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docs/source/overview/running.rst

@@ -30,7 +30,7 @@ This is a two step process:
 
 
 Inherit |EKO| or grids from Existing Theory
-"""""""""""""""""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""""""""
 
 You can reuse the |EKO| from a different theory by running::
 
@@ -62,69 +62,70 @@ Generating FONLL FK Tables
 --------------------------
 
 In order to generate FK tables with (numerical) |FONLL| the different flavor schemes
-need to be evolved separately and joined together in a single FK table only 
-in the final step. 
+need to be evolved separately and joined together in a single FK table only
+in the final step.
 
-There are 2 workflows possible, one in which all the steps are performed individually 
-and one that is more automatize. 
+There are 2 workflows possible, one in which all the steps are performed individually
+and one that is more automatize.
 
 The automatize workflows always assumes that |FONLL| is performed both for
 charm and bottom effects.
 
 The manual procedure works as follow:
 
-  1. Generate 7 theories for all the different flavor patches with command:
+  1. Generate 7 theories for all the different flavor patches with command::
 
       pineko fonll_tcards THEORY_ID
 
     The different flavor patches are named following the convention:
 
-      * THEORY_ID00 : |FFNS| :math:`n_f=3`
-      * THEORY_ID01 : |FFN0| :math:`n_f=3`
-      * THEORY_ID02 : massless component of |FFNS| :math:`n_f=4`
-      * THEORY_ID03 : massive component of |FFNS| :math:`n_f=4`
-      * THEORY_ID05 : massless component of |FFNS| :math:`n_f=5`
-      * THEORY_ID06 : massive component of |FFNS| :math:`n_f=5`
-    
+      * ``THEORY_ID00`` : |FFNS| :math:`n_f=3`
+      * ``THEORY_ID01`` : |FFN0| :math:`n_f=3`
+      * ``THEORY_ID02`` : massless component of |FFNS| :math:`n_f=4`
+      * ``THEORY_ID03`` : massive component of |FFNS| :math:`n_f=4`
+      * ``THEORY_ID05`` : massless component of |FFNS| :math:`n_f=5`
+      * ``THEORY_ID06`` : massive component of |FFNS| :math:`n_f=5`
+
     where for |FFNS| :math:`n_f=4,5` massive and massless parts are splitted to
     allow for a damping option.
 
   2. Generate the grids corrisponding to all the 7 theories with the external program.
-  
+
   3. Generate the operator cards for each theory with the usual command.
-  4. Generate the ekos for each theory with the usual commands.
-     Note that in principle only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
+     Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
      So you might speed up the procedure taking advantage of inherit-ekos.
-
+
+  4. Generate the ekos for each theory with the usual commands.
+
   5. Generate the FK tables each of the 7 theories with the usual commands.
 
-  6. Combine the various FK tables into a single file, using the command:
+  6. Combine the various FK tables into a single file, using the command::
 
       pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
 
-    where the first 3 theories are needed to perform |FONLL| on charm effects, 
+    where the first 3 theories are needed to perform |FONLL| on charm effects,
     while the last 4 are needed to include also bottom effects.
 
-The automatize procedure can be faster, but it might be less
-flexible. In this case the workflows is:
+The automatize procedure can be faster, but it might be less flexible.
+In this case the workflows is:
 
-  1. Generate 7 theories for all the different flavor patches with command:
+  1. Generate 7 theories for all the different flavor patches with the command::
 
       pineko fonll_tcards THEORY_ID
-    
-    See above for the naming convention
-  
+
+    See above for the intermediate theories naming convention.
+
   2. Generate the grids corrisponding to all the 7 theories with the external program.
 
-  3. Generate the ekos for only 3 theories and inherit the others using the command:
+  3. Generate the ekos for only 3 theories and inherit the others running::
 
       pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
 
-    Note: this is usually an expensive operation as multiple ekos are run sequentially. 
+    Note: this is usually an expensive operation as multiple ekos are run sequentially.
     Depending on the resources that you have available it might be more convinient
     to call the command separately for each DATASET.
-  
-  4. Generate the final |FONLL| FK table directly using:
+
+  4. Generate the final |FONLL| FK table directly running::
 
       pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...