Update README.md

example/test_problem/Hydro/ClusterMerger/README.md

@@ -14,6 +14,86 @@
    - [[Miscellaneous Options | Installation: Simulation-Options#miscellaneous-options]]
 
 
+# Default setup
+1. Units:
+   1. External (for `Input__TestProb` only)
+      | [L] | [M]  |
+      |---  |---   |
+      | kpc | km/s |
+
+   2. Internal (for all other input files and internal usage)
+      | [L] | [M]         | [T]       | [V] = [L]/[T] | [D] = [M]/[L]^3  |
+      |---  |---          |---        |---            |---               |
+      | kpc | 1.0e14 Msun | 1.0e1 Gyr | ~ 9.8e1 km/s  | ~ 6.8e-27 g/cm^3 |
+
+2. Default resolution ~ 15 kpc ([[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]] = 3)
+
+
+# Note
+1. Mimic the merging cluster simulation setup of Flash provided by John ZuHone
+   [John ZuHone, 2011, ApJ, 728, 54](https://dx.doi.org/10.1088/0004-637X/728/1/54)
+   [(arXiv:1004.3820)](https://arxiv.org/abs/1004.3820), but the initial conditions
+   are somewhat different.
+
+2. Run the script `download_ic.sh` to download the initial condition files for this test.
+   These files are generated by John ZuHone.
+
+3. Alternatively, you can construct the ICs yourself using the `cluster_generator` package.
+
+   Install cluster_generator from GitHub and run the included `gamer_cluster_ics.py` script
+   1. Clone the git repository to somewhere else probably
+      ```bash
+      git clone https://github.com/jzuhone/cluster_generator
+      ```
+   2. Move to the directory
+      ```bash
+      cd cluster_generator
+      ```
+   3. [Optional] Update SciPy to version >= 1.13.0
+   4. Install package
+      ```bash
+      python -m pip install .
+      ```
+   5. Go back to the `gamer_cluster_ics.py` script and run with `python gamer_cluster_ics.py`
+
+> [!WARNING]
+> This package is under development and currently has poor documentation, contact [jzuhone@gmail.com](mailto:jzuhone@gmail.com) for details
+
+4. No need to set [[PAR_NPAR | Particles#PAR_NPAR ]] in `Input__Parameter` since it will be reset automatically.
+
+5. Some handy yt analysis scripts and a notebook are put in `yt_script`
+
+   For example, to generate the slice plots, one can
+
+   1. Move to directory
+      ```bash
+      cd yt_script
+      ```
+   2. Edit `idx_start` and `idx_end` in `plot_slice-z.py`.
+   3. Execute the script
+      ```bash
+      python plot_slice-z.py
+      ```
+      or
+      ```bash
+      mpirun -np NUMBER_OF_CPU_CORES_YOU_HAVE python plot_slice-z.py
+      ```
+# Compilation flags
+- Must enable
+   - [[MODEL=HYDRO | Installation: Simulation-Options#MODEL]]
+   - [[GRAVITY | Installation: Simulation-Options#GRAVITY]]
+   - [[PARTICLE | Installation: Simulation-Options#PARTICLE]]
+   - [[SUPPORT_HDF5 | Installation: Simulation-Options#SUPPORT_HDF5]]
+   - [[NPAR_ATT_USER=0 | Installation: Simulation-Options#NPAR_ATT_USER]]
+   - [[NCOMPT_PASSIVE_USER | Installation: Simulation-Options#NCOMP_PASSIVE_USER]]>= `Merger_cool_NumHalos` + `Merger_coll_UseMetals`
+     (these are parameters in Input__TestProb)
+- Must disable
+   - [[COMOVING | Installation: Simulation-Options#COMOVING]]
+- Available options
+   - [[MHD | Installation: Simulation-Options#MHD]]
+   - [[Miscellaneous Options | Installation: Simulation-Options#miscellaneous-options]]
+
+
 # Default setup
 1. Units:
    1. External (for `Input__TestProb` only)