Changeset 4072 for trunk/LMDZ.COMMON/libf/evolution/deftank/README

Timestamp:

Feb 16, 2026, 11:41:37 AM (3 weeks ago)

Author:

jbclement

Message:

PEM:
Modify the PEM semantics to standardize file/functions/variable names and avoid ambiguity: workflow = repetion of cycles; cycle = PCM phase + PEM phase; PCM phase = 2+ PCM runs of 1 year each, PEM phase = 1 PEM run of 'x' years.
JBC

File:

• trunk/LMDZ.COMMON/libf/evolution/deftank/README (modified) (9 diffs)

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

@@ -1 @@
-   *    .          .   +     .    *        .  +      .    .       .      
-            +         _______  ________  ____    ____      *           + 
+   *    .          .   +     .    *        .  +      .    .       .
+            +         _______  ________  ____    ____      *           +
   +   .        *     |_   __ \|_   __  ||_   \  /   _|          .       *
-           .     .     | |__) | | |_ \_|  |   \/   |  *        *      .  
-        .              |  ___/  |  _| _   | |\  /| |      .        .     
- .  *          *      _| |_    _| |__/ | _| |_\/_| |_                  * 
-             +       |_____|  |________||_____||_____|   +     .         
+           .     .     | |__) | | |_ \_|  |   \/   |  *        *      .
+        .              |  ___/  |  _| _   | |\  /| |      .        .
+ .  *          *      _| |_    _| |__/ | _| |_\/_| |_                  *
+             +       |_____|  |________||_____||_____|   +     .
    .      *          .   *       .   +       *          .        +      .
 
-   
+
 This folder contains all the files needed to run and work with the Planetary Evolution Model (PEM).
 
@@ -24 +24 @@
 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 Mars planet physics package; 
+    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 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
@@ -31 +31 @@
 Usage:
 ------
-To run a PEM simulation, do: ./launchPEM.sh [options]
+To run a PEM simulation, do: ./pem_workflow.sh [options]
 Options:
     1) None: to start a simulation from scratch;
-    2) 're': to relaunch a simulation from a starting point (interactive prompt).
+    2) 're': to resume 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.
+The Bash file ''pem_workflow.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:
@@ -46 +46 @@
       /!\ 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 necessary PEM files: "pem_workflow.sh", "pem_workflow_lib.sh", "pcm_run.job", "pem_run.job", "run_PEM.def" and "obl_ecc_lsp.asc";
     > the optional PEM files: "diagevol.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM.
 
@@ -52 +52 @@
 
 Before a simulation, you have to set up some parameters/options in:
-    > "launchPEM.sh";
-    > "PCMrun.job";
-    > "PEMrun.job";
+    > "pem_workflow.sh";
+    > "pcm_run.job";
+    > "pem_run.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".
+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 "ini_pem_orbit.sh" can do it automatically with "obl_ecc_lsp.asc".
 
 Outputs:
@@ -63 +63 @@
     > the usual outputs of the PCM: "restartfi.nc", "restart.nc", "diagfi.nc", etc;
     > the XIOS outputs of the PCM: "Xoutdaily4pem*.nc"/"Xoutyearly4pem*.nc";
-    > the outputs of the chained simulation: "launchPEM.log", "launchPEM.info" and possibly "kill_launchPEM.sh";
+    > the outputs of the chained simulation: "pem_workflow.log", "pem_workflow.sts" and possibly "kill_pem_workflow.sh";
     > the usual outputs of the PEM: "restartfi.nc", "restart.nc"/"restart1D.txt" and "diagevol.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.
+If you run a simulation by submitting jobs, the script "kill_pem_workflow.sh" is automatically generated. It can be used to kill the jobs related to your chained simulation in the queue of the job scheduler.
 
 Deftank files:
 --------------
-# launchPEM.sh:
+# pem_workflow.sh:
   Bash script file to launch the chained simulation of PEM and PCM runs.
   The user has to specify:
       > n_mars_years, n_earth_years -> the number of Mars/Earth years to be simulated in total (> 0);
-      > nPCM_ini -> the number of initial PCM years (>= 2);
-      > nPCM -> the number of PCM years between each PEM run (>= 2, usually 2);
-      > 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.
+      > n_pcm_runs_ini -> the number of initial PCM years (>= 2);
+      > n_pcm_runs -> the number of PCM years between each PEM run (>= 2, usually 2);
+      > exec_mode -> the execution 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) None: to start a simulation from scratch;
-      2) 're': to relaunch a simulation from a starting point (interactive prompt).
+      2) 're': to resume a simulation from a starting point (interactive prompt).
 
-# liblaunchPEM.sh:
-  Library of bash functions used by the PEM launching script "launchPEM.sh".
+# pem_workflow_lib.sh:
+  Library of bash functions used by the PEM workflow script "pem_workflow.sh".
 
-# PCMrun.job:
+# pcm_run.job:
   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 headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" execution 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:
+# pem_run.job:
   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 headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" execution 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 should be adapted.
@@ -101 +101 @@
 
 # run_PEM.def
-  All the possible parameters to define a PEM run (read in "conf_pem.F90").
-  It needs to be included in "run_PCM.def" with "INCLUDEDEF=run_PEM.def".
+  All the possible parameters to define a PEM run (read in "config.F90").
+  It needs to include in "run_PCM.def" with "INCLUDEDEF=run_PEM.def".
 
 # obl_ecc_lsp.asc [default], obl_ecc_lsp_pos.asc [future years]
@@ -108 +108 @@
 
 # modify_startfi_orbit.sh:
-  Bash script file to modify orbital parameters in the file "startfi.nc". They should be consistent with Laskar's data in "obl_ecc_lsp.asc" at the same date if orbital parameters are meant to vary during the simulation. See also "inipem_orbit.sh".
+  Bash script file to modify orbital parameters in the file "startfi.nc". They should be consistent with Laskar's data in "obl_ecc_lsp.asc" at the same date if orbital parameters are meant to vary during the simulation. See also "ini_pem_orbit.sh".
 
 # modify_startfi_var.sh:
   Bash script file to modify the value of a variable in a file "startfi.nc".
 
-# inipem_orbit.sh:
+# ini_pem_orbit.sh:
   Bash script file to set the orbital parameters of a file "startfi.nc" from Laskar's data contained in "obl_ecc_lsp.asc" according to the initial date 'pem_ini_earth_date' defined in "run_PEM.def". See also "modify_startfi_orbit.sh".
 
@@ -128 +128 @@
   Python script file to output the stratification data from the "startpem.nc" files.
 
-# visu_evol_layering.py:
+# visu_layering_evol.py:
   Python script file to output the stratification data over time from the "startpem.nc" files.