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

@@ -78,19 +78,19 @@ with category names
 
 -   **SIMULATION I/O** – I/O-related parameter
 
--   `GEOMETRY` – selection of the coordinate system
+-   **GEOMETRY** – selection of the coordinate system
 
--   `DOMAIN SETTINGS` – physical/numerical domain specifications
+-   **DOMAIN SETTINGS** – physical/numerical domain specifications
 
--   `BOUNDARY CONDITIONS` – selection of boundary conditions
+-   **BOUNDARY CONDITIONS** – selection of boundary conditions
 
--   `MESH REFINEMENT` – AMR-related parameters
+-   **MESH REFINEMENT** – AMR-related parameters
 
--   `USER-SPECIFIC PARAMETERS` – freely usuable parameter
+-   **USER-SPECIFIC PARAMETERS** – freely usuable parameter
 
--   `SOLVER SPECIFICATIONS` – selection of solver options
+-   **SOLVER SPECIFICATIONS** – selection of solver options
 
--   `PHYSICS SPECIFICATIONS` – selection of physics options
+-   **PHYSICS SPECIFICATIONS** – selection of physics options
 
 A parameter section starts with its category name preceded by the
 `>`-character. The associated parameters follow in lines where a line
@@ -121,7 +121,7 @@ variable named `_C` defined in the header `nirvana.h`. A certain
 variable `V` in `_C` is then addressed by `_C.V`, e.g., `_C.geometry`
 for the type of coordinate system.
 
-`SIMULATION I/O`:
+**SIMULATION I/O**:
 
         >SIMULATION I/O ----------------------------------------------------------------
     01   NEW  ./MODLAST                                >mode:{NEW,RES,MOD,ANA},fname
@@ -186,7 +186,7 @@ for the type of coordinate system.
         [here](3.3-Output-data#snapshot-files)) is renewed
         overwriting existing older files.
 
-`GEOMETRY`:
+**GEOMETRY**:
 
         >GEOMETRY ----------------------------------------------------------------------
     01   CART  0.00e+00  0.00e+00  0.00e+00      >geometry,omega[0-2]
@@ -205,7 +205,7 @@ for the type of coordinate system.
         component `_C.omega[0]` is accepted as relevant representing
         rotation around the geometric axis.
 
-`DOMAIN SETTINGS`:
+**DOMAIN SETTINGS**:
 
         >DOMAIN SETTINGS ---------------------------------------------------------------
     01    0.000000e+00  6.280000e+00  0160       >lo[0],up[0],dim[0] 
@@ -262,7 +262,7 @@ for the type of coordinate system.
         the number of MPI threads, i.e.
         `_C.bnx`×`_C.bny`×`_C.bnz`=number of MPI threads.
 
-`BOUNDARY CONDITIONS`:
+**BOUNDARY CONDITIONS**:
 
         >BOUNDARY CONDITIONS -----------------------------------------------------------
     01  PPPPPP                                   >bc[0-5]:{I,O,A,M,R,C,P,D,F,U}
@@ -351,7 +351,7 @@ for the type of coordinate system.
         -   `U`: user-defined boundary conditions (cf.
             [here](3.2-User-interfaces#defining-boundary-conditions)).
 
-`MESH REFINEMENT`:
+**MESH REFINEMENT**:
 
         >MESH REFINEMENT ---------------------------------------------------------------
     01    0  2                                         >imr,amr
@@ -448,7 +448,7 @@ for the type of coordinate system.
         be resolved by at least one grid cell. A zero or negative value
         means that the Field-length-based criterion is disabled.
 
-`USER-SPECIFIC PARAMETERS`:
+**USER-SPECIFIC PARAMETERS**:
 
         >USER-SPECIFIC PARAMETERS ------------------------------------------------------
     01   0.00000e+00  0.00000e+00  0.00000e+00   >param[0-2] /
@@ -470,7 +470,7 @@ for the type of coordinate system.
 
     -   `_C.flag[0-7]`: freely usable parameter of `int` type.
 
-`SOLVER SPECIFICATIONS`:
+**SOLVER SPECIFICATIONS**:
 
         >SOLVER SPECIFICATIONS ---------------------------------------------------------
     01   RK3 CU CCT 5.0e-01                      >mhd_solver_{time,flux,ef},mhd_courant
@@ -569,7 +569,7 @@ for the type of coordinate system.
 
     -   `_C.dt0_reduce`: reduction factor of the first timestep.
 
-`PHYSICS SPECIFICATIONS`:
+**PHYSICS SPECIFICATIONS**:
 
         >PHYSICS SPECIFICATIONS --------------------------------------------------------
     01   Y  7.94e+05                             >mf,permeability_rel
@@ -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.
-        [here](3.2-User-interfaces#user-defined-cooling/heating-function)).
+        [User-defined cooling/heating function](3.2-User-interfaces#user-defined-cooling/heating-function)).
 
 -   `11` (`_C.tracer`)
 
@@ -842,7 +842,7 @@ considered primary.
 The mesh is represented by the master mesh pointer `gm` which is the
 only argument passed to function `configUser()`. The problem-relevant
 variables have to be assigned for each superblock `g` in `gm`. Recall
-the explanations about the [mesh data
+in this context the explanations about the [mesh data
 structure](3.1-Code-basics\#mesh-data-structure).
 
 There are two types of primary variables: cell-averaged variables and
@@ -1209,7 +1209,7 @@ cells otherwise.
 There are a number of predefined BC types (standard BC) which can be
 selected in the parameter interface `nirvana.par` under category
 BOUNDARY CONDITION. There, standard types are specified by letters
-{I,O,D,M,A,R,C,F,P}.
+{I,O,D,M,A,R,C,F,P} (cf. [Specification of main simulation parameters](3.2-User-interfaces#specification-of-main-simulation-parameters)). 
 
 #### User-defined BC
 
@@ -1337,7 +1337,7 @@ coefficient can be found in testproblem
 `/nirvana/testproblems/VISC/problem1`.
 
 User-defined viscosity is enabled by appropriate choice in the parameter
-interface `nirvana.par` under the category `PHYSICS SPECIFICATIONS`
+interface `nirvana.par` under the category PHYSICS SPECIFICATIONS
 (code parameter: `_C.viscosity`).
 
 #### Thermal conduction
@@ -1386,7 +1386,7 @@ conduction coefficient *κ* in the isotropic heat flux
 
 User-defined thermal conduction is enabled by appropriate choice in the
 parameter interface `nirvana.par` under the category
-`PHYSICS SPECIFICATIONS` (code parameter: `_C.conduction`).
+PHYSICS SPECIFICATIONS (code parameter: `_C.conduction`).
 
 #### Ohmic diffusion
 
@@ -1421,7 +1421,7 @@ evaluated at cell-centroid coordinates
 
 User-defined Ohmic diffusion is enabled by appropriate choice in the
 parameter interface `nirvana.par` under the category
-`PHYSICS SPECIFICATIONS` (code parameter: `_C.diffusion`).
+PHYSICS SPECIFICATIONS (code parameter: `_C.diffusion`).
 
 ## User-defined coefficient for ambipolar diffusion
 
@@ -1465,7 +1465,7 @@ ambipolar diffusion coefficient can be found in testproblem
 
 User-defined ambipolar diffusion is enabled by appropriate choice in the
 parameter interface `nirvana.par` under the category
-`PHYSICS SPECIFICATIONS` (code parameter: `_C.APdiffusion`).
+PHYSICS SPECIFICATIONS (code parameter: `_C.APdiffusion`).
 
 ## User-defined body force
 
@@ -1503,7 +1503,7 @@ for a body force can be found in testproblem
 `/nirvana/testproblems/MHD/problem21`.
 
 The body force is enabled by specification in the parameter interface
-`nirvana.par` under the category `PHYSICS SPECIFICATIONS` (code
+`nirvana.par` under the category PHYSICS SPECIFICATIONS (code
 parameter: `_C.force`).
 
 ## User-defined cooling/heating function
@@ -1557,7 +1557,7 @@ testproblem `/nirvana/testproblems/HEATLOSS/problem2`.
 
 User-defined cooling/heating is enabled by appropriate choice in the
 parameter interface `nirvana.par` under the category
-`PHYSICS SPECIFICATIONS` (code parameter: `_C.heatloss`).
+PHYSICS SPECIFICATIONS (code parameter: `_C.heatloss`).
 
 ## User-defined equation of state
 
@@ -1720,7 +1720,7 @@ table `_TABLT`.
 `TDeos()` in module `utilTD.c` and in the numerical procedure.*
 
 A tabulated EOS is enabled by appropriate choice in the parameter
-interface `nirvana.par` under category `PHYSICS SPECIFICATIONS` (code
+interface `nirvana.par` under category PHYSICS SPECIFICATIONS (code
 paramter: `_C.eos`).
 
 ## User-defined initial/restricted mesh refinement
@@ -1840,16 +1840,16 @@ The parameter file `NCCM.par` serves as user interface to the
 multi-species framework/NCCM. `NCCM.par` is grouped into the category
 sections
 
--   `SPECIES SPECIFICATION` – selection of species.
+-   **SPECIES SPECIFICATION** – selection of species.
 
--   `REACTIONS SPECIFICATION` – selection of chemical reactions.
+-   **REACTIONS SPECIFICATION** – selection of chemical reactions.
 
--   `THERMAL PROCESSES SPECIFICATION` – selection of microphysical
+-   **THERMAL PROCESSES SPECIFICATION** – selection of microphysical
     thermal processes.
 
 A section starts with the category name preceded by the ’`>`’-character.
 
-:
+**SPECIES SPECIFICATION**:
 
     >SPECIES SPECIFICATION ---------------------------------------------------------
     > LABEL      H__D__He_C__N__O__Ne_Mg_Si_Fe   CHARGE  MASSFRAC
@@ -1897,7 +1897,7 @@ values.*
 *Note 2: A specie electron with label e- is automatically generated by
 the code.*
 
-`REACTIONS SPECIFICATION`:
+**REACTIONS SPECIFICATION**:
 
     >REACTIONS SPECIFICATION -------------------------------------------------------
     > ID   STCOEFF REACTANT [& STCOEFF REACTANT] > STCOEFF PRODUCT [& STCOEFF PRODUCT]
@@ -1938,7 +1938,7 @@ mass conservation as well as the existence of the labels of involved
 species. This rection check can be disabled by setting the macro
 `CHECK_REACTIONS` to `NO` in `nirvanaUser.h`.*
 
-`THERMAL PROCESSES SPECIFICATION`:
+**THERMAL PROCESSES SPECIFICATION**:
 
     >THERMAL PROCESSES SPECIFICATION -----------------------------------------------
     >ON/OFF