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

@@ -1912,11 +1912,15 @@ species. The following species are currently contained:
 
 -   chemical elements H, D, He, C, N, O, Ne, Mg, Si, Fe and their ions
 
--   negatively charged elements H$^-$, C$^-$, O$^-$
+-   negatively charged elements H<sup>-</sup>, C<sub>-</sup>, O<sup>-</sup>
 
--   molecules H$_2$, H$_2$+, H$_3^+$, HD, O$_2$, C$_2$, O$_2^+$, CH,
-    CH$^+$, CH$_2$, CH$_2^+$, CH$_3^+$, OH, OH$^+$, CO, CO$^+$, H$_2$O,
-    H$_2$O$^+$, H$_3$O$^+$, HCO$^+$ and HOC$^+$
+-   molecules H<sub>2</sub>, H<sub>2</sub><sup>+</sup>, 
+    H<sub>3</sub><sup>+</sup>, HD, O<sub>2</sub>, C<sub>2</sub>, 
+    O<sub>2</sub><sup>+</sup>, CH, CH<sup>+</sup>, CH<sub>2</sub>, 
+    CH<sub>2</sub><sup>+</sup>, CH<sub>3</sub><sup>+</sup>, OH, 
+    OH<sup>+</sup>, CO, CO<sup>+</sup>, H<sub>2</sub>O,
+    H<sub>2</sub>O<sup>+</sup>, H<sub>3</sub>O<sup>+</sup>, 
+    HCO<sup>+</sup> and HOC<sup>+</sup>
 
 Each species is defined by a unique label `LABEL` (eg., He+, Fe+16,
 HOC+), its chemical signature (H\_\_D\_\_He_C\_\_N\_\_O\_\_Ne_Mg_Si_Fe),
@@ -1961,7 +1965,7 @@ grouped into the following categories:
 
 -   subnetworks for the ionization structure of each element
 
--   subnetworks for H$_2$ formation and HD formation
+-   subnetworks for H<sub>2</sub> formation and HD formation
 
 -   C-bearing and O-bearing chemical cycles
 
@@ -2021,7 +2025,7 @@ NCCM currently includes the following processes:
 -   fine-structure line cooling of the metals C, N, O, Ne, Mg, Si and Fe
 
 -   chemical-, rotovibrational line- and collision-induced cooling of
-    H$_2$
+    H<sub>2</sub>
 
 -   rotovibrational line cooling of HD
 
@@ -2029,7 +2033,7 @@ NCCM currently includes the following processes:
 
 -   rotovibrational line cooling of CO
 
--   rotovibrational line cooling of H$_2$O
+-   rotovibrational line cooling of H<sub>2</sub>O
 
 -   rotational line cooling of OH
 
@@ -2084,7 +2088,7 @@ values (given in brackets).
 
     -   `HLLD_PRESSURE_CORR` ({YES,NO}): option to enable/disable the
         low Mach pressure correction term in the HLLD Riemann solver
-        according to [@MM21]
+        according to [MM21](#references)
 
     -   `BORIS_CORR` ({YES,NO,AUTO}): option to enable/disable the Boris
         correction (cf. [Code features](#code-features))
@@ -2092,15 +2096,15 @@ values (given in brackets).
     -   `BORIS_CRED`: reduced speed of light in Boris correction
 
     -   `BORIS_CRED_MIN`: lower limit of reduced speed of light in units
-        $2|{\bf v}|+c_s$
+        2|**v**|+c<sub>s</sub>
 
     -   `BORIS_AUTO_CA_MAX`: Alfven speed threshold in units
-        $2|{\bf v}|+c_s$ above which the Boris correction is avtivated
+        2|**v**|+c<sub>s</sub> above which the Boris correction is avtivated
         when `BORIS_CORR`=`AUTO`
 
 -   MESH REFINEMENT
 
-    -   `MAXLEVEL` ($<128$): maximum refinement level
+    -   `MAXLEVEL` (<128): maximum refinement level
 
     -   `NOBR` ({YES,NO}): option to prevent mesh refinement at domain
         boundaries
@@ -2119,7 +2123,7 @@ values (given in brackets).
     -   `MG_ITMAX`: maximum number of multigrid iterations before
         termination
 
-    -   `MG_TOL` (typical: $10^{-6}$): error tolerance in the multigrid
+    -   `MG_TOL` (typical: 10<sup>-6</sup>): error tolerance in the multigrid
         solver
 
     -   `MG_N_SUBLEVELS` (1,2): number of sublevels (below zero level)
@@ -2143,17 +2147,17 @@ values (given in brackets).
     -   `MG_BASE_CHEB_ACC` ({YES,NO}): option to enable Chebyshev
         acceleration in the
 
-    -   `MG_MAX_ANISO_X` ($\ge 1$): allowed y,z-to-x anisotropy
+    -   `MG_MAX_ANISO_X` (<=1): allowed y,z-to-x anisotropy
 
-    -   `MG_MAX_ANISO_Y` ($\ge 1$): allowed z-to-y anisotropy base level
+    -   `MG_MAX_ANISO_Y` (<=1): allowed z-to-y anisotropy base level
         solver
 
 -   RKL SCHEME
 
-    -   `RKL_COURANT_EXPL` ($<0.5$): explicit Courant number used in the
+    -   `RKL_COURANT_EXPL` (<0.4): explicit Courant number used in the
         RKL solver
 
-    -   `RKL_MAX_COURANT` (typical: $<1000$): maximum Courant-like
+    -   `RKL_MAX_COURANT` (typical: <1000): maximum Courant-like
         number allowed in the RKL solver
 
     -   `RKL_DT_LIM`: RKL-related timestep limit as fraction of the
@@ -2161,14 +2165,14 @@ values (given in brackets).
 
 -   HEATLOSS SOLVER
 
-    -   `HEATLOSS_TOL` (typical: $10^{-5}$): relative error tolerance in
+    -   `HEATLOSS_TOL` (typical: 10<sup>-5</sup>): relative error tolerance in
         heatloss solver
 
     -   `HEATLOSS_ATOL`: absolute error tolerance in heatloss solver
 
 -   CHEMICAL REACTIONS SOLVER
 
-    -   `REACTIONS_TOL` (typical: $10^{-5}$): relative error tolerance
+    -   `REACTIONS_TOL` (typical: 10<sup>-5</sup>): relative error tolerance
         in NCCM solver
 
     -   `REACTIONS_ATOL_X`: absolute error tolerance for number
@@ -2206,18 +2210,17 @@ values (given in brackets).
 
 **ANALYTICAL EOS-RELATED MACROS**
 
--   `PUSR(rho,eth)`: user-defined expression for the pressure $p$ as a
-    function of $\varrho$ (`rho`) and $\varepsilon$ (`eth`)
+-   `PUSR(rho,eth)`: user-defined expression for the pressure *p* as a
+    function of 𝜚 (`rho`) and *ε* (`eth`)
 
 -   `CS2USR(rho,eth)`: user-defined expression for the square of sound
-    speed $c_s^2(\varrho,\varepsilon)$
+    speed *c*<sub>s</sub><sup>2</sup>(𝜚,*ε*)
 
--   `TUSR(rho,eth)`: user-defined expression for the temperature
-    $T(\varrho,\varepsilon)$
+-   `TUSR(rho,eth)`: user-defined expression for the temperature *T*(𝜚,*ε*)
 
 -   `ETUSR(rho,eth)`: user-defined expression of the thermal energy
-    density $\varepsilon(\varrho)$ as a function of $\varrho$ in
-    simulations without energy equation. Otherwise identity.
+    density *ε*(𝜚) as a function of 𝜚 in simulations without energy equation. 
+    Otherwise identity.
 
 ### References