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These instructions can also be found in the *README*. The software needs to be compiled (see [CAXS installation page](/dblain/pytheas/wikis/how-to-install)).
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In this section we will describe how to quickly run an *Exo-REM* simulation. We will use the `inputs/example.nml` coming with all distributed versions of *Exo-REM* as a starting point.
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# Setup
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1. Put [GEISA 2015](http://cds-espri.ipsl.fr/cgi-bin/geisa/geisa2015_format) - formatted lines data of the species of your choice inside the _data/lines_ directory. These data needs to contains **at least** GEISA parameters A to D. If your species name is "speciesName", the lines file needs to be named "speciesName.dat".
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2. Copy the file _data/species/H2O.nml_, rename the copy as _speciesName.nml_ and edit it to suit your needs. ("nml" is the extension used for [Fortran namelists](http://jules-lsm.github.io/vn4.3/namelists/intro.html)).
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3. Edit the file _inputs/input_parameters.nml_ to suit your needs. **Be careful:**
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- `n_levels` must match the number of values of `pressure_space`;
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- if `use_profile_mode` is `True`, `n_levels` must also match the number of values of `temperature_space`;
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- if `use_profile_mode` is `False`, `size_thermospace` must match the number of values of `temperature_space`;
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- `n_species` must match the number of values of `species_names` and `species_vmr`;
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- `species_names` values must be the names used for the _data/lines_ and _data/species_files.
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# Setup for Rey et al. 2017 CH4 lines
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1. Get Rey et al. CH4 lines from [here](http://theorets.tsu.ru/molecules.ch4.hybrid) (both strong lines and weak lines).
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2. Put the lines files inside the _data/lines/CH4_ directory (`mkdir` it if it doesn't exists yet).
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3. Follow the "setup" steps above from step 2. **Be sure to exactly write "CH4" for the _data/species_ file name and for the species name**.
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# Prerequisites
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1. Verify if the collision-induced absorption (CIA) files are inside the _data/cia_ directory. If you want to use other CIA files, respect the same format and use "CIAname.cia.txt" as file name (e.g. "H2-He.cia.txt").
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2. If you intend to use clouds, verify if the cloud optical constants (OCST) files are inside the _data/cloud_optical_constants_ directory. If you want to use other OCST files, respect the same format and use "cloudName.ocst.txt" as file name (e.g. "H2O.ocst.txt").
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3. Put k-coefficients of desired absorbers inside the _data/k_coefficients_tables_ directory. You can use directly *CKC* outputs converted into HDF5 using *txt2h5*, or e.g. *[petitRADTRANS](https://petitradtrans.readthedocs.io/en/latest/content/available_opacities.html)* k-tables. If your absorber name is "absorberName", the lines file needs to be named "absorberName.ktable.exorem.h5" (e.g. H2O.ktable.exorem.h5). You can download compressed *Exo-REM* k-tables [here](https://gitlab.obspm.fr/dblain/exorem/-/tree/master/data/k_coefficients).
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4. If you intend to use stellar spectra, you can download them e.g. [here](http://svo2.cab.inta-csic.es/theory/newov2/index.php?models=bt-settl). You **must** modify them in order to respect the *Exo-REM* data format (see section data format).
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5. Verify if all the condensates and gases thermochemical tables are in the _data/thermochemical_tables_ directory. If you want to add more species to the chemical model, respect the same format and use "speciesName.tct.dat" as file name (e.g. "H2O.tct.dat").
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6. Put a temperature profile as a priori inside the _inputs/atmospheres/temperature_profiles_ directory. The *Exo-REM* data format must be respected. You should have received an example of such a file with your *Exo-REM* distribution.
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# Running CAXS
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1. Open a terminal.
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2. `cd` yourself into CAXS' _bin_ directory.
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3. Launch the calculations by executing (replace `X` by the number of processes you want to use):
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```bash
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mpiexec -np X caxs.exe
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```
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Alternatively, if you want to use only 1 process, you can execute (you still need to have OpenMPI installed):
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```bash
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./caxs.exe
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```
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4. By default, at the end of the calculations, the results are stored in the _outputs_ directory. |
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\ No newline at end of file |
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# Setup
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7. Copy and edit the file _inputs/example.nml_ to suit your needs. **Be careful:**
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- `n_cia` must match the number of values of `cia_names`;
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- `n_species` must match the number of values of `species_names` **and** `species_mode`;
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- `n_clouds` must match the number of values of all the cloud parameters **except** `cloud_mode` and `clouf_fraction`;
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- `species_names` and `cia_names` values must be the names used for the _data/cia_ and _data/k_coefficients_tables_ files. |
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\ No newline at end of file |