R-CESM Input/Output Files¶
In this section, we’ll list the input files required for running the model, and the files that result from a successful or unsuccessful model run.
Please note that for models like ROMS configurable options are chosen during both compilation and running phases. Since the source code always contain files required during compilation stage, their list is not presented here. But the important files for the compilation phase are discussed in detail. Since the files needed during model running phase (for a new experiment) are not available as a package like the R-CESM source code, their list is presented for each component model. Again, most important among these are discussed in detail. Please use the input files for the Gulf of Mexico test case (Chapter [cha:qkstart]) as a reference for setting up a new experiment. Only a basic description is provided in this chapter and for information on tools and procedure for creating some of these input files, please see Chapter [cha:tools].
Note
If the model run involves many restart runs, keep the input files (for the running phase) which are invariant across the runs in a separate directory and make symbolic links in the run directory as required.
ROMS Input Files¶
Compilation Phase¶
For the ROMS model, some of the scheme/parametrization choices are made pre-compilation using header files (.h). File txgla_3dnudg.h in $SRCROOT/components/roms directory is the ROMS header file for the low-resolution Gulf of Mexico test case. A copy of the header file used during compilation will be available in src ‘exec/include’ directory (Section
[sec:comp]).
Running Phase¶
For ROMS, the 3D nudging file is required only if the 3D nudging is turned on (see Section [sec:3Dnudg]). All other files are required for realistic configurations (ROMS do have the options to provide grid, boundary and initial files through analytical functions for idealized configurations). A list of ROMS input files are given in Table [tab:inpR].
Grid File¶
ROMS grid file (netCDF) contains all the grid related information needed by ROMS model. In addition model grid cell latitude and logitude, grid file contains several parameters like grid cell area, model bathymetry and land-sea mask.
Boundary Condition File¶
For open lateral boundaries, ROMS require time varying data for temperature, salinity, u and v velocities and sea surface height. This is provided through the boundary condition netCDF file.
Inidial Condition or Restart File¶
For the very first run, ROMS need initial condition file with full 3D model state (temperature, salinity, u nad v velocities and sea surface height). For a restart run, this is provided through model generated restart files.
3D Nudging File¶
ROMS can be configured with 3-dimentional nudging to specified data to make sure model is not drifting too far away from the specified data (typically from ocean reanalysis products). The data can be climatology or inter-annually varying depending on the application. Nudging can be along few grid points along the open boundaries or throughout the entire ROMS domain (like in the Gulf of Mexico test case). Irrespective of this choice, the 3D nudging data should always be for the entire 3D model domain (a ROMS requirement) and time varying.
WRF Input Files¶
Running Phase¶
WRF input netCDF and namelist files are listed in Table [tab:inpW], which are mandatory for all cases.
required only for restart runs.
#
Filename
File Type
Description
1
wrfinput_d01.nc
netCDF
Grid file
2
wrflowinp_d01
netCDF
Lower boundary conditions
3
wrfbdy_d01
netCDF
Lateral boundary conditions
4
#atm.r.2010-01-04.∗.nc | netCDF | WRF restart files
5
namelist.input
txt
WRF namelist/options file
For WRF there are serveral table files in addition to input netCDF and namelist files. All files in a WRF directory (R-CESM-1.0.0/models/atm/wrf/3.5.1/WRFV3/run/*) are linked to run directory as table files and no check has been done to see which all of these files are mandatory for running R-CESM and which all reduntant. A list of table files are given in Table [tab:inpWtable].
# |
Filename |
# |
Filename |
1 |
aerosol.formatted |
24 |
ETAMPNEW_….._rain |
2 |
aerosol_lat.formatted |
25 |
ETAMPNEW_….._rain_DBL |
3 |
aerosol_lon.formatted |
26 |
GENPARM.TBL |
4 |
aerosol_plev.formatted |
27 |
grib2map.tbl |
5 |
CAM_ABS_DATA |
28 |
gribmap.txt |
6 |
CAM_AEROPT_DATA |
29 |
LANDUSE.TBL |
7 |
CAMtr_volume_mixing_ratio.A1B |
30 |
MPTABLE.TBL |
8 |
CAMtr_volume_mixing_ratio.A2 |
31 |
ozone.formatted |
9 |
CAMtr_volume_mixing_ratio.RCP4.5 |
32 |
ozone_lat.formatted |
10 |
CAMtr_volume_mixing_ratio.RCP6 |
33 |
ozone_plev.formatted |
11 |
CAMtr_volume_mixing_ratio.RCP8.5 |
34 |
RRTM_DATA |
12 |
CLM_ALB_ICE_DFS_DATA |
35 |
RRTM_DATA_DBL |
13 |
CLM_ALB_ICE_DRC_DATA |
36 |
RRTMG_LW_DATA |
14 |
CLM_ASM_ICE_DFS_DATA |
37 |
RRTMG_LW_DATA_DBL |
15 |
CLM_ASM_ICE_DRC_DATA |
38 |
RRTMG_SW_DATA |
16 |
CLM_DRDSDT0_DATA |
39 |
RRTMG_SW_DATA_DBL |
17 |
CLM_EXT_ICE_DFS_DATA |
40 |
SOILPARM.TBL |
18 |
CLM_EXT_ICE_DRC_DATA |
41 |
tr49t67 |
19 |
CLM_KAPPA_DATA |
42 |
tr49t85 |
20 |
CLM_TAU_DATA |
43 |
tr67t85 |
21 |
co2_trans |
44 |
URBPARM.TBL |
22 |
ETAMPNEW_DATA |
45 |
URBPARM_UZE.TBL |
23 |
ETAMPNEW_DATA_DBL |
46 |
VEGPARM.TBL |
namelist.input¶
Please adapt the namelist.input file provided with Gulf of Mexico test case for a new application rather than using namelist.input file available with independant WRF distribution. Please note that the domain decomposition (processor tiling) is automatically determined by R-CESM and there is no field in namelist.input to control this aspect for the WRF component. Please see Section 3.2.3 for details about processor specifying options for R-CESM.
R-CESM/Coupler Input Files¶
Compilation Phase¶
Files during compilation R-CESM
Running Phase¶
For R-CESM and its coupler, there are several input files which are listed in Table [tab:inpC]. Please provide all of these files even if some of the component models (like ice) are not used. All files which do not belong exclusively to either ROMS or WRF is included in this category. The acronym “IO” implies input-output. (Some words are used interchangably: ocean/ROMS, atmosphere/WRF, data ocean/xroms in Table [tab:inpC] and this will be corrected in the future.)
24 is only required for restart runs.
rpointer Files¶
The rpointer here means “restart pointer” which informs R-CESM about restart date and time. There are 5 rpointer files, one for each component as shown below:
atmosphere/WRF: |
rpointer.atm |
data ocean: |
rpointer.docn |
driver/coupler: |
rpointer.drv |
ROMS: |
rpointer.roms |
ocean: |
rpointer.ocn (symbolic link to rpointer.roms) |
Please note that the time format for these files are different (like 2010-01-04_00_00_00 for atm and 2010-01-04-00000 for drv). The rpointer.drv file use acronym cpl in it (like TXGLO.cpl.r.2010-01-04-00000.nc) instead of drv. Also there are two entries for the rpointer.docn and other have just one entry. The usage details of rpointer files are listed below.
For the very first run from initial condition files, set the entries in all rpointer files to expected restart date.
For all successfull runs, the rpointer files are automatically updated with the most recet restart date and time.
If you intend to continue a run from most recent restart files, just these updated rpointer files to the restart run directory.
If you are making restart run from a different restart file, please update the rpointer files accordingly.
For restart runs, the first entry in rpointer files should correspond to the restart date and time.
TXGLO.atm.r.2010-04-20_00_00_00.nc
TXGLO.atm.r.2010-04-30_00_00_00.nc
Please note that the restart file writing frequency is not determined by rpointer files but by the value of “restart_n” in drv_in (see Section [sec:rstfr] for details).
docn_ocn_in¶
The syntax for years in the streams entry of “docn_ocn_in” is as follows:
streams = "docn.streams.txt.prescribed YrAlign yrFirst yrLast"
It appears that the YrAlign should be same as YrFirst always!!!!!
drv_in¶
The number of processors/cores (PEs) for running R-CESM and its component models should be clearly mentioned in drv_in (&ccsm_pes namelist). If drv_in is edited to update PE count or layout, pleae edit the ocean.in (Section 1.2.5) and run_R-CESM.job file (Section 4.1) accordingly. Please note that the total number of PEs are devided between atm_ntasks and ocn_ntasks. Also, atm_rootpe is 0 and ocn_rootpe is same as atm_ntasks. All other component model mirrors the settings for the atm. Two examples for total PE counts of 552 and 120 are provided in Table [tab:pe].
sum of number of atm model PE (atm_ntasks) and ocn model PE (ocn_ntasks). Please note that the root PE for atm is 0 and that for ocn in atm_ntasks. Other component models mirror atm model settings.
ccsm_pe
Total
Total
field
PE=552
PE=120
atm_ntasks
168
40
atm_nthreads
1
1
atm_rootpe
0
0
atm_pestride
1
1
atm_layout
‘concurrent’
‘concurrent’
lnd_ntasks
168
40
lnd_nthreads
1
1
lnd_rootpe
0
0
lnd_pestride
1
1
lnd_layout
‘concurrent’
‘concurrent’
ocn_ntasks
384
80
ocn_nthreads
1
1
ocn_rootpe
168
40
ocn_pestride
1
1
ocn_layout
‘concurrent’
‘concurrent’
ice_ntasks
168
40
ice_nthreads
1
1
ice_rootpe
0
0
ice_pestride
1
1
ice_layout
‘concurrent’
‘concurrent’
glc_ntasks
168
40
glc_nthreads
1
1
glc_rootpe
0
0
glc_pestride
1
1
glc_layout
‘concurrent’
‘concurrent’
cpl_ntasks
168
40
cpl_nthreads
1
1
cpl_rootpe
0
0
cpl_pestride
1
1
docn.streams.txt.prescribed¶
This file provides path and filenames for the domain info file (eg. domain.txglo.nc) and the xROMS sea surface temperature (SST) and ice fields (eg. \(*\)_xroms_sstice.nc). Please update the value for “<filePath>” and “<fileNames>” for both “<domainInfo>” and “<fieldInfo>” entries as appropriate.
Mapping Weight Files¶
Coupled model components can have different resolutions. R-CESM requires precomputed interpolation weights to map surface quantities between different coupled model components. Interpolation options like bilinear and averaging options like area-average are available with the ESMF tool.
For a detailed discussion on mapping weight files and how to make them, please see Section 5.2 in :raw-latex:`\citet{montuoro17}`.
xroms_sstice.nc¶
R-CESM need data for SST and ice over entire domain. With xROMS set up (Section [sec:frxroms]), user has to provide an xROMS file with SST and ice for the entire xROMS domain. SST for the bigger domain is typycally available in WRF lower boundary input files. Current test cases use ice as 0 everywhere.
A simple approach is to use matlab to interpolate WRF SST onto xROMS grid and then write the interpolated SST to a proper xROMS SST netCDF file (use the file from Gulf of Mexico test case as a reference).
Other Input Files¶
Other files required by R-CESM during running phase are listed in Table [tab:inpO].
executable.
All Output Files¶
Complete list of output files from a R-CESM run is provided in Table [tab:outC].
Sl. |
Filename |
File Type | Purpose |
||
|---|---|---|---|---|
1 |
*.log |
txt |
Log files from each component |
|
2 |
rsl.error.* | txt | WRF std error |
|||
2 |
rsl.out.* |
txt |
WRF std error |
|
2 |
rpointer.* |
txt | restart file pointers |
||
2 |
<case>.atm.hi.<time>.nc |
netCDF |
WRF output file |
|
2 |
<case>.ocn.hi.<time>.nc |
netCDF |
ROMS output file |
|
2 |
<case>.docn.rs1.<time>.nc | netCDF | DOCN restart file |
|||
2 |
<case>.clm2.h0.<time>.nc | netCDF | CLM 4.0 monthly output file |
|||
2 |
<case>.<comp>.r.<time>.nc | netCDF | Restart files from each component |
|||
2 |
<case>.clm2.h0.<time>.nc | netCDF | CLM 4.0 monthly output file |
|||
2 |
<case>.clm2.rh0.<time>.nc | netCDF | CLM 4.0 restart file |
|||