Add ELBDM test problems

doc/wiki/Test-Problem-related/Test-Problems:-AGORA_IsolatedGalaxy.md

@@ -40,7 +40,7 @@
    [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)
 2. Other references
    - [AGORA website](https://sites.google.com/site/santacruzcomparisonproject/)
-   - [AGORA initial condition](http://goo.gl/8JzbIJ)
+   - [AGORA initial condition](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)

doc/wiki/Test-Problem-related/Test-Problems:-DiskHeating.md

@@ -0,0 +1,143 @@
+> [!CAUTION]
+> Please do not edit this file(page) manually since the workflow will overwrite your changes.
+>
+> This file(page) is automatically generated by the workflow `Update test problem wiki page` using the script `tool/wiki/sync_test_problem_pages.py`.
+>
+> The workflow is triggered by push changes to any of `example/test_problem/*/*/README.md` and `tool/wiki/sync_test_problem_pages.py`.
+
+
+# Compilation flags
+- Must enable
+   - [[MODEL=ELBDM | Installation: Simulation-Options#MODEL]]
+   - [[GRAVITY | Installation: Simulation-Options#GRAVITY]]
+   - [[PARTICLE | Installation: Simulation-Options#PARTICLE]]
+   - [[STORE_PAR_ACC | Installation: Simulation-Options#STORE_PAR_ACC]]
+   - [[SUPPORT_HDF5 | Installation: Simulation-Options#SUPPORT_HDF5]]
+   - [[SUPPORT_GSL | Installation: Simulation-Options#SUPPORT_GSL]] (optional, only useful for thin disk)
+- Must disable
+   - [[COMOVING | Installation: Simulation-Options#COMOVING]]
+- Available options
+   - [[Miscellaneous Options | Installation: Simulation-Options#miscellaneous-options]]
+
+
+# Quick start
+0. Generate `gamer`
+   1. Copy `generate_make.sh` to the directory `src`
+   2. Generate `Makefile`
+      ```bash
+      sh generate_make.sh
+      ```
+   3. Compile `gamer`
+      ```bash
+      make clean
+      make -j 4
+      ```
+
+1. Download initial conditions of `m_22=0.4`, `M_h=7e10` Msun halo and stellar disk with
+   ```bash
+   sh download_ic.sh
+   ```
+
+2. Ensure [[PAR_INIT | #PAR_INIT]] = 1 and [[OPT__INIT]] = 3 in `Input__Parameter`
+
+3. Default [[END_T | ]] is 2.5e-1 (about 3.5 Gyr) as in [Yang et al. 2023](https://doi.org/10.1093/mnras/stae793) and [[OUTPUT_DT | ]] is 1.0e-2 (about 0.14 Gyr)
+
+4. To switch to a high-resolution run, command `ln -sf ic_files/PAR_IC_0.4_M7 PAR_IC`
+   Set [[PAR_NPAR | ]]=80000000, [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=3, and change all values in `Input__Flag_NParPatch` to `800`
+
+
+# General initial condition setup
+1. Disk
+
+   a. Generate the disk via modified [GALIC](https://github.com/HsunYeong/GALIC.git)
+      The snapshots have the filenames `snap_XXX.hdf5`
+
+   b. Set the filename, units in `get_par_ic.py` to match the GALIC set-up
+
+   c. Set center to be location of the soliton in `get_par_ic.py`
+
+   d. Execute `get_par_ic.py`, it will generate `PAR_IC`
+
+2. Halo
+
+   a. If the data is binary file `UM_IC`
+
+      * Set [[OPT__INIT | ]] = 3 and [[PAR_INIT | ]] = 1
+      * `Input__UM_IC_RefineRegion` is required
+
+   b. If the data is GAMER snapshot
+
+      * Command `ln -s Data_XXXXXX RESTART` to create a soft link
+      * Set [[OPT__INIT | ]] = 2 and [[PAR_INIT | ]] = 2 in `Input__Parameter`
+      * Turn on `AddParWhenRestart` and `AddParWhenRestartByFile` in `Input__TestProb`
+      * Set `AddParWhenRestartNPar` in `Input__TestProb`
+      * Turn on [[OPT__RESTART_RESET | ]] in `Input__Parameter`
+      # Recommand to turn off `AddParWhenRestart`, `AddParWhenRestartByFile`, [[OPT__RESTART_RESET | ]] right after the simulation starts
+
+   c. The code for [FDM halo reconstruction](https://github.com/calab-ntu/psidm-halo-reconstruction)
+
+3. Thin disk (optional)
+
+   a. Create a soft link for restart
+      ```bash
+      ln -s Data_XXXXXX RESTART
+      ```
+
+   b. Set [[OPT__INIT | ]] = 2 and [[PAR_INIT | ]] = 2 and turn on [[OPT__RESTART_RESET | ]] in Input__Parameter
+
+   c. Turn on `AddParWhenRestart` in `Input__TestProb`
+
+   d. Set `AddParWhenRestartNPar`, `Disk_Mass`, `Disk_R`, and `DispTableFile` in `Input__TestProb`
+
+
+# Analysis scripts
+1. `particle_proj.py`, `plot_halo_slice.py`
+
+   * Plot the projection of disk particles or halo density slice
+   * Output files: `particle_proj_*.png`, `Data_*_Slice_x_Dens.png`
+
+2. `plot_halo_density.py`, `plot_halo_potential.py`
+
+   * Compute and plot shell-averaged halo density or gravitational potential profiles
+   * Output files: `Data_*_1d-Profile_radius_Dens.png`, `Halo_Dens_Data_*.npy`,
+                   `Data_*_1d-Profile_radius_Pote.png`, `Halo_Pote_Data_*.npy`
+
+3. `data_disk.py`
+
+   * Compute the disk information (rotation speed, velocity dispersion, surface density, scale height, etc.)
+   * Output files: `Data_Disk_*.npy`
+
+4. `data_halo.py`
+
+   * Compute the halo information (enclosed mass, velocity dispersion, etc.)
+   * Required files: `Halo_Dens_*.npy` (generated by `plot_halo_density.py`) and `Halo_Pote_*.npy` (by `plot_halo_potential.py`)
+   * Output files: `Data_Halo_*.npy`
+
+5. `vel_distribution.py`
+
+   * Compute the velocity distribution in 2-kpc-wide radial bins centered on R = 4, 6, 8, 10 kpc
+   * Output files: `Vel_data_*.npz`, `vel_*.png`
+
+6. `get_heating.py`
+
+   * Compute the theoretical heating rate of the stellar disk as a function of radius
+   * Required files: `Data_Disk_*.npy` (generated by `data_disk.py`), `Data_Halo_*.npy` (by `data_halo.py`)
+   * Output files: `Heating_*.npz`
+
+7. `get_heating_rate_theory.py`
+
+   * Get the time-averaged theoretical heating rate
+   * Required files: `Heating_*.npz` (generated by `get_heating.py`)
+   * Output files: printed plain text
+
+8. `get_heating_rate_simulation.py`
+
+   * Compute ensemble- and time-averaged disk heating rates measured from simulation data
+   * Required files: `Vel_data_*.npz` (generated by `vel_distribution.py`)
+   * Output files: `sigma_z_sqr.png` and printed plain text
+
+9. `plot_data_example.py`
+
+   * An example script to plot the angle-averaged disk rotation curve and shell-averaged density profile
+   * Required files: `Data_Disk_*.npy` (generated by `data_disk.py`) and/or `Data_Halo_*.npy` (by `data_halo.py`)
+   * Output files: `Rotation_Curve.png`, `Halo_Density_Profile.png`

doc/wiki/Test-Problem-related/Test-Problems:-GaussianWavePacket.md

@@ -0,0 +1,26 @@
+> [!CAUTION]
+> Please do not edit this file(page) manually since the workflow will overwrite your changes.
+>
+> This file(page) is automatically generated by the workflow `Update test problem wiki page` using the script `tool/wiki/sync_test_problem_pages.py`.
+>
+> The workflow is triggered by push changes to any of `example/test_problem/*/*/README.md` and `tool/wiki/sync_test_problem_pages.py`.
+
+
+# Compilation flags
+- Must enable
+   - [[MODEL=ELBDM | Installation: Simulation-Options#MODEL]]
+- Must disable
+   - [[GRAVITY | Installation: Simulation-Options#GRAVITY]]
+   - [[PARTICLE | Installation: Simulation-Options#PARTICLE]]
+- Available options
+   - [[Miscellaneous Options | Installation: Simulation-Options#miscellaneous-options]]
+
+
+# Default setup
+1. Evolve the Gaussian wave packet for half of box
+2. Apply the analytical solution as user-defined BC
+   --> Set [[OPT__BC_FLU_* | ]] = 4
+
+
+# Note
+1. Only support 1D --> Use `Gau_XYZ` to control the propagation direction

doc/wiki/Test-Problem-related/Test-Problems:-HaloMerger.md

@@ -0,0 +1,90 @@
+> [!CAUTION]
+> Please do not edit this file(page) manually since the workflow will overwrite your changes.
+>
+> This file(page) is automatically generated by the workflow `Update test problem wiki page` using the script `tool/wiki/sync_test_problem_pages.py`.
+>
+> The workflow is triggered by push changes to any of `example/test_problem/*/*/README.md` and `tool/wiki/sync_test_problem_pages.py`.
+
+
+Compilation flags:
+========================================
+Enable : MODEL=ELBDM, GRAVITY (, PARTICLE, SUPPORT_GSL)
+Disable: COMOVING
+
+
+# Default setup
+1. Code units
+   (1) UNIT_L = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
+              = 1437.814521231748 kpc
+   (2) UNIT_V = 100 km/s
+   (3) UNIT_D = rho_bg (background matter density at z=0)
+              = 38.06 Msun/kpc^3
+       --> Mass density and wavefunction are normalized to rho_bg
+   (4) UNIT_T = 14068.4678922741 Myr
+   (5) UNIT_M = 1.131e+11 Msun
+
+2. ELBDM_MASS              1.0e-22
+   ELBDM_REMOVE_MOTION_CM  0
+   ELBDM_TAYLOR3_AUTO      0
+
+3. OPT__BC_FLU_*           1  (periodic)
+   OPT__BC_POT             2  (isolated)
+
+4. MAX_LEVEL               3
+   OPT__FLAG_RHO           1
+
+5. END_T                   0.25
+
+# Note
+1. Simulate the merger of halos and solitons in an external potential
+
+2. Edit `Input_TestProb_Halo` to specify the parameters for the halos
+   a. Add new parameters with increasing indexes if the number of halos is more than 2
+   b. For `HaloMerger_Halo_InitMode` == 1
+      - The initial condition of halos is constructed by reading the `HALO_IC` file as a table and performing linear interpolation
+         - Note that this `HALO_IC` has nothing to do with the built-in option [[OPT__INIT | ]] = 3
+      - The `HALO_IC` must be single AMR level
+         - If there is a halo `UM_IC` (for [[OPT__INIT | ]] = 3) that has multiple AMR levels (and there is `Input__UM_IC_RefineRegion`),
+           the Python script `Make_UM_IC_uniform.py` is provided to convert it to
+           a single-level `UM_IC` with the specified level, which can be used as the `HALO_IC`
+           (However, those levels higher than Target_lv+log_2( 2*PatchSize ) cannot be handled and will be ignored)
+         - If converting the halo UM_IC to be single-level is not feasible,
+           switching to the initialization option [[OPT__INIT | ]] = 3 to load a multi-level `UM_IC` is also an alternative
+           (However, only one `UM_IC` can be loaded and all the parameters in `Input_TestProb_Halo` will not be used)
+      - Note that `HaloMerger_Halo_*_CenCoord*` in `Input__TestProb_Halo` is the `HALO_IC` box center rather than the exact halo center
+
+3. Edit `Input_TestProb_Soliton` to specify the parameters for the solitons
+   a. Add new parameters with increasing indexes if the number of solitons is more than 2
+   b. For `HaloMerger_Soliton_InitMode` == 1
+      - The initial condition of solitons is constructed by reading the table of soliton density profile
+        (the density profile will be rescaled to the given core radius or core density if `HaloMerger_Soliton_*_DensProf_Rescale` == 1)
+   c. For `HaloMerger_Soliton_InitMode` == 2
+      - The initial condition of solitons is constructed by using the analytical formula of soliton density profile
+
+4. Edit `Input_TestProb_ParCloud` to specify the parameters for the particle clouds
+   a. Add new parameters with increasing indexes if the number of particle clouds is more than 2
+   b. For `HaloMerger_ParCloud_InitMode` == 1
+      - The initial condition of particle clouds is constructed by reading the table of density profile and using `Par_EquilibriumIC()`
+      - The default particle clouds use the HaloDensityProfile (see Note 7. below) to represent the CDM halos
+      - Enable compilation options: [[PARTICLE | ]], [[SUPPORT_GSL | ]]
+      - Set the parameter [[OPT__FREEZE_FLUID | ]] to 1 in `Input__Parameter` for particle-only simulations
+
+5. Turn on [[OPT__EXT_POT | ]] == 1 to add external potential
+   a. The external potential of a uniform-density sphere, which is proportional to r^2 inside and proportional to 1/r outside
+
+6. Download the default `HALO_IC` file: `sh download_ic.sh`
+   a. Halo mass = 4.0960e+09 Msun
+   b. Without soliton
+   c. N = 640, L = 0.0646921095 Mpc/h, single-precision
+
+7. Generate the default HaloDensityProfile and SolitonDensityProfile: `python Make_DensityProfile.py`
+   a. The parameters for the halo density profile are used to fit the ELBDM halo
+
+8. Some examples of yt visualization scripts are put in `plot_script`
+
+9. The corresponding wavelength is 0.00083778702 Mpc/h when ELBDM_MASS = 1.0e-22 and velocity = 1.0*100 km/s
+   -> Make sure the resolution is high enough to resolve the wavelength
+
+10. The input halos and solitons may overlap with each other initially
+   -> Their wavefunctions, instead of densities, are added directly
+   -> Note that the interference will cause the density distribution to be different from the sum of individual density

doc/wiki/Test-Problem-related/Test-Problems:-IsolatedHalo.md

@@ -0,0 +1,105 @@
+> [!CAUTION]
+> Please do not edit this file(page) manually since the workflow will overwrite your changes.
+>
+> This file(page) is automatically generated by the workflow `Update test problem wiki page` using the script `tool/wiki/sync_test_problem_pages.py`.
+>
+> The workflow is triggered by push changes to any of `example/test_problem/*/*/README.md` and `tool/wiki/sync_test_problem_pages.py`.
+
+
+# Compilation flags
+- Must enable
+   - [[MODEL=ELBDM | Installation: Simulation-Options#MODEL]]
+   - [[GRAVITY | Installation: Simulation-Options#GRAVITY]]
+- Must disable
+   - [[COMOVING | Installation: Simulation-Options#COMOVING]]
+- Available options
+   - [[Miscellaneous Options | Installation: Simulation-Options#miscellaneous-options]]
+
+
+# Default setup
+1. Code units
+   (1) UNIT_L = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
+   (2) UNIT_V = 100 km/s
+   (3) UNIT_D = rho_bg (background matter density at z=0)
+       --> Mass density and wavefunction are normalized to rho_bg
+
+2. ELBDM
+   | Parameter name         | value   |
+   |---                     |---      |
+   | ELBDM_MASS             | 8.0e-23 |
+   | ELBDM_REMOVE_MOTION_CM | 1       |
+   | ELBDM_TAYLOR3_AUTO     | 0       |
+
+3. Boundary conditions
+   | Parameter name | value |
+   |---             |---    |
+   | OPT__BC_FLU_*  | 1     |
+   | OPT__BC_POT    | 2     |
+
+4. AMR
+   | Parameter name | value |
+   |---             |---    |
+   | MAX_LEVEL      | 0     |
+
+
+# Libyt covering_grid setup
+1. Code units
+   (1) UNIT_L = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
+   (2) UNIT_V = 100 km/s
+   (3) UNIT_D = rho_bg (background matter density at z=0)
+       --> Mass density and wavefunction are normalized to rho_bg
+
+2. ELBDM
+   | Parameter name         | value   |
+   |---                     |---      |
+   | ELBDM_MASS             | 8.0e-23 |
+   | ELBDM_REMOVE_MOTION_CM | 1       |
+   | ELBDM_TAYLOR3_AUTO     | 0       |
+
+3. Boundary conditions
+   | Parameter name | value |
+   |---             |---    |
+   | OPT__BC_FLU_*  | 1     |
+   | OPT__BC_POT    | 2     |
+
+4. AMR
+   | Parameter name | value |
+   |---             |---    |
+   | MAX_LEVEL      | 0     |
+   | OPT__FLAG_RHO  | 1     |
+
+5. End simulation condition
+   | Parameter name | value         |
+   |---             |---            |
+   | END_T          | 5.7116620e-03 |
+   | END_STEP       | 32            |
+
+6. libyt
+   | Parameter name | value                                    |
+   |---             |---                                       |
+   | YT_SCRIPT      | libyt_script/inline_script_covering_grid |
+   | YT_VERBOSE     | 1                                        |
+
+
+# Note
+1. Download the IC file
+   ```bash
+   sh download_ic.sh
+   ```
+
+2. Some examples of yt visualization scripts are put in `yt_script`
+
+3. Simulate a single isolated halo extracted from a cosmological simulation
+
+4. About libyt covering_grid test
+   a. Use submit script `./libyt_script/submit_gamer.job` for job submission
+
+   b. Put `./libyt_script/inline_script_covering_grid.py` under the same folder as gamer
+
+   c. For determining the `left_edge` and `dims` in function `ds.covering_grid`:
+      `left_edge`: LV1 resolution is 0.175/512/2 ; region covered by LV1 box (by `ds.covering_grid`) is 0.175/512/2*512; 0.04375 = (0.175 - 0.175/512/2*512)/2
+      `dims`:      Plan to cover region with half of the simulation box length, i.e. will have 256X256X256 base level cells -> refine to MAX_LEVEL=1 -> LV1 cells is 512X512X512
+
+   d. Use `plot_slice-dens_covering_grid.py` to extract density slices from `.npz` files
+
+   e. Use `make_movie.sh` to convert `.png` pictures into `.mp4`