chore(docs): Sync wiki to doc/wiki [skip-cd]

jzuhone · Jan 11, 2025 · b226061 · b226061
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diff --git a/doc/wiki/Adding-New-Simulations.md b/doc/wiki/Adding-New-Simulations.md
@@ -8,8 +8,8 @@ Mandatory steps are marked by &#x1F4CC;.
 5. [Add Problem-specific Grid Fields and Particle Attributes](#v-add-problem-specific-grid-fields-and-particle-attributes)
 6. [Add Problem-specific Functionalities](#vi-add-problem-specific-functionalities)
    *  [Output](#output)
-   *  [Initial Condition by File - Fluid](#initial-condition-by-file---fluid)
-   *  [Initial Condition by File - Particle](#initial-condition-by-file---particle)
+   *  [Initial Condition from Files - Grids](#initial-condition-from-files---grids)
+   *  [Initial Condition from Files - Particles](#initial-condition-from-files---particles)
    *  [Work Before Output](#work-before-output)
    *  [Refinement Criteria](#refinement-criteria)
    *  [Work Before Refine](#work-before-refine)
@@ -382,10 +382,9 @@ Other user-specified functionalities such as refinement criteria and
 timestep constraints can be added in a similar way and are outlined below.
 
 
-### Initial Condition by File - Fluid
+### Initial Condition from Files - Grids
 * **Description:**
-This funciton will overwrite the [[setting the fluid field | Initial-Conditions#IC-File-Grids]]
-from the `UM_IC`.
+Provide a custom routine for [[Setting IC from Files - Grids | Initial-Conditions#IC-File-Grids]].
 * **Prototype:**
 `void Init_ByFile_NewProblem( real fluid_out[], const real fluid_in[], const int nvar_in,
                               const double x, const double y, const double z, const double Time,
@@ -397,10 +396,9 @@ from the `UM_IC`.
 * **Example:**
 `src/Init/Init_ByFile.cpp` &#8594; `Init_ByFile_Default()`
 
-### Initial Condition by File - Particle
+### Initial Condition from Files - Particles
 * **Description:**
-This funciton will overwrite the
-[[initialize particle attributes routine from a file | Initial-Conditions#IC-File-Particles]].
+Provide a custom routine for [[Setting IC from Files - Particles | Initial-Conditions#IC-File-Particles]].
 * **Prototype:**
 `void Par_Init_ByFile_NewProblem();`
 * **Function Pointer:**

diff --git a/doc/wiki/Initial-Conditions.md b/doc/wiki/Initial-Conditions.md
@@ -361,6 +361,10 @@ routine will add grids to levels [[OPT__UM_IC_LEVEL | Runtime-Parameters:-Initia
 [[ MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]
 in the regions satisfying any refinement criterion.
 
+A custom routine for assigning data to each cell from the loaded data
+can be specified using the function pointer
+[[Init_ByFile_User_Ptr | Adding-New-Simulations#initial-condition-from-files---grids]].
+
 The initial condition file `UM_IC` can be loaded concurrently by multiple
 MPI processes using [[OPT__UM_IC_LOAD_NRANK | Runtime-Parameters:-Initial-Conditions#OPT__UM_IC_LOAD_NRANK]].
 
@@ -446,6 +450,10 @@ They have the floating-point types for now but will be changed to integers in th
 For `PTYPE_TRACER`, one must also enable the compilation option
 [[--tracer | Installation:-Option-List#--tracer]].
 
+A custom routine for assigning particle attributes from the loaded data
+can be specified using the function pointer
+[[Par_Init_ByFile_User_Ptr | Adding-New-Simulations#initial-condition-from-files---particles]].
+
 Note that it is not required to adopt [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=3 and
 [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=3 at the same time. In other words,
 it is perfectly fine to set the grid initial condition from an analytical

diff --git a/doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md b/doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md
@@ -103,15 +103,9 @@ For variables with `Default/Min/Max` labeled as `Depend`, click the parameter na
 | [[ FB_RSEED \| Runtime-Parameters:-Feedback#FB_RSEED ]]                                              |             456 |               0 |            None | random seed [456] |
 | [[ FB_SNE \| Runtime-Parameters:-Feedback#FB_SNE ]]                                                  |               0 |            None |            None | supernova explosion feedback [0] |
 | [[ FB_USER \| Runtime-Parameters:-Feedback#FB_USER ]]                                                |               0 |            None |            None | user-defined feedback [0] |
-| [[ FLAG_ANGULAR_CEN_X \| Runtime-Parameters:-Refinement#FLAG_ANGULAR_CEN_X ]]                        |            -1.0 |            None |            None | x center coordinate for OPT__FLAG_ANGULAR (<0=auto -> box center) [-1.0] |
-| [[ FLAG_ANGULAR_CEN_Y \| Runtime-Parameters:-Refinement#FLAG_ANGULAR_CEN_Y ]]                        |            -1.0 |            None |            None | y center coordinate for OPT__FLAG_ANGULAR (<0=auto -> box center) [-1.0] |
-| [[ FLAG_ANGULAR_CEN_Z \| Runtime-Parameters:-Refinement#FLAG_ANGULAR_CEN_Z ]]                        |            -1.0 |            None |            None | z center coordinate for OPT__FLAG_ANGULAR (<0=auto -> box center) [-1.0] |
 | [[ FLAG_BUFFER_SIZE \| Runtime-Parameters:-Refinement#FLAG_BUFFER_SIZE ]]                            |              -1 |            None |             PS1 | number of buffer cells for the flag operation (0~PATCH_SIZE; <0=auto -> PATCH_SIZE) [-1] |
 | [[ FLAG_BUFFER_SIZE_MAXM1_LV \| Runtime-Parameters:-Refinement#FLAG_BUFFER_SIZE_MAXM1_LV ]]          |              -1 |            None |             PS1 | FLAG_BUFFER_SIZE at the level MAX_LEVEL-1 (<0=auto -> REGRID_COUNT) [-1] |
 | [[ FLAG_BUFFER_SIZE_MAXM2_LV \| Runtime-Parameters:-Refinement#FLAG_BUFFER_SIZE_MAXM2_LV ]]          |              -1 |            None |             PS1 | FLAG_BUFFER_SIZE at the level MAX_LEVEL-2 (<0=auto) [-1] |
-| [[ FLAG_RADIAL_CEN_X \| Runtime-Parameters:-Refinement#FLAG_RADIAL_CEN_X ]]                          |            -1.0 |            None |            None | x center coordinate for OPT__FLAG_RADIAL (<0=auto -> box center) [-1.0] |
-| [[ FLAG_RADIAL_CEN_Y \| Runtime-Parameters:-Refinement#FLAG_RADIAL_CEN_Y ]]                          |            -1.0 |            None |            None | y center coordinate for OPT__FLAG_RADIAL (<0=auto -> box center) [-1.0] |
-| [[ FLAG_RADIAL_CEN_Z \| Runtime-Parameters:-Refinement#FLAG_RADIAL_CEN_Z ]]                          |            -1.0 |            None |            None | z center coordinate for OPT__FLAG_RADIAL (<0=auto -> box center) [-1.0] |
 | [[ FLU_GPU_NPGROUP \| Runtime-Parameters:-GPU#FLU_GPU_NPGROUP ]]                                     |              -1 |            None |            None | number of patch groups sent into the CPU/GPU fluid solver (<=0=auto) [-1] |
 
 # G
@@ -228,7 +222,6 @@ For variables with `Default/Min/Max` labeled as `Depend`, click the parameter na
 | [[ OPT__FIXUP_ELECTRIC \| Runtime-Parameters:-Hydro#OPT__FIXUP_ELECTRIC ]]                           |               1 |            None |            None | correct coarse grids by the fine-grid boundary electric field [1] ##MHD ONLY## |
 | [[ OPT__FIXUP_FLUX \| Runtime-Parameters:-Hydro#OPT__FIXUP_FLUX ]]                                   |          Depend |          Depend |          Depend | correct coarse grids by the fine-grid boundary fluxes [1] ##HYDRO and ELBDM ONLY## |
 | [[ OPT__FIXUP_RESTRICT \| Runtime-Parameters:-Hydro#OPT__FIXUP_RESTRICT ]]                           |               1 |            None |            None | correct coarse grids by averaging the fine-grid data [1] |
-| [[ OPT__FLAG_ANGULAR \| Runtime-Parameters:-Refinement#OPT__FLAG_ANGULAR ]]                          |               0 |            None |            None | flag: angular resolution (Input__Flag_AngularResolution) [0] |
 | [[ OPT__FLAG_CRAY \| Runtime-Parameters:-Refinement#OPT__FLAG_CRAY ]]                                |               0 |            None |            None | flag: cosmic-ray energy (Input__Flag_CRay) [0] ##COSMIC_RAY ONLY## |
 | [[ OPT__FLAG_CURRENT \| Runtime-Parameters:-Refinement#OPT__FLAG_CURRENT ]]                          |               0 |            None |            None | flag: current density in MHD (Input__Flag_Current) [0] ##MHD ONLY## |
 | OPT__FLAG_ENGY_DENSITY                                                                               |               0 |            None |            None | flag: energy density (Input_Flag_EngyDensity) [0] ##ELBDM ONLY## |
@@ -246,7 +239,6 @@ For variables with `Default/Min/Max` labeled as `Depend`, click the parameter na
 | [[ OPT__FLAG_NPAR_PATCH \| Runtime-Parameters:-Refinement#OPT__FLAG_NPAR_PATCH ]]                    |               0 |               0 |               2 | flag: # of particles per patch (Input__Flag_NParPatch): (0=off, 1=itself, 2=itself+siblings) [0] |
 | [[ OPT__FLAG_PAR_MASS_CELL \| Runtime-Parameters:-Refinement#OPT__FLAG_PAR_MASS_CELL ]]              |               0 |            None |            None | flag: total particle mass per cell (Input__Flag_ParMassCell) [0] |
 | [[ OPT__FLAG_PRES_GRADIENT \| Runtime-Parameters:-Refinement#OPT__FLAG_PRES_GRADIENT ]]              |               0 |            None |            None | flag: pressure gradient (Input__Flag_PresGradient) [0] ##HYDRO ONLY## |
-| [[ OPT__FLAG_RADIAL \| Runtime-Parameters:-Refinement#OPT__FLAG_RADIAL ]]                            |               0 |            None |            None | flag: radial resolution (Input__Flag_RadialResolution) [0] |
 | [[ OPT__FLAG_REGION \| Runtime-Parameters:-Refinement#OPT__FLAG_REGION ]]                            |               0 |            None |            None | flag: specify the regions **allowed** to be refined -> edit "Flag_Region.cpp" [0] |
 | [[ OPT__FLAG_RHO \| Runtime-Parameters:-Refinement#OPT__FLAG_RHO ]]                                  |               0 |            None |            None | flag: density (Input__Flag_Rho) [0] |
 | [[ OPT__FLAG_RHO_GRADIENT \| Runtime-Parameters:-Refinement#OPT__FLAG_RHO_GRADIENT ]]                |               0 |            None |            None | flag: density gradient (Input__Flag_RhoGradient) [0] |