find . -name \*.txt -type f -exec /Users/ruess/Downloads/pandoc-2.7.2/bin/pandoc -f mediawiki -t markdown -o {}.md {} \;
then replace all .txt.md files by .txt
and finally run git mv on all .txt files to convert to .md files

fermi_surface/perform_calculations.md

+##### Step-by-step recipe {#step_by_step_recipe}
+
+#### Setting the inputcard and writing out the \$\\mathcal{T}\$-matrix and Green\'s function {#setting_the_inputcard_and_writing_out_the_mathcalt_matrix_and_greens_function}
+
+`   - Create the folder **__fermi__** and copy on it the following files : `*`potential`*`, `*`inputcard`*`, `*`shapefun`*` and `*`kkr.x`*`.`\
+`   - Write-out the t-matrix and Green-function:`\
+`      - Set the running option `*`FERMIOUT`*\
+`      - Set the temperature to 0.00`\
+`      - Increase the cluster size (`*`R_xy`*` and `*`R_z`*`) such that there are at least 300 atoms in the cluster.`\
+`      - Define the energy contour, with only one energy point. e.g `<file>
+
+EMIN EMAX TEMPR NPOL NPT1 NPT2 NPT3 E E 000.0 0 0 1 0 </file> where *E*
+is the energy.
+
+`      - Set `*`STEPS=1`*`.`\
+`    - Run one single iteration : `*`mpirun`` ``-np`` ``XX`` ``kkr.x`*`. Some TBkkr* files should be written out. These files contain the Green function and t-matrix of the system.`
+
+#### Perform the Fermi surface calculation {#perform_the_fermi_surface_calculation}
+
+`  - Create the folder **__surf__** and copy on it the following files : `*`Pkkr.x`*` and `*`__**fermi**__/TBkkr*`*` : ((Some of these files can be quite big. So creating links might be the better idea: e.g. `*`ln`` ``-s`` ``**__fermi__**/TBkkr_*`` ``.`*`))`\
+`  - Set the `[`inputFs`](fermi_surface:inputfs_file "wikilink")` file.`\
+`  - Start the calculation : `*`mpirun`` ``-np`` ``XX`` ``Pkkr.x`*
+
+#### Spin and velocity calculations {#spin_and_velocity_calculations}
+
+Depending on the kind of set for which the calculations are done create
+the folder \*\*\_\_surf\_vis\_\_\*\* (for the visualization set) or
+\*\*\_\_surf\_int\_\_\*\* (for the integration set). The visualization
+set will be treated in this paragraph but all the steps are similar for
+the integration set.
+
+`  - Copy all the content of the **__surf__** folder into the new folder : `*`cp`` ``-r`` ``surf`` ``surf_vis`*\
+`  - Set the `[`inputFS`` ``for`` ``spin`` ``and`` ``velocity`](fermi_surface:inputfs_file_for_spin_and_group_velocity "wikilink")` calculations in **__surf_vis__**.`\
+`  - Start the calculation : `*`mpirun`` ``-np`` ``XX`` ``Pkkr.x`*