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Update 3.2 User interfaces 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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......@@ -149,7 +149,7 @@ for the type of coordinate system.
*base* container filename of the snapshot. The base container
filename is `NIR#` or `NIRLAST#` with `#`=`_C.model` but
excluding the dot and post-dot container id (cf.
\[here\](3.3-Output-data\#snapshot-files)).
\[Output data\](3.3-Output-data\#snapshot-files)).
- `02` (`_C.mod_max`, `_C.time_max`)
......@@ -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))
[Output data](3.3-Output-data#log-file)) and monitoring file
`nirvana.mon` (cf. [Output data](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.
[Output data](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)).
[Data analysis](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
[Output data](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)).
[Defining BC](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-refinement)).
[User-defined mesh refinement](3.2-User-interfaces#user-defined-mesh-refinement)).
`_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
[AMR](3.1-Code-basics#adaptive-mesh-refinement)). A zero or
negative value means that the respective component is disabled
for a mesh refinement check.
......@@ -426,7 +426,7 @@ 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
[AMR](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.
......@@ -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
[AMR](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.
......@@ -529,7 +529,7 @@ for the type of coordinate system.
- `_C.viscosity_courant`: CFL-analog number in the expression for
the fluid viscosity timestep. A typical value in case of STD is
< 0.5. Values much larger than 1 are possible in the case of
<0.5. Values much larger than 1 are possible in the case of
RKL.
- `03` (`_C.diffusion_solver`, `_C.diffusion_courant`)
......@@ -595,7 +595,7 @@ for the type of coordinate system.
- `_C.permeability_rel`: relative magnetic permeability
*μ*<sub>*r**e**l*</sub>
( = *μ*/*μ*<sub>0</sub>, *μ*<sub>0</sub> = 4*π* ⋅ 10<sup> − 7</sup>`V` ⋅ `m`<sup> − 1</sup> ⋅ `A`<sup> − 1</sup> ⋅ `s`<sup> − 1</sup>).
( = *μ*/*μ*<sub>0</sub>, *μ*<sub>0</sub> = 4*π*⋅10<sup>−7</sup>V⋅m<sup>−1</sup>⋅A<sup>−1</sup>⋅s<sup>−1</sup>).
*Note: The Gaussian unit system can be mimicked by choosing a
value
......@@ -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))
[User-defined EOS](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)).
[User-defined EOS](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.*
......@@ -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.
[User-defined cooling/heating function](3.2-User-interfaces#user-defined-cooling/heating-function)).
[User-defined cooling/heating function](3.2-User-interfaces#user-defined-cooling-and-heating-function)).
- `11` (`_C.tracer`)
......@@ -836,7 +836,7 @@ components are not allocated in the HD case. Likewise, arrays for
`_C.tracer`=0 respective `_C.species`=0. Furthermore, derived variables
like the temperature must not be assigned here. If the TESTFIELDS
infrastructure is used testfield fluctuation variables,
**b**<sub>*t*</sub>, *t* = 0, *N*<sub>*t*</sub> − 1, are to be
**b**<sub>*t*</sub>, *t*=0,*N*<sub>*t*</sub>−1, are to be
considered primary.
The mesh is represented by the master mesh pointer `gm` which is the
......