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

@@ -180,7 +180,7 @@ possible values or a numeric range.
 
 -   `01` (`_C.geometry`, `_C.omega[0-2]`)
 
-    -   `_C.geometry` ({CART,CYL,SPH}): choice of coordinate system where
+    -   `_C.geometry` ({CART,CYL,SPH}): choice of coordinate system
         - CART: Cartesian
         - CYL: cylindrical
         - SPH: spherical
@@ -203,32 +203,32 @@ possible values or a numeric range.
 
 -   `01` (`_C.lo[0]`, `_C.up[0]`, `_C.dim[0]`)
 
-    -   `_C.lo[0]`,\_C.up\[0\]: lower,upper **x**-coordinate of the
+    -   `_C.lo[0]`,\_C.up\[0\]: lower,upper x-coordinate of the
         computational domain.
 
     -   `_C.dim[0]`: number of *base-level* grid points in
-        **x**-direction. `_C.dim[0]` must be an integral factor of 4, and
+        x-direction. `_C.dim[0]` must be an integral factor of 4, and
         excludes ghost cells which are automatically added by the code.
 
 -   `02` (`_C.lo[1]`, `_C.up[1]`, `_C.dim[1]`)
 
-    -   `_C.lo[1]`,`_C.up[1]`: lower,upper **y**-coordinate of the
+    -   `_C.lo[1]`,`_C.up[1]`: lower,upper y-coordinate of the
         computational domain. In case of spherical geometry
         ($y\equiv \theta$) `_C.lo[1]`,`_C.up[1]` have to be specified in
         units of $\pi$.
 
     -   `_C.dim[1]`: number of *base-level* grid points in
-        **y**-direction. `_C.dim[1]` must be a multiple factor of 4.
+        y-direction. `_C.dim[1]` must be a multiple factor of 4.
 
 -   `03` (`_C.lo[2]`, `_C.up[2]`, `_C.dim[2]`)
 
-    -   `_C.lo[2]`,`_C.up[2]`: lower,upper **z**-coordinate of the
+    -   `_C.lo[2]`,`_C.up[2]`: lower,upper z-coordinate of the
         computational domain. In case of cylindrical- or spherical
         geometry ($z\equiv \phi$) `_C.lo[2]`,`_C.up[2]` have to be
         specified in units of $\pi$.
 
     -   `_C.dim[2]`: number of *base-level* grid points in
-        **z**-direction. `_C.dim[2]` must be a multiple factor of 4. If
+        z-direction. `_C.dim[2]` must be a multiple factor of 4. If
         `_C.dim[2]`=0 the simulation is assumed 2D, i.e., axisymmetric
         in case of cylindrical- or spherical coordinates.
 
@@ -242,7 +242,7 @@ possible values or a numeric range.
         SFC-decomposition is automatically used instead.
 
     -   `_C.bnx`,`_C.bny`,`_C.bnz`: number of domain subdivisions in
-        **x,y,z**-direction in case \_C.partitioning_type=BLOCK. Numbers
+        x,y,z-direction in case \_C.partitioning_type=BLOCK. Numbers
         must be chosen such that the grid dimension of subdomains is a
         multiple factor of 4 in each coordinate direction. Moreover, the
         total number of subdomains must equal the number of MPI threads,
@@ -259,9 +259,9 @@ possible values or a numeric range.
         conditions. The type of boundary condition at a physical domain
         boundary is characterized by a single capital letter. It are
         grouped in a 6-letters word with the individual letter
-        representing, from left to right, the lower-**x** (`_C.bc[0]`),
-        upper-**x** (`_C.bc[1]`), lower-**y** (`_C.bc[2]`), upper-**y**
-        (`_C.bc[3]`), lower-**z** (`_C.bc[4]`) and upper-**z** (`_C.bc[5]`)
+        representing, from left to right, the lower-x (`_C.bc[0]`),
+        upper-x (`_C.bc[1]`), lower-y (`_C.bc[2]`), upper-y
+        (`_C.bc[3]`), lower-z (`_C.bc[4]`) and upper-z (`_C.bc[5]`)
         domain boundary. Possible boundary condition types are
         ($u_{i/o}$: inner/outer-domain boundary values of a variable
         $u$):
@@ -298,14 +298,14 @@ possible values or a numeric range.
             $u_o=u_i$ for the perpendicular magnetic field component.
 
         -   `R`: reflection-on-axis (only of relevance in cylindrical
-            geometry at the **y**-lower boundary at $R=0$ or in
-            spherical geometry at the **y**-lower/upper boundaries at
+            geometry at the y-lower boundary at $R=0$ or in
+            spherical geometry at the y-lower/upper boundaries at
             $\theta =0,\pi$) - reflecting conditions at the geometric
             axis. Same as M except for the azimutal magnetic field
             component for which $u_o=-u_i$.
 
         -   `C`: reflection-at-center (only of relevance in spherical
-            geometry at the **x**-lower boundary at $r=0$) - reflecting
+            geometry at the x-lower boundary at $r=0$) - reflecting
             conditions at the coordinate center. Same as M except for
             the non-radial magnetic field components for which
             $u_o=-u_i$.
@@ -317,9 +317,9 @@ possible values or a numeric range.
             (pseudo-vacuum condition) for the magnetic field.
 
         -   `F`: free boundary (only of relevance in cylindrical
-            geometry at the **y**-lower boundary at $R=0$ or in
-            spherical geometry at the **y**-lower/upper boundaries at
-            $\theta =0,\pi$ and **x**-lower boundary at $r=0$) -
+            geometry at the y-lower boundary at $R=0$ or in
+            spherical geometry at the y-lower/upper boundaries at
+            $\theta =0,\pi$ and x-lower boundary at $r=0$) -
             'natural' boundary condition at the geometric axis. Boundary
             values are not set explictely but are implicitly given by
             $\pi$-shifted values. Note that when a `F`-type boundary
@@ -578,11 +578,11 @@ possible values or a numeric range.
         from the momentum equation and the induction equation is not
         solved.
 
-    -   `_C.permeability_rel`: relative magnetic permeability $\mu_{rel}$
-        ($=\mu /\mu_0$,$\mu_0 =4\pi\cdot 10^{-7}V\cdot m^{-1}\cdot A^{-1}\cdot s^{-1}$).
+    -   `_C.permeability_rel`: relative magnetic permeability 
+        $\mu_{rel} (=\mu /\mu_0,\,\mu_0 =4\pi\cdot 10^{-7}V\cdot m^{-1}\cdot A^{-1}\cdot s^{-1})$.
 
         **Important:** The Gaussian unit system can be mimicked by
-        choosing a value `_C.permeability_rel` $=10^7$ so that
+        choosing a value `_C.permeability_rel`$=10^7$ so that
         the magnetic permeability is $\mu =4\pi$.
 
 -   `02` (`_C.viscosity`, `_C.viscosity_coeff`)