3-NIRVANA-user-guide/3.2-User-interfaces.md

@@ -149,7 +149,7 @@ for the type of coordinate system.
         *base* container filename of the snapshot. The base container
         filename is `NIR#` or `NIRLAST#` with `#`=`_C.model` but
         excluding the dot and post-dot container id (cf.
-        \[here\](3.3-Output-data\#snapshot-files)).
+        \[Output data\](3.3-Output-data\#snapshot-files)).
 
 -   `02` (`_C.mod_max`, `_C.time_max`)
 
@@ -168,22 +168,22 @@ for the type of coordinate system.
 
     -   `_C.freq_log`: interval in units of timestep cycles at which the
         NIRVANA log file `nirvana.log` (cf.
-        [here](3.3-Output-data#log-file)) and monitoring file
-        `nirvana.mon` (cf. [here](3.3-Output-data#monitoring-file))
+        [Output data](3.3-Output-data#log-file)) and monitoring file
+        `nirvana.mon` (cf. [Output data](3.3-Output-data#monitoring-file))
         is updated.
 
     -   `_C.freq_nir`: interval in units of timestep cycles at which
         NIRVANA snapshots (cf.
-        [here](3.3-Output-data#snapshot-files)) are produced.
+        [Output data](3.3-Output-data#snapshot-files)) are produced.
 
     -   `_C.freq_ana`: interval in units of timestep cycles at which the
         user interface function `analysisUser()` is called for
         user-specific analysis tasks (cf.
-        [here](3.5-Data-analysis#runtime-data-analysis)).
+        [Data analysis](3.5-Data-analysis#runtime-data-analysis)).
 
     -   `_C.freq_walltime`: interval in seconds at which the special
         snapshot `NIRLAST.#` (cf.
-        [here](3.3-Output-data#snapshot-files)) is renewed
+        [Output data](3.3-Output-data#snapshot-files)) is renewed
         overwriting existing older files.
 
 **GEOMETRY**:
@@ -349,7 +349,7 @@ for the type of coordinate system.
             concerning MPI and AMR.*
 
         -   `U`: user-defined boundary conditions (cf.
-            [here](3.2-User-interfaces#defining-boundary-conditions)).
+            [Defining BC](3.2-User-interfaces#defining-boundary-conditions)).
 
 **MESH REFINEMENT**:
 
@@ -364,7 +364,7 @@ for the type of coordinate system.
 
     -   `_C.imr` (≤`MAXLEVEL`): maximal requested refinement level in a
         user-defined initially refined mesh (cf.
-        [here](3.2-User-interfaces#user-defined-initial/restricted-mesh-refinement)).
+        [User-defined mesh refinement](3.2-User-interfaces#user-defined-mesh-refinement)).
         `_C.imr` cannot be larger than the macro `MAXLEVEL` defined in
         the header file `nirvanaUser.h`.
 
@@ -379,7 +379,7 @@ for the type of coordinate system.
         field strength (`_C.amr_eps[3]`) and tracer variables
         (`_C.amr_eps[4]`) in the derivatives-based mesh refinement
         criterion (cf.
-        [here](3.1-Code-basics#adaptive-mesh-refinement)). A zero or
+        [AMR](3.1-Code-basics#adaptive-mesh-refinement)). A zero or
         negative value means that the respective component is disabled
         for a mesh refinement check.
 
@@ -426,7 +426,7 @@ for the type of coordinate system.
 
     -   `_C.amr_Jeans` (typical value: 0.2): threshold in the
         Jeans-length-based mesh refinement criterion (cf.
-        [here](3.1-Code-basics#adaptive-mesh-refinement)). The value
+        [AMR](3.1-Code-basics#adaptive-mesh-refinement)). The value
         `_C.amr_Jeans` defines the fraction of local Jeans length to be
         resolved by at least one grid cell. A zero or negative value
         means that the Jeans-length-based criterion is disabled.
@@ -443,7 +443,7 @@ for the type of coordinate system.
 
     -   `_C.amr_Field` (typical value: 0.2): threshold in the
         Field-length-based mesh refinement criterion (cf.
-        [here](3.1-Code-basics#adaptive-mesh-refinement)). The value
+        [AMR](3.1-Code-basics#adaptive-mesh-refinement)). The value
         `_C.amr_Field` defines the fraction of the local Field length to
         be resolved by at least one grid cell. A zero or negative value
         means that the Field-length-based criterion is disabled.
@@ -529,7 +529,7 @@ for the type of coordinate system.
 
     -   `_C.viscosity_courant`: CFL-analog number in the expression for
         the fluid viscosity timestep. A typical value in case of STD is
-         < 0.5. Values much larger than 1 are possible in the case of
+         <0.5. Values much larger than 1 are possible in the case of
         RKL.
 
 -   `03` (`_C.diffusion_solver`, `_C.diffusion_courant`)
@@ -595,7 +595,7 @@ for the type of coordinate system.
 
     -   `_C.permeability_rel`: relative magnetic permeability
         *μ*<sub>*r**e**l*</sub>
-        ( = *μ*/*μ*<sub>0</sub>, *μ*<sub>0</sub> = 4*π* ⋅ 10<sup> − 7</sup>`V` ⋅ `m`<sup> − 1</sup> ⋅ `A`<sup> − 1</sup> ⋅ `s`<sup> − 1</sup>).
+        ( = *μ*/*μ*<sub>0</sub>, *μ*<sub>0</sub> = 4*π*⋅10<sup>−7</sup>V⋅m<sup>−1</sup>⋅A<sup>−1</sup>⋅s<sup>−1</sup>).
 
         *Note: The Gaussian unit system can be mimicked by choosing a
         value
@@ -737,11 +737,11 @@ for the type of coordinate system.
 
         -   USER: user-defined analytic EOS. This choice requires the
             specification of special macros (cf.
-            [here](3.2-User-interfaces#user-defined-equation-of-state))
+            [User-defined EOS](3.2-User-interfaces#user-defined-equation-of-state))
 
         -   TAB: user-defined tabulated EOS. This choice requires the
             generation of look-up tables (cf.
-            [here](3.2-User-interfaces#user-defined-equation-of-state)).
+            [User-defined EOS](3.2-User-interfaces#user-defined-equation-of-state)).
 
         *Note: The choice of an isothermal EOS or polytropic EOS is not
         compatible with solving for an energy equation.*
@@ -772,7 +772,7 @@ for the type of coordinate system.
         cooling/heating function coded in the interfaces
         `sourceCoolingUser.c` for cooling and `sourceHeatingUser.c`
         for heating (cf.
-        [User-defined cooling/heating function](3.2-User-interfaces#user-defined-cooling/heating-function)).
+        [User-defined cooling/heating function](3.2-User-interfaces#user-defined-cooling-and-heating-function)).
 
 -   `11` (`_C.tracer`)
 
@@ -836,7 +836,7 @@ components are not allocated in the HD case. Likewise, arrays for
 `_C.tracer`=0 respective `_C.species`=0. Furthermore, derived variables
 like the temperature must not be assigned here. If the TESTFIELDS
 infrastructure is used testfield fluctuation variables,
-**b**<sub>*t*</sub>, *t* = 0, *N*<sub>*t*</sub> − 1, are to be
+**b**<sub>*t*</sub>, *t*=0,*N*<sub>*t*</sub>−1, are to be
 considered primary.
 
 The mesh is represented by the master mesh pointer `gm` which is the