Merge pull request #476 from xuanweishan/rename_wiki_files

Rename wiki files

Author: hyschive

.github/workflows/update_all_parameter_page.yml

@@ -27,14 +27,14 @@ jobs:
           python sync_runtime_parameter.py
       - name: move markdown
         run: |
-          mv tool/wiki/Runtime-Parameters:-All.md doc/wiki/Runtime-Parameters-related
+          mv tool/wiki/[Runtime-Parameters]-All.md doc/wiki/Runtime-Parameters-related
       - name: set git config
         run: |
           git config --global user.email "${{env.GIT_AUTHOR_EMAIL}}"
           git config --global user.name "${{env.GIT_AUTHOR_NAME}}"
       - name: make a commit and push if the file changed
         run: |
-          git diff --exit-code doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md || \
-          ( git add doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md && \
+          git diff --exit-code doc/wiki/Runtime-Parameters-related/[Runtime-Parameters]-All.md || \
+          ( git add doc/wiki/Runtime-Parameters-related/[Runtime-Parameters]-All.md && \
           git commit -m "[Workflow] Update all parameters wiki page" && \
           git push )

doc/wiki/Adding-New-Simulations.md

@@ -96,7 +96,7 @@ For details see
 
 2. Magnetic field IC — choose one of the following two methods
 (only necessary when enabling
-[[--mhd | Installation:-Option-List#--mhd]]):
+[[--mhd | [Installation]-Option-List#--mhd]]):
 
     * Specify the magnetic field IC by editing the function `SetBFieldIC()`
 or specify the vector potential IC by editing a function linking to the function pointer
@@ -109,7 +109,7 @@ uniform-mesh binary file. For details see
 
 3. Particles IC — choose one of the following two methods
 (only necessary when enabling
-[[--particle | Installation:-Option-List#--particle]]):
+[[--particle | [Installation]-Option-List#--particle]]):
 
     * Specify a particle initialization function.
         1. Define the function `Par_Init_ByFunction_NewProblem()`.
@@ -200,7 +200,7 @@ during the runtime.
     ```
 
 4. Add these parameters to the input file `Input__TestProb`
-(see [[Input__TestProb | Runtime-Parameters:-Input__TestProb]]
+(see [[Input__TestProb | [Runtime-Parameters]-Input__TestProb]]
 for the file format).
 This file must be put in the same directory as the executable `gamer`
 when running the code.
@@ -220,7 +220,7 @@ when running the code.
 
 It takes 4 small steps to add a new grid field:
 
-1. Set [[ --passive | Installation:-Option-List#--passive]]
+1. Set [[ --passive | [Installation]-Option-List#--passive]]
 to `N` (for `N` new fields) when generating the Makefile.
 
 2. Declare a global integer variable on the top of the problem source
@@ -232,7 +232,7 @@ file to store the new field index. For example,
 
     Note that some field index variables have been pre-declared in
 `include/Field.h` (e.g., `Idx_Metal` for the field `Metal` used by,
-for example, [[ GRACKLE_METAL | Runtime-Parameters:-Chemistry-and-Radiation#GRACKLE_METAL ]]).
+for example, [[ GRACKLE_METAL | [Runtime-Parameters]-Chemistry-and-Radiation#GRACKLE_METAL ]]).
 Whenever applicable, skip this step and use these pre-declared index variables
 directly.
 
@@ -267,12 +267,12 @@ It controls whether the new field will be floored to `TINY_NUMBER` to ensure pos
     The fifth parameter should be set to either `NORMALIZE_YES` or `NORMALIZE_NO`.
 It controls whether the new field will be renormalized by the total gas density
 after every update when enabling
-[[ OPT__NORMALIZE_PASSIVE | Runtime-Parameters:-Hydro#OPT__NORMALIZE_PASSIVE ]].
+[[ OPT__NORMALIZE_PASSIVE | [Runtime-Parameters]-Hydro#OPT__NORMALIZE_PASSIVE ]].
 
     The sixth parameter should be set to either `INTERP_FRAC_YES` or `INTERP_FRAC_NO`.
 It controls whether the new field will be converted to mass fraction during interpolation
 when enabling
-[[ OPT__INT_FRAC_PASSIVE_LR | Runtime-Parameters:-Hydro#OPT__INT_FRAC_PASSIVE_LR ]].
+[[ OPT__INT_FRAC_PASSIVE_LR | [Runtime-Parameters]-Hydro#OPT__INT_FRAC_PASSIVE_LR ]].
 
     One must also set the function pointer `Init_Field_User_Ptr` in the problem
 initialization function `Init_TestProb_Hydro_NewProblem()`.
@@ -283,7 +283,7 @@ initialization function `Init_TestProb_Hydro_NewProblem()`.
 
 > [!NOTE]
 > The built-in field `Metal` with the field index `Idx_Metal`
-will be added automatically when enabling [[ GRACKLE_METAL | Runtime-Parameters:-Chemistry-and-Radiation#GRACKLE_METAL ]].
+will be added automatically when enabling [[ GRACKLE_METAL | [Runtime-Parameters]-Chemistry-and-Radiation#GRACKLE_METAL ]].
 
 4. Assign initial values to the new field in `SetGridIC()` using the corresponding
 field index. For example,
@@ -305,8 +305,8 @@ field index. For example,
 Adding a new particle attribute is very similar to adding a new grid field.
 So we only highlight the differences in each of the 4 steps above.
 
-1. Set [[ --par_attribute_flt | Installation:-Option-List#--par_attribute_flt ]] and
-[[ --par_attribute_int | Installation:-Option-List#--par_attribute_int ]]
+1. Set [[ --par_attribute_flt | [Installation]-Option-List#--par_attribute_flt ]] and
+[[ --par_attribute_int | [Installation]-Option-List#--par_attribute_int ]]
 instead when generating the Makefile.
 
 2. Declare a global integer variable on the top of the problem source
@@ -394,7 +394,7 @@ The following example illustrates the procedure to add a problem-specific
     ```
 
 4. Turn on the corresponding runtime option
-[[OPT__OUTPUT_USER | Runtime-Parameters:-Outputs#OPT__OUTPUT_USER]].
+[[OPT__OUTPUT_USER | [Runtime-Parameters]-Outputs#OPT__OUTPUT_USER]].
 when running the code.
 
     ```
@@ -415,7 +415,7 @@ Provide a custom routine for [[Setting IC from Files - Grids | Initial-Condition
 * **Function Pointer:**
 `Init_ByFile_User_Ptr`
 * **Runtime Option:**
-[[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=3
+[[OPT__INIT | [Runtime-Parameters]-Initial-Conditions#OPT__INIT]]=3
 * **Example:**
 `src/Init/Init_ByFile.cpp` → `Init_ByFile_Default()`
 
@@ -427,7 +427,7 @@ Provide a custom routine for [[Setting IC from Files - Particles | Initial-Condi
 * **Function Pointer:**
 `Par_Init_ByFile_User_Ptr`
 * **Runtime Option:**
-[[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=3
+[[PAR_INIT | [Runtime-Parameters]-Particles#PAR_INIT]]=3
 * **Example:**
 `src/Particle/Par_Init_ByFile.cpp` → `Par_Init_ByFile_Default()`
 ### Work Before Output
@@ -448,14 +448,14 @@ None
 ### Refinement Criteria
 * **Description:**
 Add user-specified refinement criteria. See
-[[OPT__FLAG_USER | Runtime-Parameters:-Refinement#OPT__FLAG_USER]]
+[[OPT__FLAG_USER | [Runtime-Parameters]-Refinement#OPT__FLAG_USER]]
 for details.
 * **Prototype:**
 `bool Flag_NewProblem( const int, const int, const int, const int, const int, const double );`
 * **Function Pointer:**
 `Flag_User_Ptr`
 * **Runtime Option:**
-[[OPT__FLAG_USER | Runtime-Parameters:-Refinement#OPT__FLAG_USER]]
+[[OPT__FLAG_USER | [Runtime-Parameters]-Refinement#OPT__FLAG_USER]]
 * **Example:**
 `src/Refine/Flag_User.cpp`
 
@@ -479,7 +479,7 @@ Add user-specified timestep constraints.
 * **Function Pointer:**
 `Mis_GetTimeStep_User_Ptr`
 * **Runtime Option:**
-[[OPT__DT_USER | Runtime-Parameters:-Timestep#OPT__DT_USER]]
+[[OPT__DT_USER | [Runtime-Parameters]-Timestep#OPT__DT_USER]]
 * **Example:**
 `src/Miscellaneous/Mis_GetTimeStep_User.cpp`
 
@@ -492,7 +492,7 @@ Add user-specified (i.e., inflow) boundary conditions.
 `BC_User_Ptr` for the cell-centered fluid variables and
 `BC_BField_User_Ptr` for the face-centered magnetic field
 * **Runtime Option:**
-[[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]] = 4
+[[OPT__BC_FLU_* | [Runtime-Parameters]-Hydro#OPT__BC_FLU_XM]] = 4
 * **Example:**
 `src/TestProblem/ELBDM/ExtPot/Init_TestProb_ELBDM_ExtPot.cpp`
 → `BC()`
@@ -510,7 +510,7 @@ Using the vector potential is recommended since it reduces the divergence-free e
 Note that one still needs to define `MHD_ResetByUser_BField_Ptr` when using the vector potential
 (see the example below).
 * **Restriction:**
-  * [[INIT_SUBSAMPLING_NCELL | Runtime-Parameters:-Initial-Conditions#INIT_SUBSAMPLING_NCELL]] has no effect on resetting the initial magnetic field.
+  * [[INIT_SUBSAMPLING_NCELL | [Runtime-Parameters]-Initial-Conditions#INIT_SUBSAMPLING_NCELL]] has no effect on resetting the initial magnetic field.
   * To ensure that the reset magnetic field satisfies the divergence-free condition to the machine precision,
 one must (i) use the vector potential and (ii) ensure that the reset fields do not touch any coarse-fine
 AMR interfaces. Supporting resetting a divergence-free magnetic field across coarse-fine AMR interfaces
@@ -525,7 +525,7 @@ will be implemented in the future.
 * **Function Pointer:**
 `Flu_ResetByUser_Func_Ptr`, `MHD_ResetByUser_BField_Ptr`, `MHD_ResetByUser_VecPot_Ptr`
 * **Runtime Option:**
-[[OPT__RESET_FLUID | Runtime-Parameters:-Hydro#OPT__RESET_FLUID]], [[OPT__RESET_FLUID_INIT | Runtime-Parameters:-Hydro#OPT__RESET_FLUID_INIT]]
+[[OPT__RESET_FLUID | [Runtime-Parameters]-Hydro#OPT__RESET_FLUID]], [[OPT__RESET_FLUID_INIT | [Runtime-Parameters]-Hydro#OPT__RESET_FLUID_INIT]]
 * **Example:**
 `src/Fluid/Flu_ResetByUser.cpp`, `src/Model_Hydro/MHD_ResetByUser.cpp`, `src/TestProblem/Hydro/BlastWave/MHD_ResetByUser_BlastWave.cpp`
 
@@ -537,7 +537,7 @@ Perform user-specified simulation diagnostics.
 * **Function Pointer:**
 `Aux_Record_User_Ptr`
 * **Runtime Option:**
-[[OPT__RECORD_USER | Runtime-Parameters:-Miscellaneous#OPT__RECORD_USER]]
+[[OPT__RECORD_USER | [Runtime-Parameters]-Miscellaneous#OPT__RECORD_USER]]
 * **Example:**
 `src/Auxiliary/Aux_Record_User.cpp`
 
@@ -582,7 +582,7 @@ for details.
 * **Function Pointer:**
    * `Init_ExtAcc_Ptr`
 * **Runtime Option:**
-[[OPT__EXT_ACC | Runtime-Parameters:-Gravity#OPT__EXT_ACC]]
+[[OPT__EXT_ACC | [Runtime-Parameters]-Gravity#OPT__EXT_ACC]]
 * **Example:**
    * `src/TestProblem/Hydro/Plummer/Init_TestProb_Hydro_Plummer.cpp`
    * `src/TestProblem/Hydro/Plummer/ExtAcc_Plummer.cpp`
@@ -598,7 +598,7 @@ for details.
 * **Function Pointer:**
    * `Init_ExtPot_Ptr`
 * **Runtime Option:**
-[[OPT__EXT_POT | Runtime-Parameters:-Gravity#OPT__EXT_POT]]
+[[OPT__EXT_POT | [Runtime-Parameters]-Gravity#OPT__EXT_POT]]
 * **Example:**
    * `src/TestProblem/Hydro/Plummer/Init_TestProb_Hydro_Plummer.cpp`
    * `src/TestProblem/Hydro/Plummer/ExtPot_Plummer.cpp`
@@ -612,20 +612,20 @@ Add a user-specified equation of state. See [[here | equation-of-state]] for det
    * `EoS_Init_Ptr`
    * `Eos_End_Ptr`
 * **Compilation Option:**
-[[--eos | Installation:-Option-List#--eos]]
+[[--eos | [Installation]-Option-List#--eos]]
 * **Example:**
    * `src/EoS/User_Template`
    * `src/EoS/Gamma`
 
 ### Feedback
 * **Description:**
-Add a user-specified feedback. See [[FB_USER | Runtime-Parameters:-Feedback#FB_USER]] for details.
+Add a user-specified feedback. See [[FB_USER | [Runtime-Parameters]-Feedback#FB_USER]] for details.
 * **Function Pointer:**
    * `FB_Init_User_Ptr`
 * **Compilation Option:**
-[[--feedback | Installation:-Option-List#--feedback]]
+[[--feedback | [Installation]-Option-List#--feedback]]
 * **Runtime Option:**
-[[FB_USER | Runtime-Parameters:-Feedback#FB_USER]]
+[[FB_USER | [Runtime-Parameters]-Feedback#FB_USER]]
 * **Example:**
    * `src/TestProblem/Hydro/Plummer/FB_Plummer.cpp`
 
@@ -637,7 +637,7 @@ Store user-specified variables in HDF5 snapshots.
 * **Function Pointer:**
    * `Output_HDF5_UserPara_Ptr`
 * **Compilation Option:**
-[[SUPPORT_HDF5 | Installation: Simulation-Options#SUPPORT_HDF5]]
+[[--hdf5 | [Installation]-Option-Lists#--hdf5]]
 * **Runtime Option:**
 None
 * **Example:**

…ibute-related/Contribute:-Update-Wiki.md …bute-related/[Contribute]-Update-Wiki.mddoc/wiki/Contribute-related/Contribute:-Update-Wiki.md renamed to doc/wiki/Contribute-related/[Contribute]-Update-Wiki.md doc/wiki/Contribute-related/Contribute:-Update-Wiki.md renamed to doc/wiki/Contribute-related/[Contribute]-Update-Wiki.md

@@ -4,7 +4,7 @@ This guide provides step-by-step instructions for setting up and using Visual St
 
 ### Prerequisites
 
-- **Quick Start**: Follow the [[Quick Start | Quick-Start]] guide to download GAMER and complete at least one [[demo | Quick-Start:-1D-Shock-Tube]].
+- **Quick Start**: Follow the [[Quick Start | Quick-Start]] guide to download GAMER and complete at least one [[demo | [Quick-Start]-1D-Shock-Tube]].
 - **Visual Studio Code**: Download and install VS Code from [https://code.visualstudio.com/](https://code.visualstudio.com/).
 - **C/C++ Extension**: Install the "C/C++" extension from the VS Code Marketplace.
 

doc/wiki/Developing-with-VS-Code.md

@@ -2,18 +2,18 @@
 ## Compilation Options
 
 Related options:
-[[--model | Installation:-Option-List#--model]],  
-[[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]],  
-[[--wave_scheme | Installation:-Option-List#--wave_scheme]],  
-[[--conserve_mass | Installation:-Option-List#--conserve_mass]],  
-[[--laplacian_four | Installation:-Option-List#--laplacian_four]],  
-[[--gramfe_scheme | Installation:-Option-List#--gramfe_scheme]],  
-[[--hybrid_scheme | Installation:-Option-List#--hybrid_scheme]],  
-[[--self_interaction | Installation:-Option-List#--self_interaction]],  
+[[--model | [Installation]-Option-List#--model]],  
+[[--elbdm_scheme | [Installation]-Option-List#--elbdm_scheme]],  
+[[--wave_scheme | [Installation]-Option-List#--wave_scheme]],  
+[[--conserve_mass | [Installation]-Option-List#--conserve_mass]],  
+[[--laplacian_four | [Installation]-Option-List#--laplacian_four]],  
+[[--gramfe_scheme | [Installation]-Option-List#--gramfe_scheme]],  
+[[--hybrid_scheme | [Installation]-Option-List#--hybrid_scheme]],  
+[[--self_interaction | [Installation]-Option-List#--self_interaction]],  
 
 
 ## Runtime Parameters
-[[Runtime parameters: ELBDM | Runtime-Parameters:-ELBDM]]
+[[Runtime parameters: ELBDM | [Runtime-Parameters]-ELBDM]]
 
 Other related parameters:
 TBF.

…iki/ELBDM-related/ELBDM-Hybrid-Scheme.md …i/ELBDM-related/[ELBDM]-Hybrid-Scheme.mddoc/wiki/ELBDM-related/ELBDM-Hybrid-Scheme.md renamed to doc/wiki/ELBDM-related/[ELBDM]-Hybrid-Scheme.md doc/wiki/ELBDM-related/ELBDM-Hybrid-Scheme.md renamed to doc/wiki/ELBDM-related/[ELBDM]-Hybrid-Scheme.md

@@ -3,10 +3,10 @@
 To enable GPU:
 1. Generate the `Makefile` and recompile the code (see [[Installation]] for details)
     1. Set
-[[GPU_COMPUTE_CAPABILITY | Installation:-Machine-Configuration-File#4-GPU-compute-capability]]
-according to the GPU architecture on your system in the [[configuration file | Installation:-Machine-Configuration-File]]
+[[GPU_COMPUTE_CAPABILITY | [Installation]-Machine-Configuration-File#4-GPU-compute-capability]]
+according to the GPU architecture on your system in the [[configuration file | [Installation]-Machine-Configuration-File]]
     2. Generate `Makefile` with
-[[--gpu | Installation:-Option-List#--gpu]]=`true`
+[[--gpu | [Installation]-Option-List#--gpu]]=`true`
     3. Recompile the code with `make clean; make`
 
 2. [Query the GPUs on your system](#query-gpus) [optional]
@@ -17,12 +17,12 @@ according to the GPU architecture on your system in the [[configuration file | I
 ## Compilation Options
 
 Related options:
-[[--gpu | Installation:-Option-List#--gpu]],  
-[[--gpu_regcount_flu | Installation:-Option-List#--gpu_regcount_flu]]  
+[[--gpu | [Installation]-Option-List#--gpu]],  
+[[--gpu_regcount_flu | [Installation]-Option-List#--gpu_regcount_flu]]  
 
 
 ## Runtime Parameters
-[[Runtime parameters: GPU | Runtime-Parameters:-GPU]]
+[[[Runtime parameters] GPU | [Runtime-Parameters]-GPU]]
 
 Other related parameters: none
 
@@ -69,7 +69,7 @@ and there are currently two running jobs using GPU ID 0 and 1, respectively.
 
 On a node with <var>N</var><sub>GPU</sub>, each GPU has a unique
 ID in the range 0 to <var>N</var><sub>GPU</sub>-1. GAMER uses the runtime
-parameter [[OPT__GPUID_SELECT | Runtime-Parameters:-GPU#OPT__GPUID_SELECT]] to set the GPU ID
+parameter [[OPT__GPUID_SELECT | [Runtime-Parameters]-GPU#OPT__GPUID_SELECT]] to set the GPU ID
 associated with each MPI process.
 
 * `OPT__GPUID_SELECT = -2`: set by CUDA runtime. Typically, this

…-related/ELBDM-Spectral-Interpolation.md …elated/[ELBDM]-Spectral-Interpolation.mddoc/wiki/ELBDM-related/ELBDM-Spectral-Interpolation.md renamed to doc/wiki/ELBDM-related/[ELBDM]-Spectral-Interpolation.md doc/wiki/ELBDM-related/ELBDM-Spectral-Interpolation.md renamed to doc/wiki/ELBDM-related/[ELBDM]-Spectral-Interpolation.md

@@ -1,3 +1,3 @@
 TBF.
 
-- [[ Update Wiki | Contribute:-Update-Wiki ]]
+- [[ Update Wiki | [Contribute]-Update-Wiki ]]