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Update 3.2 User interfaces
authored
Jan 10, 2021
by
Udo Ziegler
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3-NIRVANA-user-guide/3.2-User-interfaces.md
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6a5c1e77
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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`
)
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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
...
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@@ -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]
...
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@@ -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
...
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...
...
