fermi_surface/perform_calculations.md

-##### Step-by-step recipe {#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}
+## Setting the inputcard and writing out the $`\mathcal{T}`$-matrix and Green's 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>
+   - 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
+```
+EMIN EMAX TEMPR NPOL NPT1 NPT2 NPT3
+E E 000.0 0 0 1 0
+```
+where `E` is the energy.
 
-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.
 
-`      - 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 {#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) file.
+  - Start the calculation : `mpirun -np XX Pkkr.x`
 
-`  - 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}
+#### 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
+the folder **surf\_vis** (for the visualisation set) or
+**surf\_int** (for the integration set). The visualisation
 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`*
+  - 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) calculations in **__surf_vis__**.
+  - Start the calculation : `mpirun -np XX Pkkr.x`