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| Ticket | Owner | Reporter | Resolution | Summary |
|---|---|---|---|---|
| #680 | Done | IMPORTANT: stations and floats in nesting applications | ||
| Description |
STATIONS: The routine read_stapar.F that reads the stations input script (stations.in) was updated so the CPP option STATIONS is more robust across nested grids. Only one stations.in input script is needed in nested applications. As in ocean.in, we just need to use the plural symbol == after the KEYWORD for relevant nested grids parameters. For example, in a four nested grids application we can have: ! Switch to control the writing of stations data within nested and/or multiple
! connected grids, [1:Ngrids].
Lstations == T T T T
! Logical switches (TRUE/FALSE) to activate writing of fields in STATION
! output file, [Sout(:,ng), ng=1, Ngrids].
Sout(idUvel) == 4*T ! u 3D U-velocity
Sout(idVvel) == 4*T ! v 3D V-velocity
Sout(idu3dE) == 4*F ! u_eastward 3D U-eastward at RHO-points
Sout(idv3dN) == 4*F ! v_northward 3D V-nortward at RHO-points
Sout(idWvel) == 4*T ! w 3D W-velocity
Sout(idOvel) == 4*T ! omega 3D omega vertical velocity
Sout(idUbar) == 4*T ! ubar 2D U-velocity
Sout(idVbar) == 4*T ! vbar 2D V-velocity
Sout(idu2dE) == 4*F ! ubar_eastward 2D U-eastward at RHO-points
Sout(idv2dN) == 4*F ! vbar_northward 2D V-northward at RHO-points
Sout(idFsur) == 4*T ! zeta free-surface
Sout(idBath) == 4*T ! bath time-dependent bathymetry
Sout(idTvar) == 8*T ! temp, salt, ... all (NT) tracers
Sout(idUsms) == 4*T ! sustr surface U-stress
Sout(idVsms) == 4*T ! svstr surface V-stress
Sout(idUbms) == 4*T ! bustr bottom U-stress
Sout(idVbms) == 4*T ! bvstr bottom V-stress
Sout(idUbrs) == 4*F ! bustrc bottom U-current stress
Sout(idVbrs) == 4*F ! bvstrc bottom V-current stress
Sout(idUbws) == 4*F ! bustrw bottom U-wave stress
Sout(idVbws) == 4*F ! bvstrw bottom V-wave stress
Sout(idUbcs) == 4*F ! bustrcwmax bottom max wave-current U-stress
Sout(idVbcs) == 4*F ! bvstrcwmax bottom max wave-current V-stress
Sout(idUbot) == 4*F ! Ubot bed wave orbital U-velocity
Sout(idVbot) == 4*F ! Vbot bed wave orbital V-velocity
Sout(idUbur) == 4*F ! Ur bottom U-velocity above bed
Sout(idVbvr) == 4*F ! Vr bottom V-velocity above bed
Sout(idW2xx) == 4*F ! Sxx_bar 2D radiation stress, Sxx component
Sout(idW2xy) == 4*F ! Sxy_bar 2D radiation stress, Sxy component
Sout(idW2yy) == 4*F ! Syy_bar 2D radiation stress, Syy component
Sout(idU2rs) == 4*F ! Ubar_Rstress 2D radiation U-stress
Sout(idV2rs) == 4*F ! Vbar_Rstress 2D radiation V-stress
Sout(idU2Sd) == 4*F ! ubar_stokes 2D U-Stokes velocity
Sout(idV2Sd) == 4*F ! vbar_stokes 2D V-Stokes velocity
Sout(idW3xx) == 4*F ! Sxx 3D radiation stress, Sxx component
Sout(idW3xy) == 4*F ! Sxy 3D radiation stress, Sxy component
Sout(idW3yy) == 4*F ! Syy 3D radiation stress, Syy component
Sout(idW3zx) == 4*F ! Szx 3D radiation stress, Szx component
Sout(idW3zy) == 4*F ! Szy 3D radiation stress, Szy component
Sout(idU3rs) == 4*F ! u_Rstress 3D U-radiation stress
Sout(idV3rs) == 4*F ! v_Rstress 3D V-radiation stress
Sout(idU3Sd) == 4*F ! u_stokes 3D U-Stokes velocity
Sout(idV3Sd) == 4*F ! v_stokes 3D V-Stokes velocity
Sout(idWamp) == 4*F ! Hwave wave height
Sout(idWlen) == 4*F ! Lwave wave length
Sout(idWdir) == 4*F ! Dwave wave direction
Sout(idWptp) == 4*F ! Pwave_top wave surface period
Sout(idWpbt) == 4*F ! Pwave_bot wave bottom period
Sout(idWorb) == 4*F ! Ub_swan wave bottom orbital velocity
Sout(idWdis) == 4*F ! Wave_dissip wave dissipation
Sout(idPair) == 4*F ! Pair surface air pressure
Sout(idUair) == 4*F ! Uair surface U-wind component
Sout(idVair) == 4*F ! Vair surface V-wind component
Sout(idTsur) == 8*F ! shflux, ssflux surface net heat and salt flux
Sout(idLhea) == 4*F ! latent latent heat flux
Sout(idShea) == 4*F ! sensible sensible heat flux
Sout(idLrad) == 4*F ! lwrad longwave radiation flux
Sout(idSrad) == 4*F ! swrad shortwave radiation flux
Sout(idEmPf) == 4*F ! EminusP E-P flux
Sout(idevap) == 4*F ! evaporation evaporation rate
Sout(idrain) == 4*F ! rain precipitation rate
Sout(idDano) == 4*T ! rho density anomaly
Sout(idVvis) == 4*T ! AKv vertical viscosity
Sout(idTdif) == 4*T ! AKt vertical T-diffusion
Sout(idSdif) == 4*T ! AKs vertical Salinity diffusion
Sout(idHsbl) == 4*T ! Hsbl depth of surface boundary layer
Sout(idHbbl) == 4*F ! Hbbl depth of bottom boundary layer
Sout(idMtke) == 4*F ! tke turbulent kinetic energy
Sout(idMtls) == 4*F ! gls turbulent length scale
! Logical switches (TRUE/FALSE) to activate writing of exposed sediment
! layer properties into STATIONS output file. Currently, MBOTP properties
! are expected for the bottom boundary layer and/or sediment models:
!
! idBott( 1=isd50) grain_diameter mean grain diameter
! idBott( 2=idens) grain_density mean grain density
! idBott( 3=iwsed) settling_vel mean settling velocity
! idBott( 4=itauc) erosion_stress critical erosion stress
! idBott( 5=irlen) ripple_length ripple length
! idBott( 6=irhgt) ripple_height ripple height
! idBott( 7=ibwav) bed_wave_amp wave excursion amplitude
! idBott( 8=izdef) Zo_def default bottom roughness
! idBott( 9=izapp) Zo_app apparent bottom roughness
! idBott(10=izNik) Zo_Nik Nikuradse bottom roughness
! idBott(11=izbio) Zo_bio biological bottom roughness
! idBott(12=izbfm) Zo_bedform bed form bottom roughness
! idBott(13=izbld) Zo_bedload bed load bottom roughness
! idBott(14=izwbl) Zo_wbl wave bottom roughness
! idBott(15=iactv) active_layer_thickness active layer thickness
! idBott(16=ishgt) saltation saltation height
!
! 1 1 1 1 1 1 1
! 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6
Sout(idBott) == F F F F F F F F F F F F F F F F \
F F F F F F F F F F F F F F F F \
F F F F F F F F F F F F F F F F \
F F F F F F F F F F F F F F F F
! Number of stations to process in each nested grid. These values are
! essential because the station arrays are dynamically allocated using
! these values, [1:Ngrids].
NSTATION == 1 1 1 1
! Station locations for all grids in any desired order. The horizontal
! location for a particular station may be specified in terms of fractional
! (I,J) grid pairs (FLAG=0) or (longitude,latitude) grid pairs (FLAG=1).
! Here, FLAG is a special switch and may be used for multiple purposes.
! The GRID column indicates nested grid number to process. This value must
! be one in non-nested applications. The COMMENT section is ignored during
! reading and may be used to help documentation.
POS = GRID FLAG X-POS Y-POS COMMENT
1 0 50.0d0 40.0d0
2 0 60.0d0 65.0d0
3 0 57.0d0 30.0d0
4 0 66.0d0 25.0d0
Users need to pay attention to all the above parameters. In particular: Lstations, NSTATION, and POS. FLOATS: Similarly, one floats.in is need in nested applications when the CPP option FLOATS is activated. Currently, the floats trajectories are independent of each nested grid. That is, once that the trajectory exit a particular grid it will not continue into the other nested grids. We will figure out in the future how to allow this but it is not high in our priority list. As mentioned above, we just need to use the plural symbol == after the KEYWORD for nested grids parameters. For example, in a four nested grids application we can have: ! Switch to control the computation of floats trajectories within nested
! and/or multiple connected grids, [1:Ngrids].
!
Lfloats == T F F F
! Switch to control the printing of floats initial positions to standard
! output file, [1:Ngrids].
!
Fprint == T T T T
! Flag indicating re-start from previous solution. If FRREC = 0, a new
! NetCDF output file is created.
FRREC == 4*0
! If applicable, input script file name containing biological floats behavior
! model parameters.
FBIONAM = behavior_oyster.in
! Number of floats to release in each nested grid. These values are
! essential because the FLOATS structure in "mod_floats" is dynamically
! allocated using these values, [1:Ngrids].
NFLOATS == 1 1 1 1
! Initial floats locations for all grids:
!
! G Nested grid number
! C Initial horizontal coordinate type (0: grid units, 1: spherical)
! T Float trajectory type (1: Lagrangian, 2: isobaric, 3: Geopotential)
! N Number floats to be released at (Fx0,Fy0,Fz0)
! Ft0 Float release time (days) after model initialization
! Fx0 Initial float X-location (grid units or longitude)
! Fy0 Initial float Y-location (grid units or latitude)
! Fz0 Initial float Z-location (grid units or depth)
! Fdt Float cluster release time interval (days)
! Fdx Float cluster X-distribution parameter
! Fdy Float cluster Y-distribution parameter
! Fdz Float cluster Z-distribution parameter
POS = G, C, T, N, Ft0, Fx0, Fy0, Fz0, Fdt, Fdx, Fdy, Fdz
1 0 1 1 0.0d0 50.0d0 40.0d0 8.0d0 0.0d0 0.0d0 0.0d0 0.0d0
2 0 1 1 0.0d0 60.0d0 65.0d0 8.0d0 0.0d0 0.0d0 0.0d0 0.0d0
3 0 1 1 0.0d0 57.0d0 30.0d0 8.0d0 0.0d0 0.0d0 0.0d0 0.0d0
4 0 1 1 0.0d0 66.0d0 25.0d0 8.0d0 0.0d0 0.0d0 0.0d0 0.0d0
Users need to pay attention to the following parameters Lfloats, NFLOATS. and POS. Corrected nesting.F around Line 122 to avoid compilation problems when MASKING is not activated: # if defined MASKING || defined WET_DRY
PRIVATE :: mask_hweights
# endif
Many thanks to Jamie Pringle for bringing this to my attention. |
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| #681 | Done | IMPORTANT: replacing option SPLINES | ||
| Description |
The C-preprocessing option SPLINES have been in ROMS since the beginning. It is used to activate conservative, parabolic splines reconstruction of vertical derivatives in the following routines:
There has been several messages in the ROMS forum discussing the problems when SPLINES is used to compute vertical viscosity and vertical diffusion. This was first brought to our attention by Evgeny Logvinov when checking the stress condition (sustr = Akv * du/dz and svstr = Akv * dv/dz). He noticed that the stress condition was not holding and he got a very sharp change in du/dz and dv/dz 1m below the surface. Everything worked fine when SPLINES was not activated. Similar behavior was discussed Chris Sherwood. I know of several users that avoid using the SPLINES option because the of the surface and bottom stress condition needs to be preserved. However, it is nice is nice to have the parabolic splines reconstruction when computing either Richardson Number or Bulk Richardson Number. The vertical velocity shear (used as a squared quantity in the denominator) is a very noisy quantity so using parabolic splines yields a smoother values. Therefore, the C-preprocessing option SPLINES is removed and replaced with following three options for more flexibility:
WARNING: ROMS will issue an error message if the option SPLINES is activated after this update. The user will need to activate the SPLINES_VVISC and SPLINES_VDIFF. Also you will need to activate RI_SPLINES if using GLS_MIXING, LMD_MIXING, MY25_MIXING. Therefore, users need to update the header file for their applications. Several header files were updated in the trunk repository and test repositories. I highly recommend users to update their repositories. The new options provide more flexibility while preserving legacy codes and applications. Users should get identical results if activating the new options described above. |
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| #682 | Fixed | Profile Report | ||
| Description |
The routines wclock_on and wclock_off (timers.F) fail to report the profile timings in distributed-memory applications (MPI). This has been broken for awhile since the OpenMP directives were re-worked (see src:ticket:552). In that update the numthreads was modified in MPI to have the number of distributed nodes: CALL mpi_comm_size (OCN_COMM_WORLD, numthreads, MyError) This affected the logic in wclock_on and wclock_off in MPI applications, which needs numthreads = 1. To correct this problem, both routines were modified to have: !
! Set number of subdivisions, same as for global reductions.
!
#ifdef MPI
NSUB=1
#else
NSUB=numthreads
#endif
then, we use NSUB instead of numthreads in the conditional statement in wclock_on: IF (thread_count.eq.NSUB) thread_count=0 and in wclock_off: IF (thread_count.eq.NSUB) THEN
thread_count=0
...
END IF
I also improved the time profile report in nested grid applications. Many thanks to Kate Hedstrom for reminding me about this problem. |
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