[Workflow] Update test problem wiki pages

hsinhaoHHuang · Jan 28, 2025 · c845130 · c845130
1 parent 3aa8998
commit c845130
Show file tree

Hide file tree

Showing 43 changed files with 853 additions and 844 deletions.
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-AGORA_IsolatedGalaxy.md b/doc/wiki/Test-Problems-related/Test-Problems:-AGORA_IsolatedGalaxy.md
@@ -8,64 +8,63 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--double | Installation:-Option-List#--double]]
-   - [[--dual | Installation:-Option-List#--dual]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--dual | Installation:-Option-List#--dual]]=`DE_ENPY`
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Simulation setup
 - Units
 
-   - External (for `Input__TestProb` only)
+  - External (for `Input__TestProb` only)
 
-     See the comment of each runtime variable
+    See the comment of each runtime variable
 
-   - Internal (for all other input files and internal usage)
-     | Unit  | [L] | [M]        | [T] | [V] = [L]/[T] | [D] = [M]/[D]^3  |
-     |---    |---  |---         |---  |---            |---               |
-     | Value | kpc | 1.0e9 Msun | Myr | ~ 9.8e2 km/s  | ~ 6.8e-23 g/cm^3 |
+  - Internal (for all other input files and internal usage)
+    | Unit  | [L] | [M]        | [T] | [V] = [L]/[T] | [D] = [M]/[D]^3  |
+    |---    |---  |---         |---  |---            |---               |
+    | Value | kpc | 1.0e9 Msun | Myr | ~ 9.8e2 km/s  | ~ 6.8e-23 g/cm^3 |
 
 - Low-resolution default setup
 
-   1. Download the low-resolution initial conditions and `Input_*` by executing
-      ```bash
-      sh download_ic_low_res.sh
-      ```
+  1. Download the low-resolution initial conditions and `Input_*` by executing
+     ```bash
+     sh download_ic_low_res.sh
+     ```
 
-   2. Default resolution ~ 80 pc (root grid 128^3; [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`7`)
+  2. Default resolution ~ 80 pc (root grid 128^3; [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`7`)
 
 - High-resolution setup
 
-   1. Download the high-resolution initial conditions and `Input_*` by executing
-      ```bash
-      sh download_ic_high_res.sh
-      ```
+  1. Download the high-resolution initial conditions and `Input_*` by executing
+     ```bash
+     sh download_ic_high_res.sh
+     ```
 
-   2. Highest resolution ~ 20 pc (root grid 128^3; [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`9`)
+  2. Highest resolution ~ 20 pc (root grid 128^3; [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`9`)
 
-   3. This setup reproduces the AGORA high-resolution run presented in the GAMER-2 paper [Schive et al. 2018](https://academic.oup.com/mnras/article/481/4/4815/5106358)
+  3. This setup reproduces the AGORA high-resolution run presented in the GAMER-2 paper [Schive et al. 2018](https://academic.oup.com/mnras/article/481/4/4815/5106358)
 
 
 # Note
 - Mimic the "AgoraGalaxy" test problem setup of Enzo.
 
-   See: [Nathan Goldbaum, et al., 2015, ApJ, 814, 131](https://dx.doi.org/10.1088/0004-637X/814/2/131) [(arXiv: 1510.08458)](https://arxiv.org/abs/1510.08458) and
-   [Ji-hoon Kim, et al., 2016, ApJ, 833, 202](https://dx.doi.org/10.3847/1538-4357/833/2/202) [(arXiv: 1610.03066)](https://dx.doi.org/10.3847/1538-4357/833/2/202)
+  See: [Nathan Goldbaum, et al., 2015, ApJ, 814, 131](https://dx.doi.org/10.1088/0004-637X/814/2/131) [(arXiv: 1510.08458)](https://arxiv.org/abs/1510.08458) and
+  [Ji-hoon Kim, et al., 2016, ApJ, 833, 202](https://dx.doi.org/10.3847/1538-4357/833/2/202) [(arXiv: 1610.03066)](https://dx.doi.org/10.3847/1538-4357/833/2/202)
 
 - Other references
 
-   - [AGORA website](https://sites.google.com/site/santacruzcomparisonproject/)
-   - [AGORA initial conditions](https://goo.gl/8JzbIJ)
-   - [Enzo setup](https://bitbucket.org/enzo/enzo-dev/src/19f4a44e06f1c386573dc77b3608ba66b64d93bc/run/Hydro/Hydro-3D/AgoraGalaxy/?at=week-of-code)
-   - [Goldbaum et al. 2016](https://arxiv.org/abs/1605.00646)
-   - [yt hub](https://girder.hub.yt/#collection/5736481ddd9119000164acf1)
-   - [CloudyData_UVB table](https://github.com/grackle-project/grackle_data_files/tree/main/input)
+  - [AGORA website](https://sites.google.com/site/santacruzcomparisonproject/)
+  - [AGORA initial conditions](https://goo.gl/8JzbIJ)
+  - [Enzo setup](https://bitbucket.org/enzo/enzo-dev/src/19f4a44e06f1c386573dc77b3608ba66b64d93bc/run/Hydro/Hydro-3D/AgoraGalaxy/?at=week-of-code)
+  - [Goldbaum et al. 2016](https://arxiv.org/abs/1605.00646)
+  - [yt hub](https://girder.hub.yt/#collection/5736481ddd9119000164acf1)
+  - [CloudyData_UVB table](https://github.com/grackle-project/grackle_data_files/tree/main/input)
 
 - The low-resolution initial condition files from `sh download_ic_low_res.sh` are the same initial conditions used
   in the `AgoraGalaxy` test problem of Enzo

diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-AcousticWave.md b/doc/wiki/Test-Problems-related/Test-Problems:-AcousticWave.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--double | Installation:-Option-List#--double]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--double | Installation:-Option-List#--double]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -25,26 +25,26 @@
 
 # Note
 - Support both 1D and 3D cases
-   - set by `Acoustic_Dir`
+  - set by `Acoustic_Dir`
 - A simple gnuplot script `plot.gpt` is attached
 - `Record__L1Err` records the L1 errors
 - `AcousticWave_*_*` record the numerical and analytical solutions along the diagonal
 - For SRHD:
-   - Also enable these compilation flags:
-      - [[--srhd | Installation:-Option-List#--srhd]]
-      - [[--eos | Installation:-Option-List#--eos]]=`TAUBMATHEWS`
-      - [[--flu_scheme | Installation:-Option-List#--flu_scheme]]=`MHM`
-      - [[--flux | Installation:-Option-List#--flux]]=`HLLC`
-      - [[--slope | Installation:-Option-List#--slope]]=`PLM`
-   - In `Input__TestProb`,
-      - `Acoustic_v0` and `Acoustic_Cs` will be useless
-      - set `Acoustic_Temp_Bg = 1.0e+10` for high-temperature case
-      - set `Acoustic_Temp_Bg = 1.0e-10` for low-temperature case
-   - To check the L1 error convergence rate
-      - A L1 error plotting script `plot_L1error_SRHD.py` is attached
-      - An automatic script `Run_L1ErrorConvergenceTest_SRHD.sh` is attached
-      - Run `sh Run_L1ErrorConvergenceTest_SRHD.sh`
-      - Reference: Figure 3. in [Tseng et al. 2021, MNRAS, 504, 3298](https://doi.org/10.1093/mnras/stab1006)
+  - Also enable these compilation flags:
+    - [[--srhd | Installation:-Option-List#--srhd]]
+    - [[--eos | Installation:-Option-List#--eos]]=`TAUBMATHEWS`
+    - [[--flu_scheme | Installation:-Option-List#--flu_scheme]]=`MHM`
+    - [[--flux | Installation:-Option-List#--flux]]=`HLLC`
+    - [[--slope | Installation:-Option-List#--slope]]=`PLM`
+  - In `Input__TestProb`,
+    - `Acoustic_v0` and `Acoustic_Cs` will be useless
+    - set `Acoustic_Temp_Bg`=`1.0e+10` for high-temperature case
+    - set `Acoustic_Temp_Bg`=`1.0e-10` for low-temperature case
+  - To check the L1 error convergence rate
+    - A L1 error plotting script `plot_L1error_SRHD.py` is attached
+    - An automatic script `Run_L1ErrorConvergenceTest_SRHD.sh` is attached
+    - Run `sh Run_L1ErrorConvergenceTest_SRHD.sh`
+    - Reference: Figure 3. in [Tseng et al. 2021, MNRAS, 504, 3298](https://doi.org/10.1093/mnras/stab1006)
 
 # Links
 [[Main page of Test Problems | Test-Problems]]

diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-BlastWave.md b/doc/wiki/Test-Problems-related/Test-Problems:-BlastWave.md
@@ -8,33 +8,33 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Available options
-   - [[--mhd | Installation:-Option-List#--mhd]]
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Adopt the Lohner's error estimator on pressure as the refinement criteria
-   - `Refinement threshold`=`0.80`
+  - `Refinement threshold`=`0.80`
 
-- Maximum refinement level ([[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`3`)
+- Maximum refinement level ([[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]])=`3`
 
 
 # Note
 - Two plot scripts are attached: `plot_profile.gpt` and `plot_slice.py`
 - To reset the magnetic field during the runtime, turn on the following options.
-   1. [[OPT__RESET_FLUID | Runtime-Parameters:-Hydro#OPT__RESET_FLUID]]
-   2. `Blast_ResetB_VecPot` (optional but recommended)
+  - [[OPT__RESET_FLUID | Runtime-Parameters:-Hydro#OPT__RESET_FLUID]]
+  - `Blast_ResetB_VecPot` (optional but recommended)
 
-      Improve divergence-free
-   3. [[OPT__FLAG_USER | Runtime-Parameters:-Refinement#OPT__FLAG_USER]] (optional but recommended)
+    Improve divergence-free
+  - [[OPT__FLAG_USER | Runtime-Parameters:-Refinement#OPT__FLAG_USER]] (optional but recommended)
 
-      Refine regions within `~ 6*Blast_ResetB_r0` to the maximum level to improve divergence-free
-      (since even using vector potential, divergence-free can still break at the coarse-fine boundaries)
+    Refine regions within `~ 6*Blast_ResetB_r0` to the maximum level to improve divergence-free
+    (since even using vector potential, divergence-free can still break at the coarse-fine boundaries)
 
 # Links
 [[Main page of Test Problems | Test-Problems]]

diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Bondi.md b/doc/wiki/Test-Problems-related/Test-Problems:-Bondi.md
@@ -8,34 +8,34 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Units
-   - External (for `Input__TestProb` only)
-      | Unit  | [L] | [Dens] | [Mass] | [Temp] |
-      |---    |---  |---     |---     |---     |
-      | Value | kpc | g/cm^3 | Msun   | keV    |
+  - External (for `Input__TestProb` only)
+    | Unit  | [L] | [Dens] | [Mass] | [Temp] |
+    |---    |---  |---     |---     |---     |
+    | Value | kpc | g/cm^3 | Msun   | keV    |
 
-   - Internal (for all other input files and internal usage)
-      | Unit  | [L] | [V]      | [Dens]         | [Time] = [L]/[V]      | [Mass] = [Dens]*[L]^3 |
-      |---    |---  |---       |---             |---                    |---                    |
-      | Value | kpc | 1e3 km/s | 5.0e-25 g/cm^3 | ~ 0.978 Myr ~ 1.0 Myr | ~ 7.4e6 Msun          |
+  - Internal (for all other input files and internal usage)
+    | Unit  | [L] | [V]      | [Dens]         | [Time] = [L]/[V]      | [Mass] = [Dens]*[L]^3 |
+    |---    |---  |---       |---             |---                    |---                    |
+    | Value | kpc | 1e3 km/s | 5.0e-25 g/cm^3 | ~ 0.978 Myr ~ 1.0 Myr | ~ 7.4e6 Msun          |
 
 - Gravity dt is disabled by setting [[DT__GRAVITY | Runtime-Parameters:-Timestep#DT__GRAVITY]] to arbitrarily large
 - [[MIN_PRES | Runtime-Parameters:-Hydro#MIN_PRES]]=`1.0e-16`
 
 
 # Note
 - Dual-energy formalism is important for evolving pressure accurately in the high Mach number region (e.g., when Mach number is greater than ~10).
-   - Especially important for small [[GAMMA | Runtime-Parameters:-Hydro#GAMMA]] and large [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]
+  - Especially important for small [[GAMMA | Runtime-Parameters:-Hydro#GAMMA]] and large [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]
 - The gnuplot script `plot_diagonal.gpt` plots the simulation results along the diagonal and compare to the analytical solutions.
   The script `plot_profile.gpt` plots the shell-average profiles generated by `gamer_extract_profile`.
 - By default it runs only for 10 Bondi time.
@@ -45,9 +45,9 @@
   using [[OPT__DT_LEVEL | Runtime-Parameters:-Timestep#OPT__DT_LEVEL]]=`3` for the first step may
   result in unphysical results since the time-step would likely be over-estimated due to both the
   zero initial velocity and the disabling of [[DT__GRAVITY | Runtime-Parameters:-Timestep#DT__GRAVITY]].
-   - It's better to adopt [[OPT__DT_LEVEL | Runtime-Parameters:-Timestep#OPT__DT_LEVE]]=`2` and
-     small [[DT__FLUID_INIT| Runtime-Parameters:-Timestep#DT__FLUID_INIT]] for the first step,
-     dump data, and then restart with [[OPT__DT_LEVEL | Runtime-Parameters:-Timestep#OPT__DT_LEVEL ]]=`3`.
+  - It's better to adopt [[OPT__DT_LEVEL | Runtime-Parameters:-Timestep#OPT__DT_LEVE]]=`2` and
+    small [[DT__FLUID_INIT| Runtime-Parameters:-Timestep#DT__FLUID_INIT]] for the first step,
+    dump data, and then restart with [[OPT__DT_LEVEL | Runtime-Parameters:-Timestep#OPT__DT_LEVEL ]]=`3`.
 
 # Links
 [[Main page of Test Problems | Test-Problems]]

diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-CDM_LSS.md b/doc/wiki/Test-Problems-related/Test-Problems:-CDM_LSS.md
@@ -8,52 +8,52 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`/`ELBDM`
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`/`ELBDM`
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Cosmological constants
-   | Parameter name | Value                  |
-   |---             |---                     |
-   | A_INIT         | 0.00990099009900990099 |
-   | OMEGA_M0       | 0.315823               |
-   | HUBBLE0        | 0.6732117              |
+  | Parameter name | Value                  |
+  |---             |---                     |
+  | A_INIT         | 0.00990099009900990099 |
+  | OMEGA_M0       | 0.315823               |
+  | HUBBLE0        | 0.6732117              |
 
 - Simulation
-   | Parameter name       | Value   | Note  |
-   |---                   |---      |---    |
-   | BOX_SIZE             | 30.0    | Mpc/h |
-   | NX0_TOT              | 128     |       |
-   | MAX_LEVEL            | 5       |       |
-   | NPAR                 | 2097152 | 128^3 |
-   | OPT__FLAG_NPAR_PATCH | 2       |       |
-   | OPT__FREEZE_FLUID    | 1       |       |
+  | Parameter name       | Value   | Note  |
+  |---                   |---      |---    |
+  | BOX_SIZE             | 30.0    | Mpc/h |
+  | NX0_TOT              | 128     |       |
+  | MAX_LEVEL            | 5       |       |
+  | NPAR                 | 2097152 | 128^3 |
+  | OPT__FLAG_NPAR_PATCH | 2       |       |
+  | OPT__FREEZE_FLUID    | 1       |       |
 
 - Particle initial condition
-   | Parameter name | Value |
-   |---             |---    |
-   | PAR_IC_FORMAT  | 1     |
-   | PAR_IC_MASS    | -1.0  |
-   | PAR_IC_TYPE    | -1    |
+  | Parameter name | Value |
+  |---             |---    |
+  | PAR_IC_FORMAT  | 1     |
+  | PAR_IC_MASS    | -1.0  |
+  | PAR_IC_TYPE    | -1    |
 
 
 # Note
 - CDM cosmological large-scale structure simulations
-- Fiducial `PAR_IC` file can be downloaded with the command.
-   ```bash
-   sh download_ic.sh
-   ```
+- Fiducial `PAR_IC` file can be downloaded with the command
+  ```bash
+  sh download_ic.sh
+  ```
 - GAMER currently doesn't support particle-only simulations. So the following temporary solutions are adopted
-   1. Set gas density/energy to arbitrarily small (for [[--model | Installation:-Option-List#--model]]=`HYDRO`)
-      or wave function to zero (for [[--model | Installation:-Option-List#--model]]=`ELBDM`) in `SetGridIC()`.
-   2. Enable [[OPT__FREEZE_FLUID | Hydro#OPT__FREEZE_FLUID]]
-- Default maximum spatial resolution is 30.0/(128*2^5)~7.3 kpc/h (comoving).
+  1. Set gas density/energy to arbitrarily small (for [[--model | Installation:-Option-List#--model]]=`HYDRO`)
+     or wave function to zero (for [[--model | Installation:-Option-List#--model]]=`ELBDM`) in `SetGridIC()`.
+  2. Enable [[OPT__FREEZE_FLUID | Runtime-Parameters:-Hydro#OPT__FREEZE_FLUID]]
+- Default maximum spatial resolution is 30.0/(128\*2^5)~7.3 kpc/h (comoving).
 
 # Links
 [[Main page of Test Problems | Test-Problems]]

diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-CMZ.md b/doc/wiki/Test-Problems-related/Test-Problems:-CMZ.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Available options
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup