<p><b>mhoffman@lanl.gov</b> 2012-03-05 15:35:07 -0700 (Mon, 05 Mar 2012)</p><p>-- TRUNK COMMIT -- land_ice documents only<br>
<br>
Cleaned up the getting started document and added the new land ice grid conversion step.<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/land_ice/reference_manual/getting_started.txt
===================================================================
--- trunk/documents/land_ice/reference_manual/getting_started.txt 2012-03-05 22:26:29 UTC (rev 1593)
+++ trunk/documents/land_ice/reference_manual/getting_started.txt 2012-03-05 22:35:07 UTC (rev 1594)
@@ -1,5 +1,6 @@
-MPAS Quick Start:
+MPAS Land Ice Core Quick Start:
+=======================
Checking out the branch
$ svn checkout -username xylar@lanl.gov https://svn-mpas-model.cgd.ucar.edu/branches/land_ice_projects
@@ -11,7 +12,7 @@
-
+=======================
Building MPAS: Land Ice
$ setenv CORE land_ice (or export CORE=land_ice)
$ setenv NETCDF /usr/local/netcdf-gfortran (or export NETCDF=/usr/local/netcdf-gfortran)
@@ -24,7 +25,7 @@
-
+=============
Making a grid:
Checking out the trunk version of grid gen
$ svn checkout -username xylar@lanl.gov https://svn-mpas-model.cgd.ucar.edu/trunk/grid_gen
@@ -66,8 +67,26 @@
graph.info.part.4
etc.
+
+Next the default MPAS grid needs to be modified to include land ice variables. This is currently done with a python script.
+The script is located here: land_ice_projects/grid_tools/add_land_ice_variables_to_mpas_grid.py
+Move the script to the directory that contains your newly generated grid file (grid.nc). Run the script with:
+./add_land_ice_variables_to_mpas_grid.py -f grid.nc
+It will create a new file called land_ice_grid.nc that contains the land ice variables.
+You can confirm this with ncdump -h land_ice_grid.nc. At the end of the variable list should be:
+ double layerThicknessFractions(nVertLevels) ;
+ double thickness(Time, nCells) ;
+ double bedTopography(Time, nCells) ;
+ double beta(Time, nCells) ;
+ double normalVelocity(Time, nEdges, nVertLevels) ;
+ double tracers(Time, nCells, nVertLevelsPlus2, nTracers) ;
+
+
+
+================
+Setting up a Run:
The following assumes the following locations:
-land_ice branch is in ~/mpas_ice
+land_ice branch is in ~/mpas_ice (this should be the 'implement_core' project)
initial conditions are stored in subdirectories in ~/mpas_initial
runs are made from subdirectories in ~/mpas_runs
@@ -76,16 +95,9 @@
$ cd ~/mpas_runs/periodic_hex_01
$ ln -s ~/mpas_ice/mpas/land_ice_model.exe land_ice_model.exe
$ cp ~/mpas_ice/mpas/namelist.input.land_ice namelist.input
-$ ln -s ~/mpas_initial/periodic_hex_500_500/grid.nc grid.nc
+$ ln -s ~/mpas_initial/periodic_hex_500_500/land_ice_grid.nc grid.nc
-modify namelist.input
-$ vim namelist.input
-&sw_model
- config_test_case = 1
-...
- config_ntimesteps = 500
- config_output_interval = 50
-...
+There should be no need to modify namelist.input
if running on 2 processors:
$ ln -s ~/mpas_initial/periodic_hex_500_500/graph.info.part.2 graph.info.part.2
@@ -95,17 +107,29 @@
$ ./land_ice_model.exe
Output:
- Setting up shallow water test case 1
- -- Advection of Cosine Bell over the Pole
- Doing timestep 1
- Doing timestep 2
- Doing timestep 3
- Doing timestep 4
- Doing timestep 5
- Doing timestep 6
-...
+ Reading namelist.input
+
+ Setting up land ice test case 1
+ -- Evolution of an isothermal dome
+ Initial timestep 0000-01-01_00:00:00
+ Doing timestep 0000-01-01_00:01:00
+ timer_name total calls min max avg percent efficiency
+ 0 total time 0.62200 1 0.62200 0.62200 0.62200
+ 1 initialize 0.11700 1 0.11700 0.11700 0.11700 0.19 0.00
+ 1 time integration 0.00000 1 0.00000 0.00000 0.00000 0.00 0.00
+
look for output.nc
-Use paraview to visualize output.nc (this will have to be a separate tutorial)
+
+================
+Examining Output
+Use paraview to visualize output.nc (this will have to be a separate tutorial).
+However, paraview is limited to variables with dimensions that include nCells (or nVertices), nVertLevels. Few land ice variables meet that criterion. Hopefully this will be remedied in a future version of the paraview MPAS plugin.
+
+An alternative is to convert the output file to a regular grid that can be viewed (somwhat sloppily) in ncview (or similar tool). A script that does that conversion is here:
+land_ice_projects/grid_tools/convert_mpas_grid_to_regular_grid_netcdf.py
+
+For more rigorous examination of the output, python can be used. Python viz scripts are likely to be added to the test cases eventually.
+
</font>
</pre>