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Ticket | Owner | Reporter | Resolution | Summary |
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#374 | Fixed | WARNING: Corrected BUG in scale_factor attribute for input NetCDF files | ||
Description |
WARNING: This is a bug if you scale your data using the NetCDF scale_factor attribute which is used to compress data sometimes. Corrected a bug in get_ngfld.F, get_ngfldr.F, get_2dflf.F, get_2dfldr.F, get_3dfld.F, and get_3dfldr.F. The Fscale(ifield,ng) was rewritten as: ! ! If "scale_factor" attribute is present for a variable, the data are ! to be multiplied by this factor. Check if only water points are ! available. ! IF (foundit) THEN DO i=1,nvatt IF (TRIM(var_Aname(i)).eq.'scale_factor') THEN scale=var_Afloat(i) Fscale(ifield,ng)=Fscale(ifield,ng)*scale ELSE IF (TRIM(var_Aname(i)).eq.'water_points') THEN Iinfo(1,ifield,ng)=-ABS(Iinfo(1,ifield,ng)) Vtype=Iinfo(1,ifield,ng) END IF END DO END IF This was changed to: IF (TRIM(var_Aname(i)).eq.'scale_factor') THEN scale=var_Afloat(i) Finfo(10,ifield,ng)=scale ELSE IF (TRIM(var_Aname(i)).eq.'water_points') THEN END IF So no longer the value of Fscale(ifield,ng) is over-written. The scale value is now stored in Finfo(10,:,ng). This avoided scaling the variable twice by the scale_factor during reading in routines nf_fread*. I apologize that missed this one completely when I tested this part. Many thanks to Brian Powell for bringing this to my attention. |
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#375 | Done | Generalized coupled biology and sediment models interface | ||
Description |
I updated the interface for the various ecosystem model in ROMS. This allows a lot of flexibility and customization:
Check any of these files if you are adding a new ecosystem model into ROMS for guidance. Note that all the new ecosystem *.h files are located in ROMS/Nonlinear/Biology and included within <...> to allow the user to customize any of them in the project directory while keeping the distributed code intact (check the build script for details). The input parameters for the NEMURO model were not written in the output NetCDF file before. I missed this one. Also, notice that currently only sediment_inp.h is available for the sediment model. This will change in the future as this model evolves and more input parameters are required. I also fixed couple unbounded local arrays bugs in ecosim.h and the sink tracer indices for the silica group. |
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#376 | Done | IMPORTANT: New parameters in input script files | ||
Description |
All the input script files were updated to include new parameters:
! Harmonic/biharmonic horizontal diffusion of tracer for nonlinear model ! and adjoint-based algorithms: [1:NAT+NPT,Ngrids]. TNU2 == 0.0d0 0.0d0 ! m2/s TNU4 == 0.0d0 0.0d0 ! m4/s ad_TNU2 == 50.0d0 50.0d0 ! m2/s ad_TNU4 == 2.0d+10 2.00d+10 ! m4/s ! Harmononic/biharmonic, horizontal viscosity coefficient for nonlinear model ! and adjoint-based algorithms: [Ngrids]. VISC2 == 0.0d0 ! m2/s VISC4 == 0.0d0 ! m4/s ad_VISC2 == 50.0d0 ! m2/s ad_VISC4 == 2.0d+10 ! m4/s
! Logical switches (TRUE/FALSE) to specify which variables to consider on ! tracers point Sources/Sinks (like river runoff): [1:NAT+NPT,Ngrids]. ! See glossary below for details. LtracerSrc == T T ! temperature, salinity, inert This changes affect all ROMS input scripts: ocean.in, bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_Powell.in, npzd_iron.in, and sediment.in. The changes are simple and backward compatible. WARNING: the point sources (TS_PSOURCE) of tracers are modified as follows in ocean.in: ! LtracerSrc Logical switches (T/F) to specify which tracer variables ! to consider when the option TS_PSOURCE is activated. Only ! NAT active tracers (temperature, salinity) and NPT inert ! tracers need to be specified here: ! ! LtracerSrc(itemp,ng) for temperature (itemp=1) ! LtracerSrc(isalt,ng) for salinity (isalt=2) ! LtracerSrc(NAT+1,ng) for inert tracer 1 ! ... ... ! LtracerSrc(:,NAT+NPT) for inert tracer NPT ! ! Other biological and sediment tracers switches are specified in ! their respective input scrips. ! ! Recall that TS_PSOURCE is usually activated to add river runoff ! as a point source. At minimum, it is necessary to specify both ! temperature and salinity for all rivers. The other tracers are ! optional. ! ! This logical switch REPLACES and ELIMINATES the need to have ! or read the variable "river_flag(river)" in the input rivers ! forcing NetCDF file: ! ! double river_flag(river) ! river_flag:long_name = "river runoff tracer flag" ! river_flag:option_0 = "all tracers are off" ! river_flag:option_1 = "only temperature" ! river_flag:option_2 = "only salinity" ! river_flag:option_3 = "both temperature and salinity" ! river_flag:units = "nondimensional" ! ! This logic was too cumbersome and complicated when additional ! tracers are considered. However, this change is backward ! compatible. ! ! The LtracerSrc switch will be used to activate the reading of ! respective tracer variable from input river forcing NetCDF ! file. If you want to add other tracer variables (other than ! temperature and salinity) as a source for a particular river(s), ! you just need to specify such values on those river(s). Then, ! set the values to ZERO on the other river(s) that do NOT ! require such river forcing for that tracer. Recall that you ! need to specify the tracer values for all rivers, even if ! their values are zero. Please check any of the biological and sediment model input scripts for more details. The old logic was too cumbersome and complicated. Notice that a lot of files were changed. Notice that ana_psource.h was updated and no longer has the Lsrc argument. I am looking in more detail the river runoff (point sources) and I expect to update this capability in the future. |