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

@@ -14,7 +14,7 @@ CONTENTS
 [Specification of NCCM parameters](3.2-User-interfaces#specification-of-NCCM-parameters)  
 [User-controllable macros](3.2-User-interfaces#user-controllable-macros)
 
-### Overview
+## Overview
 
 User interfaces are certain code modules in order to generate and
 customize a simulation problem. There are three different types of user
@@ -69,7 +69,7 @@ necessary for a problem setup.
 
 -   `User.h` – freely available header file
 
-### Specification of main simulation parameters
+## Specification of main simulation parameters
 
 NIRVANA requires the parameter file `nirvana.par` as input. In this file
 the user specifies main parameters which characterize the properties of
@@ -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))
+        [here](3.3-Output-data#log-file)) and monitoring file
+        `nirvana.mon` (cf. [here](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.
+        [here](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)).
+        [here](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
+        [here](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)).
+            [here](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)).
+        [here](3.2-User-interfaces#user-defined-initial/restricted-mesh)).
         `_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
+        [here](3.1-Code-basics#adaptive-mesh-refinement)). A zero or
         negative value means that the respective component is disabled
         for a mesh refinement check.
 
@@ -426,12 +426,12 @@ 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
+        [here](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.
 
-    -   `_C.amr_dJeans` ( ≥ 0): tuning parameter for the
+    -   `_C.amr_dJeans` (≥0): tuning parameter for the
         Jeans-length-based mesh refinement criterion allowing a
         systematic reduction of the Jeans threshold with increasing
         refinement level *l* according to the expression `_C.amr_Jeans`
@@ -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
+        [here](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.
@@ -546,13 +546,13 @@ for the type of coordinate system.
 
 -   `06` (`_C.heatloss_max_change`)
 
-    -   `_C.heatloss_max_change` (typical value:  ≤ 0.1): maximal
+    -   `_C.heatloss_max_change` (typical value: ≤0.1): maximal
         allowed relative change in temperature due to the heatloss
         source term.
 
 -   `07` (`_C.reactions_max_changeX`, `_C.reactions_max_changeT`)
 
-    -   `_C.reactions_max_changeX` (typical value:  ≤ 0.1): maximal
+    -   `_C.reactions_max_changeX` (typical value: ≤0.1): maximal
         relative change of species number densities (or total number
         density) in the time integration of the chemo-thermal rate
         equations.
@@ -561,7 +561,7 @@ for the type of coordinate system.
         weight in applying the parameter `_C.reactions_max_change` to
         individual number densities and to the total number density.*
 
-    -   `_C.reactions_max_changeT` (typical value:  ≤ 0.1): maximal
+    -   `_C.reactions_max_changeT` (typical value: ≤0.1): maximal
         relative change of temperature in the time integration of the
         chemo-thermal rate equations.
 
@@ -599,8 +599,8 @@ for the type of coordinate system.
 
         *Note: The Gaussian unit system can be mimicked by choosing a
         value
-        `_``C``.``p``e``r``m``e``a``b``i``l``i``t``y``_``r``e``l` = 10<sup>7</sup>
-        so that the magnetic permeability is *μ* = 4*π*.*
+        `_``C.permeability_rel`=10<sup>7</sup>
+        so that the magnetic permeability is *μ*=4*π*.*
 
 -   `02` (`_C.viscosity`, `_C.viscosity_coeff`)
 
@@ -642,7 +642,7 @@ for the type of coordinate system.
         `_C.conduction_coeff_perp` in the anisotropic case) described
         next. The value U enables thermal conduction with a user-defined
         conduction coefficient as coded in the user interface
-        **conductionCoeffUser.c**. The value S refers to the standard
+        `conductionCoeffUser.c`. The value S refers to the standard
         Spitzer conductivity model (cf. physics guide
         [Wiki](https://gitlab.aip.de/ziegler/NIRVANA/-/wikis/A-PhysicsGuide),
         [PDF](https://gitlab.aip.de/ziegler/NIRVANA/doc/pdf/PhysicsGuide.pdf)).
@@ -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))
+            [here](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)).
+            [here](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.*
@@ -753,7 +753,7 @@ for the type of coordinate system.
         freely selectable parameter but is approximated by the
         expression*
 
-        *γ* = \[5(*n*<sub>*H*</sub>+*n*<sub>*H**e*</sub>+*n*<sub>*e*</sub>)+7*n*<sub>*H*<sub>2</sub></sub>\]/\[3(*n*<sub>*H*</sub>+*n*<sub>*H**e*</sub>+*n*<sub>*e*</sub>)+5*n*<sub>*H*<sub>2</sub></sub>\]
+        *γ*=\[5(*n*<sub>*H*</sub>+*n*<sub>*H**e*</sub>+*n*<sub>*e*</sub>)+7*n*<sub>*H*<sub>2</sub></sub>\]/\[3(*n*<sub>*H*</sub>+*n*<sub>*H**e*</sub>+*n*<sub>*e*</sub>)+5*n*<sub>*H*<sub>2</sub></sub>\]
 
     -   `_C.polytropic_constant`: polytropic constant in the polytropic
         EOS.
@@ -771,9 +771,9 @@ for the type of coordinate system.
         [PDF](https://gitlab.aip.de/ziegler/NIRVANA/doc/pdf/PhysicsGuide.pdf)).
         The value U enables the heatloss term assuming a user-defined
         cooling/heating function coded in the interfaces
-        **sourceCoolingUser.c** for cooling and **sourceHeatingUser.c**
+        `sourceCoolingUser.c` for cooling and `sourceHeatingUser.c`
         for heating (cf.
-        \[here\](3.2-User-interfaces\#user-defined-cooling/heating-function)).
+        [here](3.2-User-interfaces#user-defined-cooling/heating-function)).
 
 -   `11` (`_C.tracer`)