Tool Box Mars PEM - Revision history

Jbclement at 09:23, 4 March 2026

2026-03-04T09:23:36Z

Jbclement at 09:48, 3 March 2026

2026-03-03T09:48:11Z

Jbclement at 17:15, 26 February 2026

2026-02-26T17:15:28Z

Jbclement at 09:53, 24 October 2025

2025-10-24T09:53:12Z

Jbclement: /* Merging the PEM outputs (post-processing) */

2025-10-23T15:11:15Z

‎Merging the PEM outputs (post-processing)

Jbclement: /* Merging the PEM outputs (post-processing) */

2025-10-23T14:52:53Z

‎Merging the PEM outputs (post-processing)

Jbclement at 14:52, 23 October 2025

2025-10-23T14:52:26Z

Jbclement: /* Initialization of orbital parameters (pre-processing) */

2025-07-21T12:16:37Z

‎Initialization of orbital parameters (pre-processing)

Jbclement: /* Setting the orbital parameters (pre-processing) */

2025-07-21T12:15:42Z

‎Setting the orbital parameters (pre-processing)

Jbclement: /* Setting a variable in a NetCDF file (pre-processing) */

2025-07-21T12:14:09Z

‎Setting a variable in a NetCDF file (pre-processing)

@@ Line 8: / Line 8: @@
 * <code>modify_startfi_var.sh </code>
 * <code>multiple_exec.sh </code>
 * <code>visu_layering.py </code>
 The purpose of these tools is described in the sections below. Their usage is quite straightforward and all the parameters to be modified by the user are always gathered at the beginning of the file, in the header, with short explanations.
@@ Line 41: / Line 41: @@
 The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the ''diagevo'' files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
-=== Layering visualization over time ===
+=== Layering visualization ===
-The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the ''startevo.nc'' files.
+The Python script file <code>visu_layering.py</code> outputs the stratification data from the ''startevo.nc'' files.
-=== Layering visualization ===
+=== Layering visualization over time ===
-The Python script file <code>visu_layering.py</code> outputs the stratification data from the ''startevo.nc'' files.
+The Python script file <code>visu_layering_evo.py</code> outputs the stratification data over time from the ''startevo.nc'' files.
 [[Category:Planetary-Evolution-Model]]

@@ Line 39: / Line 39: @@
 === Merging the PEM outputs ===
-The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the ''diagpem'' files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
+The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the ''diagevo'' files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
 === Layering visualization over time ===
-The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the ''startpem.nc'' files.
+The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the ''startevo.nc'' files.
 === Layering visualization ===
-The Python script file <code>visu_layering.py</code> outputs the stratification data from the ''startpem.nc'' files.
+The Python script file <code>visu_layering.py</code> outputs the stratification data from the ''startevo.nc'' files.
 [[Category:Planetary-Evolution-Model]]

@@ Line 4: / Line 4: @@
 * <code>clean.sh </code>
 * <code>concat_pem.py </code>
-* <code>inipem_orbit.sh </code>
+* <code>ini_pem_orbit.sh </code>
 * <code>modify_startfi_orbit.sh </code>
 * <code>modify_startfi_var.sh </code>
@@ Line 21: / Line 21: @@
 === Initialization of orbital parameters ===
-The bash script file <code>inipem_orbit.sh</code> sets the orbital parameters of a file ''startfi.nc'' from Laskar's data contained in ''obl_ecc_lsp.asc'' according to the initial date 'year_earth_bp_ini' defined in ''run_PEM.def''. See also <code>modify_startfi_orbit.sh</code>.
+The bash script file <code>ini_pem_orbit.sh</code> sets the orbital parameters of a file ''startfi.nc'' from Laskar's data contained in ''obl_ecc_lsp.asc'' according to the initial date 'year_earth_bp_ini' defined in ''run_PEM.def''. See also <code>modify_startfi_orbit.sh</code>.
 === Setting the orbital parameters ===
-The bash script file <code>modify_startfi_orbit.sh</code> allows 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 <code>inipem_orbit.sh</code>.
+The bash script file <code>modify_startfi_orbit.sh</code> allows 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 <code>ini_pem_orbit.sh</code>.
 === Setting a variable in a NetCDF file ===

@@ Line 13: / Line 13: @@
 The purpose of these tools is described in the sections below. Their usage is quite straightforward and all the parameters to be modified by the user are always gathered at the beginning of the file, in the header, with short explanations.
-== Cleaning of files (post-processing) ==
+== Pre-processing ==
 The bash script file <code>clean.sh</code> cleans the folder after a PEM simulation and reset the initial starting files to prepare a new simulation.
-== Merging the PEM outputs (post-processing) ==
+=== Initialization of orbital parameters ===
-The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the "diagpem" files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
+=== Setting the orbital parameters ===
-== Initialization of orbital parameters (pre-processing) ==
+The bash script file <code>modify_startfi_orbit.sh</code> allows 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 <code>inipem_orbit.sh</code>.
-The bash script file <code>inipem_orbit.sh</code> sets the orbital parameters of a file "startfi.nc" from Laskar's data contained in "obl_ecc_lsp.asc" according to the initial date 'year_earth_bp_ini' defined in "run_PEM.def". See also <code>modify_startfi_orbit.sh</code>.
+=== Setting a variable in a NetCDF file ===
-== Setting the orbital parameters (pre-processing) ==
+The bash script file <code>modify_startfi_var.sh</code> modifies the value of a variable in a file ''startfi.nc''.
-The bash script file <code>modify_startfi_orbit.sh</code> allows 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 <code>inipem_orbit.sh</code>.
+=== Lauching multiple simulations ===
-== Setting a variable in a NetCDF file (pre-processing) ==
+The bash script <code>modify_startfi_var.sh</code> executes multiple scripts in subdirectories. It is useful to launch multiple simulations at once.
-The bash script file <code>modify_startfi_var.sh</code> modifies the value of a variable in a file "startfi.nc".
+== Post-processing ==
-== Lauching multiple simulations (pre-processing) ==
+=== Merging the PEM outputs ===
-The bash script <code>modify_startfi_var.sh</code> executes multiple scripts in subdirectories. It is useful to launch multiple simulations at once.
+The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the ''diagpem'' files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
-== Layering visualization overged time (post-processing) ==
+=== Layering visualization over time ===
-The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the "startpem.nc" files.
+The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the ''startpem.nc'' files.
-== Layering visualization (post-processing) ==
+=== Layering visualization ===
-The Python script file <code>visu_layering.py</code> outputs the stratification data from the "startpem.nc" files.
+The Python script file <code>visu_layering.py</code> outputs the stratification data from the ''startpem.nc'' files.
 [[Category:Planetary-Evolution-Model]]

@@ Line 19: / Line 19: @@
 == Merging the PEM outputs (post-processing) ==
-The Python script <code>concat_pem.sh</code> allows to concatenate along the variable 'Time' all the "diagpem" files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
+The Python script <code>concat_pem.py</code> allows to concatenate along the variable 'Time' all the "diagpem" files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.
 == Initialization of orbital parameters (pre-processing) ==