for i in jumu kkrimp kkrnano kkrsusc media playground scattering; do find . -name \*.md -type f -exec sed -i "" "s/$i\:/$i\//" {} \; ;done

scattering/perform_calculations.md

@@ -4,7 +4,7 @@ Before doing the following steps be sure that the Fermi surface
 calculation ( [Fermi surface code : Perform
 calculations](fermi_surface:perform_calculations "wikilink")) is done
 and that the host and impurity systems have converged ( [KKRimp :
-Perform impurity calculations](kkrimp:perform "wikilink")). Even if
+Perform impurity calculations](kkrimp/perform "wikilink")). Even if
 it\'s not necessary, but strongly recommended, you should use the
 folders naming defined in the two above sections.
 
@@ -13,21 +13,21 @@ folders naming defined in the two above sections.
 ### Free propagator : \$G\_0(E)\$ {#free_propagator_g_0e}
 
 ` - Create the folder **__g0__** in **__host_in_host__** : `*`mkdir`` ``-r`` ``host_in_host/g0`*\
-` - Set the **__g0__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering:folder_kkrflex "wikilink")` for **type_calculation**=**g0**`\
+` - Set the **__g0__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering/folder_kkrflex "wikilink")` for **type_calculation**=**g0**`\
 ` - Set the inputcard for a kkrflex calculation in the folder **__g0__** : `[`inputcard`` ``for`` ``kkrflex`](fermi_surface:inputcard_kkrflex "wikilink")` for **type_calculation**=**g0**`\
 ` - Run one iteration : `*`mpirun`` ``-np`` ``1`` ``kkrscatter.exe`*` ((This executable is not yet parallelized))`
 
 ### \$\\mathcal{T}(E)\$ matrix for the given impurity {#mathcalte_matrix_for_the_given_impurity}
 
 ` - Create the folder **__tmat__** in **__imp__** : `*`mkdir`` ``-r`` ``imp/tmat`*\
-` - Set the **__tmat__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering:folder_kkrflex "wikilink")` for **type_calculation**=**tmat**`\
+` - Set the **__tmat__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering/folder_kkrflex "wikilink")` for **type_calculation**=**tmat**`\
 ` - Set the inputcard for a kkrflex calculation in the folder **__tmat__** : `[`inputcard`` ``for`` ``kkrflex`](fermi_surface:inputcard_kkrflex "wikilink")` for **type_calculation**=**tmat**`\
 ` - Run one iteration : `*`mpirun`` ``-np`` ``1`` ``kkrscatter.exe`*` ((This executable is not yet parallelized))`
 
 ### Full Green\'s function : \$G\_{imp}(E)\$ {#full_greens_function_g_impe}
 
 ` - Create the folder **__gimp__** in **__imp__** : `*`mkdir`` ``-r`` ``imp/gimp`*\
-` - Set the **__gimp__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering:folder_kkrflex "wikilink")` for **type_calculation**=**gimp**`\
+` - Set the **__gimp__** folder for a kkrflex calculation : `[`folder`` ``for`` ``kkrflex`](scattering/folder_kkrflex "wikilink")` for **type_calculation**=**gimp**`\
 ` - Set the inputcard for a kkrflex calculation in the folder **__gimp__** : `[`inputcard`` ``for`` ``kkrflex`](fermi_surface:inputcard_kkrflex "wikilink")` for **type_calculation**=**gimp**`\
 ` - Run one iteration : `*`mpirun`` ``-np`` ``1`` ``kkrscatter.exe`*` ((This executable is not yet parallelized))`
 
@@ -36,20 +36,20 @@ folders naming defined in the two above sections.
 ### Compute the transition rate {#compute_the_transition_rate}
 
 ` - Create the folder **__scattering__** in **__imp__** : `*`mkdir`` ``-r`` ``imp/scattering`*\
-` - Set the **__scattering__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering:folder_pkkr "wikilink")` for **type_calculation=scattering**`\
-` - Set the inputFS file for a Pkkr calculation in the folder **__scattering__** : `[`inputFS`` ``for`` ``scattering`](scattering:inputFS_pkkr "wikilink")` for **type_calculation=scattering**`\
+` - Set the **__scattering__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering/folder_pkkr "wikilink")` for **type_calculation=scattering**`\
+` - Set the inputFS file for a Pkkr calculation in the folder **__scattering__** : `[`inputFS`` ``for`` ``scattering`](scattering/inputFS_pkkr "wikilink")` for **type_calculation=scattering**`\
 ` - Run one iteration : `*`./Pkkr.x`*` `
 
 ### Compute the life time and conductivity {#compute_the_life_time_and_conductivity}
 
 ` - Here the calculations are done in the same folder **__scattering__** since this step requires output files from the previous one.`\
-` - Set the **__scattering__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering:folder_pkkr "wikilink")` for **type_calculation=lifeT_cond**`\
-` - Set the inputFS file for a Pkkr calculation in the folder **__scattering__** : `[`inputFS`` ``for`` ``scattering`](scattering:inputFS_pkkr "wikilink")` for **type_calculation=lifeT_cond**`\
+` - Set the **__scattering__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering/folder_pkkr "wikilink")` for **type_calculation=lifeT_cond**`\
+` - Set the inputFS file for a Pkkr calculation in the folder **__scattering__** : `[`inputFS`` ``for`` ``scattering`](scattering/inputFS_pkkr "wikilink")` for **type_calculation=lifeT_cond**`\
 ` - Run one iteration : `*`./Pkkr.x`*` `
 
 ### Compute the JDOS, \$\\gamma\$-JDOS and exJDOS {#compute_the_jdos_gamma_jdos_and_exjdos}
 
 ` - Create the folder **__jdos__** in **__imp__** : `*`mkdir`` ``-r`` ``imp/jdos`*\
-` - Set the **__jdos__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering:folder_pkkr "wikilink")` for **type_calculation=jdos**`\
-` - Set the inputFS file for a Pkkr calculation in the folder **__jdos__** : `[`inputFS`` ``for`` ``scattering`](scattering:inputFS_pkkr "wikilink")` for **type_calculation=jdos**`\
+` - Set the **__jdos__** folder for Pkkr calculations : `[`folder`` ``for`` ``scattering`](scattering/folder_pkkr "wikilink")` for **type_calculation=jdos**`\
+` - Set the inputFS file for a Pkkr calculation in the folder **__jdos__** : `[`inputFS`` ``for`` ``scattering`](scattering/inputFS_pkkr "wikilink")` for **type_calculation=jdos**`\
 ` - Run one iteration : `*`./Pkkr.x`*` `