We provide a ParaView Catalyst Adaptor for CAM5 simulation with Finite Volume (fv) or Spectral Element (se) dynamic modules. We tested our code with cesm1_2_2.

Files:

catalyst_add_and_coprocess.F90: included in one of the simulation files as it needs to call functions from the simulation executable.
fv_create_data.cxx, se_create_data.cxx: initializes and stores the VTK grid.
Grid.cxx, Grid.h: manages the VTK grid.
fv_coprocess.py, se_coprocess.py: ParaView pipeline.
cesm1_2_2.patch: patch to Cam5 sources

Useful documentation:

To build CAM5 and the Catalyst adaptor:

Download ParaView source code and download CESM (Community Earth System Model) source code using instructions in:

http://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/usersguide/book1.html
Modify configure-cam.sh, gen-cam.sh, build-namelist.sh in ~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/ such that CAM_ROOT points to the location for cesm1_2_2 sources. By default the scripts assume that cesm1_2_2 is stored in ~/src/cesm_1_2_2.
Build ParaView.

Patch cesm1_2_2 sources to call the Catalyst Adaptor:
```
cd ~/src/cesm1_2_2/models/atm/cam
patch < ~/build/ParaView/CoProcessing/Adaptors/CamAdaptor/cesm1_2_2.patch
```
By default, Cam5 Adaptor saves the simulation data. See fv_coprocess.py and se_coprocess.py for the ParaView pipeline that is executed. To execute a different script you can modify those files or modify src/cpl_mct/atm_comp_mct.F90 to point to your scripts.
Configure Cam5:
```
 mkdir ~/build/cam-5.3
 cd ~/build/cam-5.3
```
Edit the configuration script by uncommenting the configuration you want or creating a different configuration. Parameters for finite volume and spectral element with different grid sizes are available. Run the configuration script.
```
~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/configure-cam.sh
```
Note you have to configure the number of MPI processors and use the same number when you run the simulation.

Build cam5:
```
make -j10
```
Create a run directory for the simulation and create the parameters for the simulation. This is where you set for how long you run the simulation and how often you save data.
```
 mkdir ~/run/cam-5.3
 cd ~/run/cam-5.3
 ~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/build-namelist.sh | grep FOUND
```
Namelists (parameters) for the simulation are listed in:

http://www.cesm.ucar.edu/cgi-bin/eaton/namelist/nldef2html-cam5_3

Different configurations need different data files. If any of the required data files are NOT FOUND download them from: https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata Don't checkout everything as the datafiles are big! First checkout individual empty directories leading to the file you are interested in:
```
cd ~/src/cesm-data
svn update --depth empty atm
cd atm
svn update --depth empty cam
cd cam
svn update --depth empty inic
cd inic
svn update --depth empty homme
cd homme
```
Then checkout the file:
```
svn update cami-mam3_0000-01-01_ne30np4_L30_c130424.nc
```
Run the simulation:
```
 ~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/run-cam.sh
```
The data fields generated by the simulation (those stored in the .nc file) are listed in:

http://www.cesm.ucar.edu/models/cesm1.2/cam/docs/ug5_3/hist_flds_fv_cam5.html

You can view the history file camrun.cam.h0.*.nc in ParaView using 'NetCDF files generic and CF conventions' reader. You can switch the dimensions viewed to be (lat,lon) or (lev, lat, lon) to get a sphere or a ball.
Optional: If you want to debug certain pio files in the simulation run:
```
 ~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/gen-cam.sh d
```
This command copies a list of .F90.in to the corresponding .F90 so that gdb works correctly over these files. When you need to rebuild run:
```
~/src/ParaView/CoProcessing/Adaptors/CamAdaptor/gen-cam.sh g
```

To dump the history file produced by the simulation in text format run ncdump camrun.cam.h0.*.nc > camrun.txt

See http://www.unidata.ucar.edu/software/netcdf/docs/netcdf_utilities_guide.html#ncdump_SYNOPSIS for more information.