This folder contains all the files needed to run the Planetary Evolution Model (PEM).

# launchPEM.sh:
  Bash script file to launch the chained simulation of PEM and PCM runs.
  The user has to specify:
      (i)   n_mars_years, n_earth_years -> the number of Mars/Earth years to be simulated in total;
      (ii)  nPCM_ini -> the number of initial PCM runs (at least 2);
      (iii) nPCM -> the number of PCM runs between each PEM run (usually 2);
      (iv)  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 supercomputer.
  The script can take an argument:
      - If there is no argument, then the script initiates a PEM simulation from scratch.
      - 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. 
  To submit chained jobs, the script works with the job schedulers SLURM and PBS/TORQUE.

# liblaunchPEM.sh:
  Library of bash functions used by the PEM launching script "launchPEM.sh".

# 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 "processiong 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 "processiong 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. This the job ID to make the PEM detect the job time limit.

# 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".

# obl_ecc_lsp.asc
  File describing orbital parameters for Mars from Laskar data. It contains the Earth year and the corresponding obliquity, eccentricity and Ls of perihelion.

# modify_startfi_orbit.sh:
  Bash script file to modify orbital parameters in the file "startfi.nc" (obliquity, eccentricity, Ls perihelion and possibly initial Ls). They should be consistent with Laskar's data in "obl_ecc_lsp.asc" to start a chained simulation at a specific date.

# modify_startfi_var.sh:
  Bash script file to modify the value of a variable in a file "startfi.nc".

# inipem_orbit.sh:
  Bash script file to modify the orbital parameters of a file "startfi.nc" according to the date set in the file "run_PEM.def".

# concat_diagpem.sh:
  Bash script file to concatenate along the variable 'Time' all the "diagpem.nc" files of the PEM into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run.

# clean.sh:
  Bash script file to clean the folder after a PEM simulation.

# multiple_exec.sh:
  Bash script to execute multiple scripts in subdirectories, useful to launch multiple simulations at once.

# visu_layering.py:
  Python script file to output the stratification data from the "startpem.nc" files.

# visu_evol_layering.py:
  Python script file to output the stratification data over time from the "startpem.nc" files.

Note:
  To run the chained simulation, be careful to have:
      (i)   the xml files for XIOS. There should be "iodef.xml", "context_lmdz_physics.xml", "file_def_physics_mars.xml" and "field_def_physics_mars.xml" which can be found in the planetary deftank folder. In "context_lmdz_physics.xml", the line for Xdiurnalave should be activated (enabled=".true.");
      (ii)  the usual def files to run the PCM. "run.def" should be renamed in "run_PCM.def";
      (iii  the starting files ("startfi.nc" and "start.nc"). The former can be modified by "modify_startfi_orbit.sh";
      (iv)  some optional files. For example, "diagfi.def" and "diagpem.def".