Changeset 3938 for trunk/LMDZ.COMMON/libf/evolution/deftank/README

Timestamp:

Oct 29, 2025, 10:02:05 AM (2 months ago)

Author:

jbclement

Message:

PEM:

• Correction of the process to balance the H2O flux from and into the atmosphere accross reservoirs: (i) computation of H2O amount going from/in the atmosphere is corrected (missing dt and wrong condition); (ii) computation of the scaling factor is corrected because we need to balance all the icetable/adsorbed/surface ice flux but it affects only sublimating/condensing surface ice flux; (iii) process of balancing is modified to be applied to every flux by scaling instead of applying it only to positive or negative flux by trimming; (iv) balance is now fully processed by the tendency before evolving the ice. This is done through dedicated subroutines.
• Correction of ice conversion between the layering algorithm and PEM ice variables (density factor was missing).
• Addition of H2O flux balance and related stopping criterion for the layering algorithm.
• Few updates for files in the deftank to be in line with the wiki Planeto pages.

JBC

File:

• trunk/LMDZ.COMMON/libf/evolution/deftank/README (modified) (3 diffs)

trunk/LMDZ.COMMON/libf/evolution/deftank/README

@@ -22 +22 @@
 ------------
 To compile the PEM, in "LMDZ.COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 pem
-Options:
+Options with example:
     1) [local]     : root name of arch files, assuming that they have been set up for your configuration;
-    2) [planet]    : mars to use the planet physics package; 
-    3) [dimensions]: 64x48x54 to define the grid you want to use.
+    2) [planet]    : mars to use the Mars planet physics package; 
+    3) [dimensions]: 64x48x54 to define the grid you want to use  (longitude x latitude x atmospheric layers).
 To run the PEM, you need a dedicated reshaping tool with consistent options. To compile it, in "LMDZ_COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 reshape_XIOS_output
-To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in "LMDZ.COMMON", do for example: ./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm
+To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in "LMDZ.COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm
 After compilation, the executable file can be found in the "bin" sub-directory.
 
 Usage:
 ------
-  To run a PEM simulation, do: ./launchPEM.sh [options]
-  Options:
-      1) None: to start a simulation from scratch;
-      2) 're': to relaunch a simulation from a starting point (interactive prompt).
+To run a PEM simulation, do: ./launchPEM.sh [options]
+Options:
+    1) None: to start a simulation from scratch;
+    2) 're': to relaunch a simulation from a starting point (interactive prompt).
+
+The Bash file ''launchPEM.sh'' is the master script to launch the PEM chained simulation. It checks if necessary files and required options for your simulation are ok.
 
 Requirements:
 -------------
-To run the PEM, you need the following files:
-    > your executable files for the PCM, the PEM and the reshaping tool with consistent dimensions;
-    > the xml files for XIOS ("iodef.xml", "context_lmdz_physics.xml", "file_def_physics_mars.xml" and "field_def_physics_mars.xml") which can be found in the PCM deftank folder;
-    > the def files you want to run the PCM ("run.def", "callphys.def", "traceur.def", etc).
+To run the PEM, you can create a folder in which you need the following files:
+    > your executable files for the PCM, the PEM and the reshaping tool with consistent options;
+    > the xml files for XIOS which can be found in the PCM deftank folder: "iodef.xml", "context_lmdz_physics.xml", "file_def_physics_mars.xml" and "field_def_physics_mars.xml";
+    > the def files you want to run the PCM: "run.def", "callphys.def", "traceur.def", etc.
       /!\ Do not forget to rename the PCM "run.def" into "run_PCM.def";
-    > the starting files you want to run the PCM ("startfi.nc", "start.nc"/"start1D.txt"/profiles);
-    > the necessary PEM files ("launchPEM.sh", "lib_launchPEM.sh", "PCMrun.job", "PEMrun.job", "run_PEM.def" and "obl_ecc_lsp.asc";
-    > the optional PEM files "diagpem.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM.
+    > the starting files you want to run the PCM: "startfi.nc", "start.nc"/"start1D.txt"/profiles;
+    > the necessary PEM files: "launchPEM.sh", "lib_launchPEM.sh", "PCMrun.job", "PEMrun.job", "run_PEM.def" and "obl_ecc_lsp.asc";
+    > the optional PEM files: "diagpem.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM.
+
+The PEM files can be found in the deftank folder.
+
+Before a simulation, you have to set up some parameters/options in:
+    > "launchPEM.sh";
+    > "PCMrun.job";
+    > "PEMrun.job";
+    > def files, especially for "run_PEM.def", "run_PCM.def", "callphys.def".
+In addition, the user has to provide a "startfi.nc" whose orbital parameters are consistent with the initial date set in "run_PEM.def". The script "inipem_orbit.sh" can do it automatically with "obl_ecc_lsp.asc".
 
 Outputs:
 --------
 The PEM simulation generates the following files:
-    > the usual outputs of the PCM ("restartfi.nc", "restart.nc", "diagfi.nc", etc);
-    > the XIOS outputs of the PCM, then reshaped ("Xdiurnalave.nc"/"data2reshape*.nc"/"data_PCM_Y*.nc");
-    > the outputs of the chained simulation ("launchPEM.log", "info_PEM.txt" and possibly "kill_launchPEM.sh");
-    > the usual outputs of the PEM ("restartfi.nc", "restart.nc"/"restart1D.txt" and "diagpem.nc").
+    > the usual outputs of the PCM: "restartfi.nc", "restart.nc", "diagfi.nc", etc;
+    > the XIOS outputs of the PCM, then reshaped: "Xdiurnalave.nc"/"data2reshape*.nc"/"data_PCM_Y*.nc";
+    > the outputs of the chained simulation: "launchPEM.log", "info_PEM.txt" and possibly "kill_launchPEM.sh";
+    > the usual outputs of the PEM: "restartfi.nc", "restart.nc"/"restart1D.txt" and "diagpem.nc".
 During the simulation, the PCM/PEM run files are renamed conveniently and stored in the sub-directories "logs" (log files), "starts" (starting files) and "diags" (diagnostic files).
 If you run a simulation by submitting jobs, the script "kill_launchPEM.sh" is automatically generated. It can be used to kill in the queue of the job scheduler the jobs related to your chained simulation.
@@ -69 +80 @@
       > mode -> the launching mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE.
   The script can take an argument:
-      1) If there is no argument, then the script initiates a PEM simulation from scratch.
-      2) If the argument is 're', then the script relaunches an existing PEM simulation. It will ask for parameters to know the starting point that you want to.
+      1) None: to start a simulation from scratch;
+      2) 're': to relaunch a simulation from a starting point (interactive prompt).
 
 # liblaunchPEM.sh:
@@ -76 +87 @@
 
 # PCMrun.job:
-  Bash script file to submit a PCM job (with SLURM or PBS/TORQUE). The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
-  The path to source the arch file should be adapted to the machine.
-  The name of the PCM executable file should be adapted.
-  The execution command should also be adapted according to the set-up.
+  Bash script file to submit a PCM job (with SLURM or PBS/TORQUE).
+  The user has to specify:
+      > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
+      > The path to source the arch file should be adapted to the machine.
+      > The name of the PCM executable file should be adapted.
+      > The execution command should also be adapted according to the set-up.
 
 # PEMrun.job:
-  Bash script file to submit PEM job (with SLURM or PBS/TORQUE).The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
-  The path to source the arch file should be adapted to the machine.
-  The name of the PEM executable file and Reshaping executable file should be adapted.
-  The PEM executable can have an optional argument which should be specified according to the set-up. Especially, the value of '--jobid' which is the job ID to make the PEM detect the job time limit.
+  Bash script file to submit PEM job (with SLURM or PBS/TORQUE).
+  The user has to specify:
+      > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
+      > The path to source the arch file should be adapted to the machine.
+      > The name of the PEM and Reshaping executable files should be adapted.
+      > The PEM executable can have an optional argument which should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job).
 
 # run_PEM.def