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version 4.2 authored by Udo Ziegler's avatar Udo Ziegler
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3-NIRVANA-user-guide/3.2-User-interfaces.md
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......@@ -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
......