ng)%MPDATA) THEN FC(i,k) = .. ELSE IF (Vadvection(itrc,ng)%HSIMT) THEN FC(i,k) = .. ELSE IF ((Vadvection(itrc,ng)%CENTERED4).or. & & (Vadvection(itrc,ng)%SPLIT_U3)) THEN FC(i,k) = .. END IF VADV_FLUX
A similar structure is found in pre_step3d.F.
- The new tracer advection strategy was tested to get identical results regardless of the parallel partitions in distributed-memory (MPI), shared-memory (OpenMP), and serial with tiled partitions. It is only possible in double precision computations. In serial precision with double precision IO, the solution are not identical because of round-off. The user needs to be aware of the computational sensitivity in parallel single-precision applications. The solution differs as a function of the tile partition.
- The HSIMT and MPDATA algorithms are not implemented in the tangent linear and adjoint codes. MPDATA is very tricky because of the recursive algorithm in the anti-diffusivity correction.
- The tracer advection switches are reported in the output NetCDF files global attribute NLM_TADV:
:NLM_TADV = "\n", "ADVECTION: HORIZONTAL VERTICAL \n", "temp: Upstream3 Centered4 \n", "salt: HSIMT HSIMT \n", "NO3: HSIMT HSIMT \n", "NH4: HSIMT HSIMT \n", "chlorophyll: HSIMT HSIMT \n", "phytoplankton: HSIMT HSIMT \n", "zooplankton: HSIMT HSIMT \n", "LdetritusN: HSIMT HSIMT \n", "SdetritusN: HSIMT HSIMT \n", "LdetritusC: HSIMT HSIMT \n", "SdetritusC: HSIMT HSIMT \n", "TIC: HSIMT HSIMT \n", "Talk: HSIMT HSIMT \n", "oxyg: HSIMT HSIMT" ;
- The old tracer advection CPP options will be ignored in ROMS. Therefore, Users may want to still keep then in the application header file to run with older versions of ROMS.
- We strongly discourage you from using the parabolic splines vertical advection (SPLINES) scheme in realistic applications! It was intended for use in idealized toy problems. It is still available for historical reasons and backward compatibility.
Change History (3)
comment:1 by , 5 years ago
| Resolution: | → Done |
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| Status: | new → closed |
comment:2 by , 5 years ago
| Description: | modified (diff) |
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comment:3 by , 5 years ago
| Description: | modified (diff) |
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