| ... | ... | @@ -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
|
| ... | ... | |
