diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-AGORA_IsolatedGalaxy.md b/doc/wiki/Test-Problems-related/Test-Problems:-AGORA_IsolatedGalaxy.md index b063a2294..67da95a8d 100644 --- 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 index 5e383dd3f..73a1678eb 100644 --- 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 index 7356dc06c..9982ab402 100644 --- 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 index 8f57ce49f..193b9aabe 100644 --- a/doc/wiki/Test-Problems-related/Test-Problems:-Bondi.md +++ b/doc/wiki/Test-Problems-related/Test-Problems:-Bondi.md @@ -8,26 +8,26 @@ # `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` @@ -35,7 +35,7 @@ # 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 index 16c309a00..580b83fde 100644 --- 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 index 42a090698..9e1ef39c5 100644 --- 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 diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-CR_Diffusion.md b/doc/wiki/Test-Problems-related/Test-Problems:-CR_Diffusion.md index 1501fb1a4..3d3c1e130 100644 --- a/doc/wiki/Test-Problems-related/Test-Problems:-CR_Diffusion.md +++ b/doc/wiki/Test-Problems-related/Test-Problems:-CR_Diffusion.md @@ -8,17 +8,16 @@ # `configure.py` options - Must enable - - [[--model | Installation:-Option-List#--model]]=`HYDRO` - - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY` - - [[--double | Installation:-Option-List#--double]] - - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]] - - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]] + - [[--model | Installation:-Option-List#--model]]=`HYDRO` + - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY` + - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]] + - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]] - 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 @@ -28,50 +27,50 @@ # Note -1. The analytical solution of `CR_Diffusion_Type`=`{0,1,2,3}` must set all fluid to be fixed but cosmic rays. +- The analytical solution of `CR_Diffusion_Type`=`{0,1,2,3}` must set all fluid to be fixed but cosmic rays. ## `CR_Diffusion_Type` - Gaussian distribution ball (`CR_Diffusion_Type`=`0`) - - All of the fluid must be fixed, except for cosmic rays. + - All of the fluid must be fixed, except for cosmic rays. - Step function ring (`CR_Diffusion_Type`=`1`) - - All fluids must be fixed, except for cosmic rays. - - This test problem is a 2D simulation. - - The analytical solution assumes the CRs diffuse along the azimuthal direction only. + - All fluids must be fixed, except for cosmic rays. + - This test problem is a 2D simulation. + - The analytical solution assumes the CRs diffuse along the azimuthal direction only. - Gaussian distribution ring (`CR_Diffusion_Type`=`2`) - - All fluids must be fixed, except for cosmic rays. - - This test problem is a 2D simulation. - - The analytical solution assumes the CRs diffuse along the azimuthal direction only. + - All fluids must be fixed, except for cosmic rays. + - This test problem is a 2D simulation. + - The analytical solution assumes the CRs diffuse along the azimuthal direction only. - Gaussian distribution plane (`CR_Diffusion_Type`=`3`) - - All fluids must be fixed, except for cosmic rays. - - The analytical solution assumes the CRs diffuse along the diagonal direction. + - All fluids must be fixed, except for cosmic rays. + - The analytical solution assumes the CRs diffuse along the diagonal direction. - CR driven blast wave (`CR_Diffusion_Type`=`4`) - - This test problem is a 3D simulation. + - This test problem is a 3D simulation. ## `CR_Diffusion_Mag_Type` - Uniform (`CR_Diffusion_Mag_Type`=`0`) - - Uniform magnetic field. + - Uniform magnetic field. - Circular (`CR_Diffusion_Mag_Type`=`1`) - - Only works for 2D simulation - - For x-y plane: `B = (-y/r, x/r, 0)` where `r = sqrt(x^2+y^2)`. - - Using `CR_Diffusion_MagX` as amplitude. + - Only works for 2D simulation + - For x-y plane: `B = (-y/r, x/r, 0)` where `r = sqrt(x^2+y^2)`. + - Using `CR_Diffusion_MagX` as amplitude. - Random (`CR_Diffusion_Mag_Type`=`2`) - - NOT divergence free! - - `-1. < B_i < 1.` + - NOT divergence free! + - `-1. < B_i < 1.` - Radial (`CR_Diffusion_Mag_Type`=`3`) - - NOT divergence free! - - Only works for 2D simulation - - For x-y plane: `B = (x/r, y/r, 0)` where `r = sqrt(x^2+y^2)`. - - Using `CR_Diffusion_MagX` as amplitude. + - NOT divergence free! + - Only works for 2D simulation + - For x-y plane: `B = (x/r, y/r, 0)` where `r = sqrt(x^2+y^2)`. + - Using `CR_Diffusion_MagX` as amplitude. - Suwa+ 2007 (`CR_Diffusion_Mag_Type`=`4`) - - Follows [Suwa+ 2007, PASJ, 59, 771](https://doi.org/10.1093/pasj/59.4.771) setup - - Using `CR_Diffusion_MagX` as amplitude. + - Follows [Suwa+ 2007, PASJ, 59, 771](https://doi.org/10.1093/pasj/59.4.771) setup + - Using `CR_Diffusion_MagX` as amplitude. ## Set simulation dimensions @@ -98,15 +97,15 @@ Not available right now. ## `yt_L1error.py` - The file structure should be like: - 
-   ./ --+-- res_0032 --+-- Data_000000
-        |              |
-        |              |-- ...
-        |
-        |-- res_0064 --+-- Data_000000
-        |              |
-        |-- ...        |-- ...
-   <\pre>
+  
+  ./ --+-- res_0032 --+-- Data_000000
+       |              |
+       |              |-- ...
+       |
+       |-- res_0064 --+-- Data_000000
+       |              |
+       |-- ...        |-- ...
+  <\pre>
 - Uncomment or comment your simulation type and set the parameters.
 
 # Links
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-CR_ShockTube.md b/doc/wiki/Test-Problems-related/Test-Problems:-CR_ShockTube.md
index def1438b5..09492fbb1 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-CR_ShockTube.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-CR_ShockTube.md
@@ -8,16 +8,16 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY`
-   - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY`
+  - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-CR_SoundWave.md b/doc/wiki/Test-Problems-related/Test-Problems:-CR_SoundWave.md
index 64f9815ed..8de42f70d 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-CR_SoundWave.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-CR_SoundWave.md
@@ -8,17 +8,17 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY`
-   - [[--double | Installation:-Option-List#--double]]
-   - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--eos | Installation:-Option-List#--eos]]=`COSMIC_RAY`
+  - [[--double | Installation:-Option-List#--double]]
+  - [[--cosmic_ray | Installation:-Option-List#--cosmic_ray]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--cr_diffusion | Installation:-Option-List#--cr_diffusion]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -28,7 +28,7 @@
 
 # Note
 - Support both 1D and 3D cases
-   - set by `CR_Acoustic_Dir`
+  - set by `CR_Acoustic_Dir`
 - A simple Python script `plot_wave.py` is attached
 - `Record__L1Err` records the L1 errors
 - `CosmicRay_AcousticWave_*_*` record the numerical and analytical solutions along the diagonal
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Caustic.md b/doc/wiki/Test-Problems-related/Test-Problems:-Caustic.md
index a24baebd1..f380a8df1 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Caustic.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Caustic.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
 - 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
@@ -26,7 +26,7 @@
 # Note
 - Ref: [Ryu, D., Ostriker, J. P., Kang, H., & Cen, R. 1993, ApJ, 414, 1](https://doi.org/10.1086/173051)
 - This test is good for testing the dual-energy formalism
-   - Without it the preshock region will be over-heated
+  - Without it the preshock region will be over-heated
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-ClusterMerger.md b/doc/wiki/Test-Problems-related/Test-Problems:-ClusterMerger.md
index 5ed465c1e..1334dbb7d 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-ClusterMerger.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-ClusterMerger.md
@@ -8,84 +8,84 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--hdf5 | Installation:-Option-List#--hdf5]]
-   - [[--par_attribute=0 | Installation:-Option-List#--par_attribute]]
-   - [[--passive | Installation:-Option-List#--passive]]>= `Merger_cool_NumHalos` + `Merger_coll_UseMetals`
-     (these are parameters in `Input__TestProb`)
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--hdf5 | Installation:-Option-List#--hdf5]]
+  - [[--par_attribute | Installation:-Option-List#--par_attribute]]=`0`
+  - [[--passive | Installation:-Option-List#--passive]]>= `Merger_cool_NumHalos` + `Merger_coll_UseMetals`
+    (these are parameters in `Input__TestProb`)
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - 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
 - Units
-   - External (for `Input__TestProb` only)
-      | Unit  | [L] | [M]  |
-      |---    |---  |---   |
-      | Value | kpc | km/s |
+  - External (for `Input__TestProb` only)
+    | Unit  | [L] | [M]  |
+    |---    |---  |---   |
+    | Value | kpc | km/s |
 
-   - Internal (for all other input files and internal usage)
-      | Unit  | [L] | [M]         | [T]       | [V] = [L]/[T] | [D] = [M]/[L]^3  |
-      |---    |---  |---          |---        |---            |---               |
-      | Value | kpc | 1.0e14 Msun | 1.0e1 Gyr | ~ 9.8e1 km/s  | ~ 6.8e-27 g/cm^3 |
+  - Internal (for all other input files and internal usage)
+    | Unit  | [L] | [M]         | [T]       | [V] = [L]/[T] | [D] = [M]/[L]^3  |
+    |---    |---  |---          |---        |---            |---               |
+    | Value | kpc | 1.0e14 Msun | 1.0e1 Gyr | ~ 9.8e1 km/s  | ~ 6.8e-27 g/cm^3 |
 
 - Default resolution ~ 15 kpc ([[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`3`)
 
 
 # Note
 - 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.
+  - [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.
 
 - Run the script `download_ic.sh` to download the initial condition files for this test.
-  These files are generated by John ZuHone.
+  - These files are generated by John ZuHone.
 
 - 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`
+  - 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
 
-- No need to set [[PAR_NPAR | Runtime-Parameters:-Particles#PAR_NPAR ]] in `Input__Parameter` since it will be reset automatically.
+- No need to set [[PAR_NPAR | Runtime-Parameters:-Particles#PAR_NPAR]] in `Input__Parameter` since it will be reset automatically.
 
 - 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
-      ```
+  - 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
+       ```
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-DiskHeating.md b/doc/wiki/Test-Problems-related/Test-Problems:-DiskHeating.md
index 9484a06b3..94762884d 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-DiskHeating.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-DiskHeating.md
@@ -8,19 +8,19 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--store_par_acc | Installation:-Option-List#--store_par_acc]]
-   - [[--hdf5 | Installation:-Option-List#--hdf5]]
-   - [[--gsl | Installation:-Option-List#--gsl]] (optional, only useful for thin disk)
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--store_par_acc | Installation:-Option-List#--store_par_acc]]
+  - [[--hdf5 | Installation:-Option-List#--hdf5]]
+  - [[--gsl | Installation:-Option-List#--gsl]] (optional, only useful for thin disk)
 - 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]]
 
-> [!NOTE]
-> DiskHeatingParticleIC uses the floating-point type for particle type and assumes single precision
+# Note
+- DiskHeatingParticleIC uses the floating-point type for particle type and assumes single precision
 
 # Quick start
 0. Generate `gamer`
@@ -60,105 +60,105 @@
 # General initial condition setup
 - Disk
 
-   1. Generate the disk via modified [GALIC](https://github.com/HsunYeong/GALIC.git).
-      The snapshots have the filenames `snap_XXX.hdf5`
+  1. Generate the disk via modified [GALIC](https://github.com/HsunYeong/GALIC.git).
+     The snapshots have the filenames `snap_XXX.hdf5`
 
-   2. Set the filename, and units in `get_par_ic.py` to match the GALIC set-up
+  2. Set the filename, and units in `get_par_ic.py` to match the GALIC set-up
 
-   3. Set center to be the location of the soliton in `get_par_ic.py`
+  3. Set center to be the location of the soliton in `get_par_ic.py`
 
-   4. Execute `get_par_ic.py`, it will generate `DiskHeatingParticleIC`
+  4. Execute `get_par_ic.py`, it will generate `DiskHeatingParticleIC`
 
 - Halo
 
-   - If the data is binary file `UM_IC`
+  - If the data is binary file `UM_IC`
 
-      1. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`3` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`1`
+    1. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`3` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`1`
 
-      2. `Input__UM_IC_RefineRegion` is required
+    2. `Input__UM_IC_RefineRegion` is required
 
-   - If the data is GAMER snapshot (`Data_XXXXXX`)
+  - If the data is GAMER snapshot (`Data_XXXXXX`)
 
-      1. Create a soft link for restart
-         ```bash
-         ln -s Data_XXXXXX RESTART
-         ```
+    1. Create a soft link for restart
+       ```bash
+       ln -s Data_XXXXXX RESTART
+       ```
 
-      2. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`2` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`2` in `Input__Parameter`
+    2. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`2` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`2` in `Input__Parameter`
 
-      3. Turn on `AddParWhenRestart` and `AddParWhenRestartByFile` in `Input__TestProb`
+    3. Turn on `AddParWhenRestart` and `AddParWhenRestartByFile` in `Input__TestProb`
 
-      4. Set `AddParWhenRestartNPar` in `Input__TestProb`
+    4. Set `AddParWhenRestartNPar` in `Input__TestProb`
 
-      5. Turn on [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] in `Input__Parameter`
-         - Recommend to turn off `AddParWhenRestart`, `AddParWhenRestartByFile`, [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] right after the simulation starts
+    5. Turn on [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] in `Input__Parameter`
+       - Recommend to turn off `AddParWhenRestart`, `AddParWhenRestartByFile`, [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] right after the simulation starts
 
-   - The code for [FDM halo reconstruction](https://github.com/calab-ntu/psidm-halo-reconstruction)
+  - The code for [FDM halo reconstruction](https://github.com/calab-ntu/psidm-halo-reconstruction)
 
 - Thin disk (optional)
 
-   1. Create a soft link for restart
-      ```bash
-      ln -s Data_XXXXXX RESTART
-      ```
+  1. Create a soft link for restart
+     ```bash
+     ln -s Data_XXXXXX RESTART
+     ```
 
-   2. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`2` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`2` and turn on [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] in `Input__Parameter`
+  2. Set [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`2` and [[PAR_INIT | Runtime-Parameters:-Particles#PAR_INIT]]=`2` and turn on [[OPT__RESTART_RESET | Runtime-Parameters:-Initial-Conditions#OPT__RESTART_RESET]] in `Input__Parameter`
 
-   3. Turn on `AddParWhenRestart` in `Input__TestProb`
+  3. Turn on `AddParWhenRestart` in `Input__TestProb`
 
-   4. Set `AddParWhenRestartNPar`, `Disk_Mass`, `Disk_R`, and `DispTableFile` in `Input__TestProb`
+  4. Set `AddParWhenRestartNPar`, `Disk_Mass`, `Disk_R`, and `DispTableFile` in `Input__TestProb`
 
 
 # Analysis scripts
 - `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`
+  - Plot the projection of disk particles or halo density slice
+  - Output files: `particle_proj_*.png`, `Data_*_Slice_x_Dens.png`
 
 - `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`, and `Halo_Pote_Data_*.npy`
+  - 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`, and `Halo_Pote_Data_*.npy`
 
 - `data_disk.py`
 
-   - Compute the disk information (rotation speed, velocity dispersion, surface density, scale height, etc.)
-   - Output files: `Data_Disk_*.npy`
+  - Compute the disk information (rotation speed, velocity dispersion, surface density, scale height, etc.)
+  - Output files: `Data_Disk_*.npy`
 
 - `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`
+  - 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`
 
 - `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`
+  - 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`
 
 - `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`
+  - 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`
 
 - `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
+  - Get the time-averaged theoretical heating rate
+  - Required files: `Heating_*.npz` (generated by `get_heating.py`)
+  - Output files: printed plain text
 
 - `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
+  - 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
 
 - `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`
+  - 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`
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-EnergyPowerSpectrum.md b/doc/wiki/Test-Problems-related/Test-Problems:-EnergyPowerSpectrum.md
index 21242f710..f64d29e27 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-EnergyPowerSpectrum.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-EnergyPowerSpectrum.md
@@ -8,15 +8,15 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--eos | Installation:-Option-List#--eos]]=`GAMMA`
-   - [[--fftw | Installation:-Option-List#--fftw]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--eos | Installation:-Option-List#--eos]]=`GAMMA`
+  - [[--fftw | Installation:-Option-List#--fftw]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--mhd | Installation:-Option-List#--mhd]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-ExtPot.md b/doc/wiki/Test-Problems-related/Test-Problems:-ExtPot.md
index 08c056746..883cf5a53 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-ExtPot.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-ExtPot.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-GaussianWavePacket.md b/doc/wiki/Test-Problems-related/Test-Problems:-GaussianWavePacket.md
index d4acb78f0..95109b5a1 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-GaussianWavePacket.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-GaussianWavePacket.md
@@ -8,23 +8,23 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Evolve the Gaussian wave packet for half of box
 - Apply the analytical solution as user-defined BC
-   - Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`4`
+  - Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`4`
 
 
 # Note
 - Only support 1D
-   - Use `Gau_XYZ` to control the propagation direction
+  - Use `Gau_XYZ` to control the propagation direction
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Gravity.md b/doc/wiki/Test-Problems-related/Test-Problems:-Gravity.md
index 45b6f66d3..6ffc10783 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Gravity.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Gravity.md
@@ -8,15 +8,15 @@
 
 # `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
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--mhd | Installation:-Option-List#--mhd]]
-   - [[--dual | Installation:-Option-List#--dual]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--dual | Installation:-Option-List#--dual]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -27,27 +27,27 @@
 
 # Note
 - This test problem will overwrite gas field to store the gravitational potential errors
-   - gas momentum x --> absolute errors of potential
-   - gas momentum y --> relative errors of potential
+  - gas momentum x --> absolute errors of potential
+  - gas momentum y --> relative errors of potential
 
-   Two output files will be generated:
-   - `PotError.bin`: binary file similar to `Data_??????` but with the gas field overwritten
-   - `PotError.txt`: text   file storing the overwritten data along the diagonal
+  Two output files will be generated:
+  - `PotError.bin`: binary file similar to `Data_??????` but with the gas field overwritten
+  - `PotError.txt`: text   file storing the overwritten data along the diagonal
 
 - Two plot scripts are provided
-   - `plot__pot_error_diagonal.gpt`: plot the text file `PotError.txt` using `gnuplot`
-   - `plot__pot_error_slice.py`: plot a slice of potential error from `PotError.bin` using `yt`
+  - `plot__pot_error_diagonal.gpt`: plot the text file `PotError.txt` using `gnuplot`
+  - `plot__pot_error_slice.py`: plot a slice of potential error from `PotError.bin` using `yt`
 
 - Currently supports 2 density profiles: NFW and Hernquist
-   - Controlled by the parameter `Gra_DensProf`.
-   - Note that errors in NFW can be very large since the total mass in NFW diverges and the adopted analytical
-     solution assumes zero potential at infinity.
-      - Numerical and analytical solutions will differ by a DC term.
+  - Controlled by the parameter `Gra_DensProf`.
+  - Note that errors in NFW can be very large since the total mass in NFW diverges and the adopted analytical
+    solution assumes zero potential at infinity.
+    - Numerical and analytical solutions will differ by a DC term.
 
 - Set `Gra_NIterProf>0` to measure the average performance of the Poisson solver
-   - The measured performance excludes the time for exchanging MPI buffer data.
-   - When adopting the isolated Poisson solver (i.e., [[OPT__BC_POT | Runtime-Parameters:-Hydro#OPT__BC_POT]]=`2`), both "NCell" and "Cells/s"
-     in `Record__PoissonPerformance` do not count the number of cells in the padded region.
+  - The measured performance excludes the time for exchanging MPI buffer data.
+  - When adopting the isolated Poisson solver (i.e., [[OPT__BC_POT | Runtime-Parameters:-Hydro#OPT__BC_POT]]=`2`), both "NCell" and "Cells/s"
+    in `Record__PoissonPerformance` do not count the number of cells in the padded region.
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-HaloMerger.md b/doc/wiki/Test-Problems-related/Test-Problems:-HaloMerger.md
index 42d5fc808..a7321de40 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-HaloMerger.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-HaloMerger.md
@@ -8,51 +8,51 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]] (optional for `HaloMerger_ParCloud_InitMode`=`1`)
-   - [[--gsl | Installation:-Option-List#--gsl]] (optional for `HaloMerger_ParCloud_InitMode`=`1`)
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]] (optional for `HaloMerger_ParCloud_InitMode`=`1`)
+  - [[--gsl | Installation:-Option-List#--gsl]] (optional for `HaloMerger_ParCloud_InitMode`=`1`)
 - 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]]
 
 
 # Default setup
 - 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
+  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
+     - Mass density and wavefunction are normalized to rho_bg
+  4. `UNIT_T` = 14068.4678922741 Myr
+  5. `UNIT_M` = 1.131e+11 Msun
 
 - ELBDM
-   | Parameter name         | value   |
-   |---                     |---      |
-   | ELBDM_MASS             | 1.0e-22 |
-   | ELBDM_REMOVE_MOTION_CM | 0       |
-   | ELBDM_TAYLOR3_AUTO     | 0       |
+  | Parameter name         | Value   |
+  |---                     |---      |
+  | ELBDM_MASS             | 1.0e-22 |
+  | ELBDM_REMOVE_MOTION_CM | 0       |
+  | ELBDM_TAYLOR3_AUTO     | 0       |
 
 - Boundary condition
-   | Parameter name | value |
-   |---             |---    |
-   | OPT__BC_FLU_*  | 1     |
-   | OPT__BC_POT    | 2     |
+  | Parameter name | Value | Note |
+  |---             |---    |--- |
+  | OPT__BC_FLU_*  | 1     | periodic |
+  | OPT__BC_POT    | 2     | isolated |
 
 - AMR
-   | Parameter name | value |
-   |---             |---    |
-   | MAX_LEVEL      | 3     |
-   | OPT__FLAG_RHO  | 1     |
+  | Parameter name | Value |
+  |---             |---    |
+  | MAX_LEVEL      | 3     |
+  | OPT__FLAG_RHO  | 1     |
 
 - Simulation
-   | Parameter name | value |
-   |---             |---    |
-   | END_T          | 0.25  |
+  | Parameter name | Value |
+  |---             |---    |
+  | END_T          | 0.25  |
 
 
 # Note
@@ -60,72 +60,72 @@
 
 - Edit `Input_TestProb_Halo` to specify the parameters for the halos
 
-   - Add new parameters with increasing indexes if the number of halos is more than 2
-
-   - 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 | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`3`
-      - The `HALO_IC` must be single AMR level
-         - If there is a halo `UM_IC` (for [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#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 | Runtime-Parameters:-Initial-Conditions#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
+  - Add new parameters with increasing indexes if the number of halos is more than 2
+
+  - 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 | Runtime-Parameters:-Initial-Conditions#OPT__INIT]]=`3`
+    - The `HALO_IC` must be single AMR level
+      - If there is a halo `UM_IC` (for [[OPT__INIT | Runtime-Parameters:-Initial-Conditions#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 | Runtime-Parameters:-Initial-Conditions#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
 
 - Edit `Input_TestProb_Soliton` to specify the parameters for the solitons
 
-   - Add new parameters with increasing indexes if the number of solitons is more than 2
+  - Add new parameters with increasing indexes if the number of solitons is more than 2
 
-   - 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`)
+  - 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`)
 
-   - For `HaloMerger_Soliton_InitMode`=`2`
-      - The initial condition of solitons is constructed by using the analytical formula of the soliton density profile
+  - For `HaloMerger_Soliton_InitMode`=`2`
+    - The initial condition of solitons is constructed by using the analytical formula of the soliton density profile
 
 - Edit `Input_TestProb_ParCloud` to specify the parameters for the particle clouds
 
-   - Add new parameters with increasing indexes if the number of particle clouds is more than 2
+  - Add new parameters with increasing indexes if the number of particle clouds is more than 2
 
-   - 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 | Installation:-Option-List#--particle]], [[--gsl | Installation:-Option-List#--gsl]]
-      - Set the parameter [[OPT__FREEZE_FLUID | Runtime-Parameters:-Hydro#OPT__FREEZE_FLUID]] to 1 in `Input__Parameter` for particle-only simulations
+  - 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 | Installation:-Option-List#--particle]], [[--gsl | Installation:-Option-List#--gsl]]
+    - Set the parameter [[OPT__FREEZE_FLUID | Runtime-Parameters:-Hydro#OPT__FREEZE_FLUID]] to 1 in `Input__Parameter` for particle-only simulations
 
 - Turn on [[OPT__EXT_POT | Runtime-Parameters:-Gravity#OPT__EXT_POT]]=`1` to add external potential
 
-   - The external potential of a uniform-density sphere, which is proportional to `r^2` inside and proportional to `1/r` outside
+  - The external potential of a uniform-density sphere, which is proportional to `r^2` inside and proportional to `1/r` outside
 
 - Download the default `HALO_IC` file
-   ```bash
-   sh download_ic.sh
-   ```
+  ```bash
+  sh download_ic.sh
+  ```
 
-   - Halo mass = 4.0960e+09 Msun
-   - Without soliton
-   - N = 640, L = 0.0646921095 Mpc/h, single-precision
+  - Halo mass = 4.0960e+09 Msun
+  - Without soliton
+  - N = 640, L = 0.0646921095 Mpc/h, single-precision
 
 - Generate the default HaloDensityProfile and SolitonDensityProfile
-   ```bash
-   python Make_DensityProfile.py
-   ```
+  ```bash
+  python Make_DensityProfile.py
+  ```
 
-   - The parameters for the halo density profile are used to fit the ELBDM halo
+  - The parameters for the halo density profile are used to fit the ELBDM halo
 
 - Some examples of yt visualization scripts are put in `plot_script`
 
 - The corresponding wavelength is 0.00083778702 Mpc/h when [[ELBDM_MASS | Runtime-Parameters:-ELBDM#ELBDM_MASS]]=`1.0e-22` and velocity = 1.0*100 km/s
 
-   - Make sure the resolution is high enough to resolve the wavelength
+  - Make sure the resolution is high enough to resolve the wavelength
 
 - 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
+  - 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
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-IsolatedHalo.md b/doc/wiki/Test-Problems-related/Test-Problems:-IsolatedHalo.md
index a744fd374..b7be927ac 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-IsolatedHalo.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-IsolatedHalo.md
@@ -8,101 +8,101 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - 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]]
 
 
 # Default setup
 - Code units
-   - `UNIT_L` = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
-   - `UNIT_V` = 100 km/s
-   - `UNIT_D` = rho_bg (background matter density at z=0)
-      - Mass density and wavefunction are normalized to rho_bg
+  - `UNIT_L` = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
+  - `UNIT_V` = 100 km/s
+  - `UNIT_D` = rho_bg (background matter density at z=0)
+    - Mass density and wavefunction are normalized to rho_bg
 
 - ELBDM
-   | Parameter name         | value   |
-   |---                     |---      |
-   | ELBDM_MASS             | 8.0e-23 |
-   | ELBDM_REMOVE_MOTION_CM | 1       |
-   | ELBDM_TAYLOR3_AUTO     | 0       |
+  | Parameter name         | Value   |
+  |---                     |---      |
+  | ELBDM_MASS             | 8.0e-23 |
+  | ELBDM_REMOVE_MOTION_CM | 1       |
+  | ELBDM_TAYLOR3_AUTO     | 0       |
 
 - Boundary conditions
-   | Parameter name | value |
-   |---             |---    |
-   | OPT__BC_FLU_*  | 1     |
-   | OPT__BC_POT    | 2     |
+  | Parameter name | Value | Note |
+  |---             |---    |--- |
+  | OPT__BC_FLU_*  | 1     | periodic |
+  | OPT__BC_POT    | 2     | isolated |
 
 - AMR
-   | Parameter name | value |
-   |---             |---    |
-   | MAX_LEVEL      | 0     |
+  | Parameter name | Value |
+  |---             |---    |
+  | MAX_LEVEL      | 0     |
 
 
 # Libyt `covering_grid` setup
 - Code units
-   - `UNIT_L` = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
-   - `UNIT_V` = 100 km/s
-   - `UNIT_D` = rho_bg (background matter density at z=0)
-      - Mass density and wavefunction are normalized to rho_bg
+  - `UNIT_L` = Mpc/h, where h=0.6955 is the present dimensionless Hubble parameter
+  - `UNIT_V` = 100 km/s
+  - `UNIT_D` = rho_bg (background matter density at z=0)
+    - Mass density and wavefunction are normalized to rho_bg
 
 - ELBDM
-   | Parameter name         | value   |
-   |---                     |---      |
-   | ELBDM_MASS             | 8.0e-23 |
-   | ELBDM_REMOVE_MOTION_CM | 1       |
-   | ELBDM_TAYLOR3_AUTO     | 0       |
+  | Parameter name         | Value   |
+  |---                     |---      |
+  | ELBDM_MASS             | 8.0e-23 |
+  | ELBDM_REMOVE_MOTION_CM | 1       |
+  | ELBDM_TAYLOR3_AUTO     | 0       |
 
 - Boundary conditions
-   | Parameter name | value |
-   |---             |---    |
-   | OPT__BC_FLU_*  | 1     |
-   | OPT__BC_POT    | 2     |
+  | Parameter name | Value | Note |
+  |---             |---    |--- |
+  | OPT__BC_FLU_*  | 1     | periodic |
+  | OPT__BC_POT    | 2     | isolated |
 
 - AMR
-   | Parameter name | value |
-   |---             |---    |
-   | MAX_LEVEL      | 0     |
-   | OPT__FLAG_RHO  | 1     |
+  | Parameter name | Value |
+  |---             |---    |
+  | MAX_LEVEL      | 1     |
+  | OPT__FLAG_RHO  | 1     |
 
 - End simulation condition
-   | Parameter name | value         |
-   |---             |---            |
-   | END_T          | 5.7116620e-03 |
-   | END_STEP       | 32            |
+  | Parameter name | Value         |
+  |---             |---            |
+  | END_T          | 5.7116620e-03 |
+  | END_STEP       | 32            |
 
 - libyt
-   | Parameter name | value                                    |
-   |---             |---                                       |
-   | YT_SCRIPT      | libyt_script/inline_script_covering_grid |
-   | YT_VERBOSE     | 1                                        |
+  | Parameter name | Value                                    |
+  |---             |---                                       |
+  | YT_SCRIPT      | libyt_script/inline_script_covering_grid |
+  | YT_VERBOSE     | 1                                        |
 
 
 # Note
 - Download the IC file
-   ```bash
-   sh download_ic.sh
-   ```
+  ```bash
+  sh download_ic.sh
+  ```
 
 - Some examples of yt visualization scripts are put in `yt_script`
 
 - Simulate a single isolated halo extracted from a cosmological simulation
 
 - About libyt `covering_grid` test
-   - Use submit script `./libyt_script/submit_gamer.job` for job submission
+  - Use submit script `./libyt_script/submit_gamer.job` for job submission
 
-   - Put `./libyt_script/inline_script_covering_grid.py` under the same folder as gamer
+  - Put `./libyt_script/inline_script_covering_grid.py` under the same folder as gamer
 
-   - 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
+  - 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 | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`1` -> LV1 cells is 512X512X512
 
-   - Use `plot_slice-dens_covering_grid.py` to extract density slices from `.npz` files
+  - Use `plot_slice-dens_covering_grid.py` to extract density slices from `.npz` files
 
-   - Use `make_movie.sh` to convert `.png` pictures into `.mp4`
+  - Use `make_movie.sh` to convert `.png` pictures into `.mp4`
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstability.md b/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstability.md
index 98cd3bd33..2594e541c 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstability.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstability.md
@@ -8,52 +8,52 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--double | Installation:-Option-List#--double]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--double | Installation:-Option-List#--double]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - 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
 - Resolution = 64^3
 - Simulation time
-   - stable -> one period
-   - unstable -> grow/decay by a factor of 50
-- Gravitational constant = 1/(4*pi) = 0.07957747154
+  - stable -> one period
+  - unstable -> grow/decay by a factor of 50
+- Gravitational constant = 1/(4\*pi) = 0.07957747154
 
 
 # Note
 - Support both hydro and MHD. For the latter, a fast-wave solution is adopted.
 - Support both 1D and 3D cases.
-   - set by `Jeans_Dir`
+  - set by `Jeans_Dir`
 - A simple gnuplot script `plot.gpt` is attached.
 - `Record__L1Err` records the L1 errors.
 - `Jeans_*` record the numerical and analytical solutions along the diagonal.
 - Example parameters
-   - Stable right-moving wave
-     ```
-     Jeans_Rho0        1.0            # background density
-     Jeans_Rho1        1.0e-6         # density perturbation amplitude
-     Jeans_P0          1.0e-2         # background pressure
-     Jeans_v0          0.0            # background velocity [0.0]
-     Jeans_B0          1.0e-2         # background magnetic field amplitude
-     Jeans_Sign       +1.0            # (>0/<0) --> (stable:right/left-moving wave; unstable:growing/decaying mode) [+1]
-     ```
-
-   - Unstable growing mode
-     ```
-     Jeans_Rho0        2.0            # background density
-     Jeans_Rho1        1.0e-6         # density perturbation amplitude
-     Jeans_P0          1.0e-2         # background pressure
-     Jeans_v0          0.0            # background velocity [0.0]
-     Jeans_B0          1.0e-2         # background magnetic field amplitude
-     Jeans_Sign       +1.0            # (>0/<0) --> (stable:right/left-moving wave; unstable:growing/decaying mode) [+1]
-     ```
+  - Stable right-moving wave
+    ```
+    Jeans_Rho0        1.0            # background density
+    Jeans_Rho1        1.0e-6         # density perturbation amplitude
+    Jeans_P0          1.0e-2         # background pressure
+    Jeans_v0          0.0            # background velocity [0.0]
+    Jeans_B0          1.0e-2         # background magnetic field amplitude
+    Jeans_Sign       +1.0            # (>0/<0) --> (stable:right/left-moving wave; unstable:growing/decaying mode) [+1]
+    ```
+
+  - Unstable growing mode
+    ```
+    Jeans_Rho0        2.0            # background density
+    Jeans_Rho1        1.0e-6         # density perturbation amplitude
+    Jeans_P0          1.0e-2         # background pressure
+    Jeans_v0          0.0            # background velocity [0.0]
+    Jeans_B0          1.0e-2         # background magnetic field amplitude
+    Jeans_Sign       +1.0            # (>0/<0) --> (stable:right/left-moving wave; unstable:growing/decaying mode) [+1]
+    ```
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstabilityComoving.md b/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstabilityComoving.md
index 612abd6c8..7ce397d60 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstabilityComoving.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-JeansInstabilityComoving.md
@@ -8,19 +8,19 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - 32^3 uniform resolution
-   - No grid refinement is adopted in this test
+  - No grid refinement is adopted in this test
 
 - [[DT__MAX_DELTA_A | Runtime-Parameters:-Timestep#DT__MAX_DELTA_A]] is set to an extremely large number so that the time-step will
   be controlled by the fluid solver
@@ -29,13 +29,17 @@
   solution, in which the solution grows exponentially. To test a STABLE solution,
   one can try the following parameters:
 
-   - `Input__Parameter`
-      - `BOX_SIZE`  = `0.5`
-      - `A_INIT`    = `1.0e-5`
-      - `OUTPUT_DT` = `2.0e-6`
-
-   - `Input__TestProb`
-      - `Jeans_RealAmp0` = `4.0e-8`
+  - `Input__Parameter`
+    | Parameter name | Value  |
+    |---             |---     |
+    | BOX_SIZE       | 0.5    |
+    | A_INIT         | 1.0e-5 |
+    | OUTPUT_DT      | 2.0e-6 |
+
+  - `Input__TestProb`
+    | Parameter name | Value  |
+    |---             |---     |
+    | Jeans_RealAmp0 | 4.0e-8 |
 
 > [!CAUTION]
 > This setup requires further verification
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Jet.md b/doc/wiki/Test-Problems-related/Test-Problems:-Jet.md
index d93fcf05b..694bc5b08 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Jet.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Jet.md
@@ -8,12 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]] (when enabling `JET_HSE`)
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]] (when enabling `JET_HSE`)
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]] (when disabling `JET_HSE`)
+  - [[--gravity | Installation:-Option-List#--gravity]] (when disabling `JET_HSE`)
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -23,8 +24,8 @@ None
 # Note
 - Ref: [Molnar, S., Schive, H-Y., et al., 2017, ApJ, 835, 57](https://arxiv.org/abs/1612.02341)
 - Recommended boundary conditions
-   - With `JET_HSE` and large `Jet_BgVel_y`: user-defined BC on -y and outflow BC on other faces
-   - Without `JET_HSE`: outflow BC on all faces
+  - With `JET_HSE` and large `Jet_BgVel_y`: user-defined BC on -y and outflow BC on other faces
+  - Without `JET_HSE`: outflow BC on all faces
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-JetICMWall.md b/doc/wiki/Test-Problems-related/Test-Problems:-JetICMWall.md
index c128364a1..f6c8d14f8 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-JetICMWall.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-JetICMWall.md
@@ -8,23 +8,23 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--srhd | Installation:-Option-List#--srhd]]
-   - [[--passive | Installation:-Option-List#--passive]]=`4`
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--srhd | Installation:-Option-List#--srhd]]
+  - [[--passive | Installation:-Option-List#--passive]]=`4`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--mhd | Installation:-Option-List#--mhd]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Units
-   | Unit  | [L]   | [M]        | [V] | [T] = [L]/[V] | [D] = [M]/[L]^3    |
-   |---    |---    |---         |---  |---            |---                 |
-   | Value | 5 kpc | 1.0e5 Msun | 1 c | ~ 16.308 kyr  | ~ 5.41e-29 g/cm**3 |
+  | Unit  | [L]   | [M]        | [V] | [T] = [L]/[V] | [D] = [M]/[L]^3    |
+  |---    |---    |---         |---  |---            |---                 |
+  | Value | 5 kpc | 1.0e5 Msun | 1 c | ~ 16.308 kyr  | ~ 5.41e-29 g/cm**3 |
 
 - Default resolution ~ 39 pc ([[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`3`)
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-KelvinHelmholtzInstability.md b/doc/wiki/Test-Problems-related/Test-Problems:-KelvinHelmholtzInstability.md
index 1c831094a..bc1d13dfd 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-KelvinHelmholtzInstability.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-KelvinHelmholtzInstability.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
 - 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
@@ -28,7 +28,7 @@
 - Random values are added to velocity in all three directions
 - yt script `plot_density.py` for visualization
 - Must disable `OPT__INIT_GRID_WITH_OMP`
-   - Otherwise all threads would share the same random seed
+  - Otherwise all threads would share the same random seed
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-LSS.md b/doc/wiki/Test-Problems-related/Test-Problems:-LSS.md
index b9bf54b1a..40fcde261 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-LSS.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-LSS.md
@@ -8,48 +8,48 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Cosmological constants
-   | Parameter name | value       |
-   |---             |---          |
-   | ELBDM_MASS     | 8.0e-23     |
-   | A_INIT         | 3.124024e-4 |
-   | OMEGA_M0       | 0.2835      |
-   | HUBBLE0        | 0.6955      |
+  | Parameter name | Value       | Note |
+  |---             |---          |--- |
+  | ELBDM_MASS     | 8.0e-23     | eV/c^2 |
+  | A_INIT         | 3.124024e-4 |  |
+  | OMEGA_M0       | 0.2835      |  |
+  | HUBBLE0        | 0.6955      |  |
 
 - Simulation
-   | Parameter name        | value |
-   |---                    |---    |
-   | BOX_SIZE              | 1.4   |
-   | MAX_LEVEL             | 3     |
-   | OPT__FLAG_RHO         | 1     |
-   | OPT__FLAG_LOHNER_DENS | 1     |
+  | Parameter name        | Value | Note |
+  |---                    |---    |--- |
+  | BOX_SIZE              | 1.4   | Mpc/h |
+  | MAX_LEVEL             | 3     |  |
+  | OPT__FLAG_RHO         | 1     |  |
+  | OPT__FLAG_LOHNER_DENS | 1     |  |
 
 - Flag tables
-   - `Input__Flag_Rho`: `example/input/Input__Flag_Rho8`
-   - `Input__Flag_Lohner`: `example/input/Input__Flag_Lohner__FLASH1_LSS_DH3.0`
+  - `Input__Flag_Rho`: `example/input/Input__Flag_Rho8`
+  - `Input__Flag_Lohner`: `example/input/Input__Flag_Lohner__FLASH1_LSS_DH3.0`
 
 
 # Note
 - Cosmological large-scale structure simulations
 
 - Download the IC file
-   ```bash
-   sh download_ic.sh
-   ```
+  ```bash
+  sh download_ic.sh
+  ```
 
 - Default maximum resolution is low
-   - Only 1.4/(256*2^3) ~ 0.7 kpc/h (comoving)
-   - Can only marginally resolve a central soliton
+  - Only 1.4/(256\*2^3) ~ 0.7 kpc/h (comoving)
+  - Can only marginally resolve a central soliton
 
 - Some yt visualization scripts are put in `plot_script`
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-LSS_Hybrid.md b/doc/wiki/Test-Problems-related/Test-Problems:-LSS_Hybrid.md
index dcc7ba977..2627b5975 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-LSS_Hybrid.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-LSS_Hybrid.md
@@ -8,113 +8,113 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Cosmological constants
-   | Parameter name | value              |
-   |---             |---                 |
-   | ELBDM_MASS     | 2.0e-23            |
-   | A_INIT         | 9.900990099e-3     |
-   | OMEGA_M0       | 0.3158230904284232 |
-   | HUBBLE0        | 0.6732117          |
+  | Parameter name | Value              | Note |
+  |---             |---                 |--- |
+  | ELBDM_MASS     | 2.0e-23            | eV/c^2 |
+  | A_INIT         | 9.900990099e-3     |  |
+  | OMEGA_M0       | 0.3158230904284232 |  |
+  | HUBBLE0        | 0.6732117          |  |
 
 - Simulation
-   | Parameter name         | value |
-   |---                     |---    |
-   | BOX_SIZE               | 2.8   |
-   | MAX_LEVEL              | 6     |
-   | OPT__FLAG_SPECTRAL     | 1     |
-   | OPT__FLAG_INTERFERENCE | 1     |
+  | Parameter name         | Value | Note |
+  |---                     |---    |--- |
+  | BOX_SIZE               | 2.8   | Mpc/h |
+  | MAX_LEVEL              | 6     |  |
+  | OPT__FLAG_SPECTRAL     | 1     |  |
+  | OPT__FLAG_INTERFERENCE | 1     |  |
 
 - Flag tables
-   - `Input__Flag_Rho`:           `example/input/Input__Flag_Rho8`
-   - `Input__Flag_Spectral`:      `example/input/Input__Flag_Spectral`
-   - `Input__Flag_Interference`:  `example/input/Input__Flag_Interference`
+  - `Input__Flag_Rho`:           `example/input/Input__Flag_Rho8`
+  - `Input__Flag_Spectral`:      `example/input/Input__Flag_Spectral`
+  - `Input__Flag_Interference`:  `example/input/Input__Flag_Interference`
 
 
 # Note
 - Cosmological large-scale structure simulations using hybrid scheme
 
 - Quickstart:
-   1. Download the IC file
-      ```bash
-      sh download_light_halo_ic.sh
-      ```
-      or
-      ```bash
-      sh download_heavy_halo_ic.sh
-      ```
-   2. For spectral interpolation:
-      -  Download spectral interpolation tables
-         ```bash
-         sh download_spectral_interpolation_tables.sh
-         ```
-      -  Set [[OPT__FLU_INT_SCHEME | ]] and [[OPT__REF_FLU_INT_SCHEME | ]] to 8
-   3. Compile GAMER and run simulation to redshift 0 with default settings.
+  1. Download the IC file
+     ```bash
+     sh download_light_halo_ic.sh
+     ```
+     or
+     ```bash
+     sh download_heavy_halo_ic.sh
+     ```
+  2. For spectral interpolation:
+     -  Download spectral interpolation tables
+        ```bash
+        sh download_spectral_interpolation_tables.sh
+        ```
+     -  Set [[OPT__FLU_INT_SCHEME | Runtime-Parameters:-Interpolation#OPT__FLU_INT_SCHEME]] and [[OPT__REF_FLU_INT_SCHEME | Runtime-Parameters:-Interpolation#OPT__REF_FLU_INT_SCHEME]] to 8
+  3. Compile GAMER and run simulation to redshift 0 with default settings.
 
 - Explanation
-   - IC
+  - IC
 
-      The wave IC consisting of two blocks of real and imaginary parts are converted to hybrid IC
-      consisting of two blocks with the density and phase fields using the Python script `elbdm_wave_to_hybrid_IC.py`
+    The wave IC consisting of two blocks of real and imaginary parts are converted to hybrid IC
+    consisting of two blocks with the density and phase fields using the Python script `elbdm_wave_to_hybrid_IC.py`
 
-      It can be used as follows:
-      ```bash
-      python elbdm_wave_to_hybrid_IC.py -resolution 256 -input UM_IC_wave -output UM_IC_hybrid
-      ```
-      to convert the input file `UM_IC_wave` with a resolution of 256 points in each dimension to the output hybrid IC `UM_IC_hybrid`.
-      Optionally, it accepts the keyword `-float8` for double precision input data.
+    It can be used as follows:
+    ```bash
+    python elbdm_wave_to_hybrid_IC.py -resolution 256 -input UM_IC_wave -output UM_IC_hybrid
+    ```
+    to convert the input file `UM_IC_wave` with a resolution of 256 points in each dimension to the output hybrid IC `UM_IC_hybrid`.
+    Optionally, it accepts the keyword `-float8` for double precision input data.
 
-      The conversion is only well-defined if the IC do not contain vortices, i.e. at high redshift for cosmological IC.
+    The conversion is only well-defined if the IC do not contain vortices, i.e. at high redshift for cosmological IC.
 
-      In a second step, the initial conditions can be rescaled using the Python script `elbdm_rescale_periodic_ic.py`.
-      It can be used as follows:
-      ```bash
-      python elbdm_rescale_periodic_ic.py -n_in 256 -n_out 64 -input UM_IC_high_resolution -output UM_IC_low_resolution
-      ```
-      and supports up- and downscaling periodic wave and hybrid IC. Optionally, it accepts the keyword `-float8` for double precision input data.
+    In a second step, the initial conditions can be rescaled using the Python script `elbdm_rescale_periodic_ic.py`.
+    It can be used as follows:
+    ```bash
+    python elbdm_rescale_periodic_ic.py -n_in 256 -n_out 64 -input UM_IC_high_resolution -output UM_IC_low_resolution
+    ```
+    and supports up- and downscaling periodic wave and hybrid IC. Optionally, it accepts the keyword `-float8` for double precision input data.
 
-   - Interpolation tables
+  - Interpolation tables
 
-      The tables can be recreated by calling
-      ```bash
-      mpirun -n 16 python3 tool/table_maker/GramFE/compute_interpolation_tables.py
-      ```
-      [[INT_SPEC_TABLE_PATH | ]] (default = "./") must be set to a folder containing the folders `interpolation_tables` and `boundary2extension_tables`
+    The tables can be recreated by calling
+    ```bash
+    mpirun -n 16 python3 tool/table_maker/GramFE/compute_interpolation_tables.py
+    ```
+    [[INT_SPEC_TABLE_PATH | Runtime-Parameters:-Interpolation#INT_SPEC_TABLE_PATH]] (default = "./") must be set to a folder containing the folders `interpolation_tables` and `boundary2extension_tables`
 
 - The simulation uses a low base-level resolution of 2.8 Mpc/h / 64 ~ 44 kpc/h (comoving).
 
-   This corresponds to a maximum wave vector k ~ 72 h/Mpc well above the cutoff power in the initial conditions for m = 2.0e-23 eV.
+  This corresponds to a maximum wave vector k ~ 72 h/Mpc well above the cutoff power in the initial conditions for m = 2.0e-23 eV.
 
-   This initial resolution has shown very good agreement with higher resolution wave initial conditions.
+  This initial resolution has shown very good agreement with higher resolution wave initial conditions.
 
 - The simulation uses the fluid solver on levels 0 - 3 and switches to the wave solver in regions of interference on level 4.
 
-   The corresponding runtime parameter [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] is set to 4.
+  The corresponding runtime parameter [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] is set to 4.
 
-   The resolution for the first level using the wave solver is 2.8 Mpc/h /(64*2^4) ~ 2.75 kpc/h (comoving) with these settings.
+  The resolution for the first level using the wave solver is 2.8 Mpc/h /(64\*2^4) ~ 2.75 kpc/h (comoving) with these settings.
 
-   This resolution has shown to be a good compromise for the starting resolution of the wave solver.
+  This resolution has shown to be a good compromise for the starting resolution of the wave solver.
 
-   Note that increasing [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] will affect performance since it will likely lead to overrefinement.
-   However, it should increase the accuracy of the hybrid scheme.
+  Note that increasing [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] will affect performance since it will likely lead to overrefinement.
+  However, it should increase the accuracy of the hybrid scheme.
 
-   On the contrary, decreasing [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] will lead to a lower-resolution at the wave-fluid boundary
-   (regardless of [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]] and [[REFINE_NLEVEL | Runtime-Parameters:-Refinement#REFINE_NLEVEL]]) and 
-   will negatively affect the accuracy of the solver.
+  On the contrary, decreasing [[ELBDM_FIRST_WAVE_LEVEL | Runtime-Parameters:-ELBDM#ELBDM_FIRST_WAVE_LEVEL]] will lead to a lower-resolution at the wave-fluid boundary
+  (regardless of [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]] and [[REFINE_NLEVEL | Runtime-Parameters:-Refinement#REFINE_NLEVEL]]) and
+  will negatively affect the accuracy of the solver.
 
 - Default maximum resolution is low
-   - Only 2.8/(64*2^6) ~ 0.7 kpc/h (comoving)
-   - Can only marginally resolve a central soliton
+  - Only 2.8/(64\*2^6) ~ 0.7 kpc/h (comoving)
+  - Can only marginally resolve a central soliton
 
 - Some yt visualization scripts are put in `plot_script`
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_ABC.md b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_ABC.md
index 487b20855..4ca32bbee 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_ABC.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_ABC.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--mhd | Installation:-Option-List#--mhd]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--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
@@ -23,10 +23,10 @@
 
 # Note
 - Reference
-   - [Zhang et al., 2018, ApJS, 236, 50](https://arxiv.org/abs/1804.03479)
+  - [Zhang et al., 2018, ApJS, 236, 50](https://arxiv.org/abs/1804.03479)
 - `ABC_NPeriod`
-   - `1` --> stable
-   - `2` --> unstable
+  - `1` --> stable
+  - `2` --> unstable
 - Initial perturbations have not been implemented yet
 
 # Links
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_LinearWave.md b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_LinearWave.md
index 096e3f3ce..d3ade5ef2 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_LinearWave.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_LinearWave.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--mhd | Installation:-Option-List#--mhd]]
-   - [[--double | Installation:-Option-List#--double]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--double | Installation:-Option-List#--double]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--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
@@ -25,7 +25,7 @@
 
 # Note
 - Support both 1D and 3D cases
-   - set by `MHDLinear_Dir`
+  - set by `MHDLinear_Dir`
 - A simple gnuplot script `plot.gpt` is attached
 - `Record__L1Err` records the L1 errors
 - `MHDLinearWave_*_*` record the numerical and analytical solutions along the diagonal
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_OrszagTangVortex.md b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_OrszagTangVortex.md
index cabbe67f4..fd7601a0f 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-MHD_OrszagTangVortex.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-MHD_OrszagTangVortex.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--mhd | Installation:-Option-List#--mhd]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--mhd | Installation:-Option-List#--mhd]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--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
@@ -25,7 +25,7 @@
 
 # Note
 - Reference
-   - [Orszag & Tang, 1998, J. Fluid Mech., 90, 129](https://doi.org/10.1017/S002211207900210X)
+  - [Orszag & Tang, 1998, J. Fluid Mech., 90, 129](https://doi.org/10.1017/S002211207900210X)
 - No z dependence
 
 # Links
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-ParticleEquilibriumIC.md b/doc/wiki/Test-Problems-related/Test-Problems:-ParticleEquilibriumIC.md
index 078b15ea6..f245a5c63 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-ParticleEquilibriumIC.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-ParticleEquilibriumIC.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--gsl | Installation:-Option-List#--gsl]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--gsl | Installation:-Option-List#--gsl]]
 - 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]]
 
 
 # Default setup
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-ParticleTest.md b/doc/wiki/Test-Problems-related/Test-Problems:-ParticleTest.md
index 63c00185e..4d4d89618 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-ParticleTest.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-ParticleTest.md
@@ -8,15 +8,15 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--tracer | Installation:-Option-List#--tracer]]
-   - [[--hdf5 | Installation:-Option-List#--hdf5]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--tracer | Installation:-Option-List#--tracer]]
+  - [[--hdf5 | Installation:-Option-List#--hdf5]]
 - 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]]
 
 
 # Default setup
@@ -35,7 +35,7 @@
 - [[OPT__FREEZE_FLUID | Runtime-Parameters:-Hydro#OPT__FREEZE_FLUID]] must be 1 for this test.
 - If [[OPT__FLAG_USER | Runtime-Parameters:-Refinement#OPT__FLAG_USER]] is set,
   a rectangle will be refined in the center of the domain.
-   - The active particle orbit is _not_ stable in this case due to self-force at refinement boundaries.
+  - The active particle orbit is _not_ stable in this case due to self-force at refinement boundaries.
 - Density of the gas must be kept very small to avoid gravitational effects from the gas.
 - Use python script `make_tracer_pngs.py` with yt to make PNG images, use
   bash script `make_tracer_movie.sh` to combine PNGs into movies with `ffmpeg`.
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Perturbation.md b/doc/wiki/Test-Problems-related/Test-Problems:-Perturbation.md
index ca7593ad7..e9edfb437 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Perturbation.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Perturbation.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme=ELBDM_HYBRID | Installation:-Option-List#--elbdm_scheme]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--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
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-PlaneWave.md b/doc/wiki/Test-Problems-related/Test-Problems:-PlaneWave.md
index ca1ab0f9a..1fada96e0 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-PlaneWave.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-PlaneWave.md
@@ -8,25 +8,25 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--double | Installation:-Option-List#--double]]
-   - [[--passive | Installation:-Option-List#--passive]]=`1`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--double | Installation:-Option-List#--double]]
+  - [[--passive | Installation:-Option-List#--passive]]=`1`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Evolve the plane wave for six periods
 - Apply the periodic BC
-   - Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`1`
+  - Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`1`
 
 
 # Note
 - Only support 1D
-   - Use `PWave_XYZ` to control the propagation direction
+  - Use `PWave_XYZ` to control the propagation direction
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Plummer.md b/doc/wiki/Test-Problems-related/Test-Problems:-Plummer.md
index 5e9304f61..8cb02b8a1 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Plummer.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Plummer.md
@@ -8,12 +8,12 @@
 
 # `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
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -22,24 +22,24 @@ None
 
 # Note
 - Test the evolution of the Plummer model
-   - `Plummer_Collision` = `0`: test the stability of a single Plummer cloud
-                           `1`: test the collision of two Plummer clouds
+  - `Plummer_Collision` = `0`: test the stability of a single Plummer cloud
+                          `1`: test the collision of two Plummer clouds
 
 - One can set [[--passive | Installation:-Option-List#--passive]]=`2`
   and `Plummer_AddColor`=`1` for `Plummer_Collision`=`1`
-   - Different clouds will be assigned with different passive scalars
+  - Different clouds will be assigned with different passive scalars
 
 - Plummer cloud(s) can have both gas and particles
-   - `Plummer_GasMFrac`: gas mass fraction
+  - `Plummer_GasMFrac`: gas mass fraction
 
 - To enable feedback
-   1. Enable `FB_USER`
-   2.  Enable `Plummer_FB_Exp` and/or `Plummer_FB_Acc`
+  1. Enable `FB_USER`
+  2. Enable `Plummer_FB_Exp` and/or `Plummer_FB_Acc`
 
 - To test mass conservation to the machine precision with mass accretion feedback
-   1. Set `Plummer_FB_ExpMMax`=`0.0` (no mass loss in explosion feedback)
-   2. Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`1` (periodic BC)
-   3. Use the gnuplot script `plot_script/plot_mass.gpt`
+  1. Set `Plummer_FB_ExpMMax`=`0.0` (no mass loss in explosion feedback)
+  2. Set [[OPT__BC_FLU_* | Runtime-Parameters:-Hydro#OPT__BC_FLU_XM]]=`1` (periodic BC)
+  3. Use the gnuplot script `plot_script/plot_mass.gpt`
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-RestrictionMismatch.md b/doc/wiki/Test-Problems-related/Test-Problems:-RestrictionMismatch.md
index 6ea0bda15..c51a743e6 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-RestrictionMismatch.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-RestrictionMismatch.md
@@ -9,9 +9,9 @@
 # Demonstration of phase mismatch after refinement and restriction
 
 ## Explanation
-This test problem demonstrates that refining and restricting the wave function in ELBDM leads to a mismatch of the phase on the coarse levels when the option [[OPT__INT_PHASE | ]] is on.
+This test problem demonstrates that refining and restricting the wave function in ELBDM leads to a mismatch of the phase on the coarse levels when the option [[OPT__INT_PHASE | Runtime-Parameters:-ELBDM#OPT__INT_PHASE]] is on.
 
-Further, it shows that the new option [[OPT__RES_PHASE | ]] remedies the mismatch immediately after restriction, but does not prevent the formation of artifacts at the coarse-fine boundary.
+Further, it shows that the new option [[OPT__RES_PHASE | Runtime-Parameters:-ELBDM#OPT__RES_PHASE]] remedies the mismatch immediately after restriction, but does not prevent the formation of artifacts at the coarse-fine boundary.
 
 It uses the `GaussianWavePacket` test with suitable initial parameters and refines a region at the center of the Gaussian wave packet.
 
@@ -43,7 +43,7 @@ However, as the plot named `ComparisonOfRestrictionMethodsAfterEvolution.png` sh
 
 The resulting mismatch is bigger than the one caused by the old restriction method.
 
-This is also shown in a series of four plots titled `Data_%06d_Slice_z_density.png` that are created from a run with the new option [[OPT__RES_PHASE | ]] turned on.
+This is also shown in a series of four plots titled `Data_%06d_Slice_z_density.png` that are created from a run with the new option [[OPT__RES_PHASE | Runtime-Parameters:-ELBDM#OPT__RES_PHASE]] turned on.
 
 The grid is unrefined in timestep `0`, refinement and restriction are performed at the end of timestep `1` and the refined fields are evolved during timestep `2`.
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Riemann.md b/doc/wiki/Test-Problems-related/Test-Problems:-Riemann.md
index 79c8d605b..a92719ede 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Riemann.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Riemann.md
@@ -8,25 +8,25 @@
 
 # `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
 - Resolution = 64x16x16, with [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`2`
 - Lohner's refinement threshold = 0.50 (on density)
-   - May not be suitable for all Riemann problems here
+  - May not be suitable for all Riemann problems here
 - Outflow boundary condition
 
 
 # Note
 - Since GAMER does not support real 1D/2D simulations, one should set the
-  root-level grid size to 16 (i.e., patch size*2) in the transverse directions
+  root-level grid size to 16 (i.e., patch size\*2) in the transverse directions
 
 - Add [[--mhd | Installation:-Option-List#--mhd]]=`true` when executing `configure.py` for the Riemann problems involving magnetic field
 
@@ -37,38 +37,46 @@
   usually lead to a non-regular solution (a compound wave)
 
 - For SRHD Riemann problems
-   - Compilation options are provided in `generate_make_Riemann_SRHD.sh`
-   - The analytical solutions can be generated by the [SRHD exact Riemann solver](https://github.com/zengbs/exact-solution-to-relativistic-riemann-problem)
+  - Compilation options are provided in `generate_make_Riemann_SRHD.sh`
+  - The analytical solutions can be generated by the [SRHD exact Riemann solver](https://github.com/zengbs/exact-solution-to-relativistic-riemann-problem)
 
-   - Setup for SRHD Ultra-relativistic limit
-      - Input__TestProb
-         - Riemann_Prob          = 10
-      - Input__Parameter
-         - BOX_SIZE              = 1.0
-         - NX0_TOT_X             = 512
-         - MAX_LEVEL             = 0
-         - OPT__OUTPUT_PRES      = 1
-         - OPT__OUTPUT_LORENTZ   = 1
-         - OPT__OUTPUT_3VELOCITY = 1
-         - OUTPUT_DT             = 0.01
-      - Plotting scripts: `plot__srhd_ur.gpt` and `plot__srhd_ur.py`
-      - The analytical solution: `ReferenceSolution/TM_EoS/SRHD_UR`
-      - Reference: Figure 4. in [Tseng et al. 2021, MNRAS, 504, 3298](https://doi.org/10.1093/mnras/stab1006)
+  - Setup for SRHD Ultra-relativistic limit
+    - `Input__TestProb`
+      | Parameter name | Value |
+      |---             |---    |
+      | Riemann_Prob   | 10    |
+    - `Input__Parameter`
+      | Parameter name        | Value |
+      |---                    |---    |
+      | BOX_SIZE              | 1.0   |
+      | NX0_TOT_X             | 512   |
+      | MAX_LEVEL             | 0     |
+      | OPT__OUTPUT_PRES      | 1     |
+      | OPT__OUTPUT_LORENTZ   | 1     |
+      | OPT__OUTPUT_3VELOCITY | 1     |
+      | OUTPUT_DT             | 0.01  |
+    - Plotting scripts: `plot__srhd_ur.gpt` and `plot__srhd_ur.py`
+    - The analytical solution: `ReferenceSolution/TM_EoS/SRHD_UR`
+    - Reference: Figure 4. in [Tseng et al. 2021, MNRAS, 504, 3298](https://doi.org/10.1093/mnras/stab1006)
 
-   - Setup for SRHD mixed ultra-relativistic and non-relativistic limits
-      - Input__TestProb
-         - Riemann_Prob          = 11
-      - Input__Parameter
-         - BOX_SIZE              = 100.0
-         - NX0_TOT_X             = 102400
-         - MAX_LEVEL             = 0
-         - OPT__OUTPUT_PRES      = 1
-         - OPT__OUTPUT_LORENTZ   = 1
-         - OPT__OUTPUT_3VELOCITY = 1
-         - OUTPUT_DT             = 0.5
-      - Plotting scripts: `plot__srhd_mixed.gpt` and `plot__srhd_mixed.py`
-      - The analytical solution: `ReferenceSolution/TM_EoS/SRHD_Mixed`
-      - Reference: Figure 5. in [Tseng et al. 2021, MNRAS, 504, 3298](https://doi.org/10.1093/mnras/stab1006)
+  - Setup for SRHD mixed ultra-relativistic and non-relativistic limits
+    - `Input__TestProb`
+      | Parameter name | Value |
+      |---             |---    |
+      | Riemann_Prob   | 11    |
+    - `Input__Parameter`
+      | Parameter name        | Value  |
+      |---                    |---     |
+      | BOX_SIZE              | 100.0  |
+      | NX0_TOT_X             | 102400 |
+      | MAX_LEVEL             | 0      |
+      | OPT__OUTPUT_PRES      | 1      |
+      | OPT__OUTPUT_LORENTZ   | 1      |
+      | OPT__OUTPUT_3VELOCITY | 1      |
+      | OUTPUT_DT             | 0.5    |
+    - Plotting scripts: `plot__srhd_mixed.gpt` and `plot__srhd_mixed.py`
+    - The analytical solution: `ReferenceSolution/TM_EoS/SRHD_Mixed`
+    - Reference: Figure 5. 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:-SelfSimilarHalo.md b/doc/wiki/Test-Problems-related/Test-Problems:-SelfSimilarHalo.md
index 11414c5e9..07beba512 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-SelfSimilarHalo.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-SelfSimilarHalo.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Soliton.md b/doc/wiki/Test-Problems-related/Test-Problems:-Soliton.md
index 89abebbd9..15dfbf41f 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Soliton.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Soliton.md
@@ -8,14 +8,14 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--unsplit_gravity | Installation:-Option-List#--unsplit_gravity]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -25,12 +25,12 @@
 
 # Note
 - `Soliton_N`=`1`: test a single soliton
-   - Set `Soliton_RSeed`<`0`
-   - Set `Soliton_EmptyRegion`=`0.0`
+  - Set `Soliton_RSeed`<`0`
+  - Set `Soliton_EmptyRegion`=`0.0`
 
 - `Soliton_N`>`1`: soliton merger
-   - Set `Soliton_RSeed`>=`0`
-   - Set `Soliton_EmptyRegion`>`0.0` (e.g., 1.0e2)
+  - Set `Soliton_RSeed`>=`0`
+  - Set `Soliton_EmptyRegion`>`0.0` (e.g., 1.0e2)
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-SphericalCollapse.md b/doc/wiki/Test-Problems-related/Test-Problems:-SphericalCollapse.md
index 6bbe9e47e..505a00af9 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-SphericalCollapse.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-SphericalCollapse.md
@@ -8,18 +8,18 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
 - Must disable
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
 - Refinement criteria: density magnitude and Lohner's error estimator for density
-   - Refinement threshold of the Lohner error estimator = 0.80
+  - Refinement threshold of the Lohner error estimator = 0.80
 - [[MAX_LEVEL | Runtime-Parameters:-Refinement#MAX_LEVEL]]=`2`
 
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear.md b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear.md
index 0672e2055..da41a57e0 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear.md
@@ -8,13 +8,12 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -26,13 +25,13 @@
 
 # Note
 - Evolve vortex pair with linear motion along x in a 2D simulation
-   - Wave function `psi_vorpair(x,y) = background + A*cos(ky*y)*exp( i*(kx*x-Omega*t+Phase0) )`
-     where `A` is a constant on the order of background, `kx` and `ky` are wavenumbers,
-     `Omega=0.5/ELBDM_ETA*(kx^2+ky^2)`, and `Phase0` is a phase constant
+  - Wave function `psi_vorpair(x,y) = background + A*cos(ky*y)*exp( i*(kx*x-Omega*t+Phase0) )`
+    where `A` is a constant on the order of background, `kx` and `ky` are wavenumbers,
+    `Omega=0.5/ELBDM_ETA*(kx^2+ky^2)`, and `Phase0` is a phase constant
 - Optionally: Add wave in `z` direction
-   - `psi(x, y, z) = psi_vorpair(x,y) + background_z * exp( i*(kz*z-ZWaveOmega*t) )`
-     where `background_z` is a constant on the order of background, `kz` is a wavenumber and
-     `Omega=0.5/ELBDM_ETA*(kz^2)`
+  - `psi(x, y, z) = psi_vorpair(x,y) + background_z * exp( i*(kz*z-ZWaveOmega*t) )`
+    where `background_z` is a constant on the order of background, `kz` is a wavenumber and
+    `Omega=0.5/ELBDM_ETA*(kz^2)`
 
 # Links
 [[Main page of Test Problems | Test-Problems]]
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear_Hybrid.md b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear_Hybrid.md
index 9b34feb34..44d95a5f6 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear_Hybrid.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairLinear_Hybrid.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -26,14 +26,14 @@
 
 # Note
 - Evolve vortex pair with linear motion along x in a 2D simulation
-   - Wave function `psi_vorpair(x,y) = background + A*cos(ky*y)*exp( i*(kx*x-Omega*t+Phase0) )`
-     where `A` is a constant on the order of background, `kx` and `ky` are wavenumbers,
-     `Omega=0.5/ELBDM_ETA*(kx^2+ky^2)`, and `Phase0` is a phase constant
+  - Wave function `psi_vorpair(x,y) = background + A*cos(ky*y)*exp( i*(kx*x-Omega*t+Phase0) )`
+    where `A` is a constant on the order of background, `kx` and `ky` are wavenumbers,
+    `Omega=0.5/ELBDM_ETA*(kx^2+ky^2)`, and `Phase0` is a phase constant
 
 - Optionally: Add wave in `z` direction
-   - `psi(x, y, z) = psi_vorpair(x,y) + background_z * exp( i*(kz*z-ZWaveOmega*t) )`
-     where `background_z` is a constant on the order of background, `kz` is a wavenumber and
-     `Omega=0.5/ELBDM_ETA*(kz^2)`
+  - `psi(x, y, z) = psi_vorpair(x,y) + background_z * exp( i*(kz*z-ZWaveOmega*t) )`
+    where `background_z` is a constant on the order of background, `kz` is a wavenumber and
+    `Omega=0.5/ELBDM_ETA*(kz^2)`
 
 - If [[--conserve_mass | Installation:-Option-List#--conserve_mass]] is enabled, mass ought to be conserved in this test because of periodic boundary conditions
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating.md b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating.md
index ef2791a38..5156a7194 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating.md
@@ -8,13 +8,12 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -24,9 +23,9 @@
 
 # Note
 - Evolve a rotating vortex pair in 2D
-   - Wave function `psi(R,phi) = background - A*J1( sqrt(2*Eta*Omega)*R )*exp( i*(phi-Omega*t+Phase0) )`,
-     where `A` is a constant on the order of background, `Eta=ELBDM_MASS/PLANCK_CONSTANT`,
-     `phi` is azimuthal angle, `R` is radius, `Omega` is angular frequency, and `Phase0` is a phase constant
+  - Wave function `psi(R,phi) = background - A*J1( sqrt(2*Eta*Omega)*R )*exp( i*(phi-Omega*t+Phase0) )`,
+    where `A` is a constant on the order of background, `Eta=ELBDM_MASS/PLANCK_CONSTANT`,
+    `phi` is azimuthal angle, `R` is radius, `Omega` is angular frequency, and `Phase0` is a phase constant
 
 - Ref: [Tzihong Chiueh et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 115101](https://doi.org/10.1088/0953-4075/44/11/115101),
   Vortex turbulence in linear Schrödinger wave mechanics
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating_Hybrid.md b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating_Hybrid.md
index 5eb081da8..ec3466bf1 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating_Hybrid.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-VortexPairRotating_Hybrid.md
@@ -8,13 +8,13 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`ELBDM`
-   - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
+  - [[--model | Installation:-Option-List#--model]]=`ELBDM`
+  - [[--elbdm_scheme | Installation:-Option-List#--elbdm_scheme]]=`ELBDM_HYBRID`
 - Must disable
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--particle | Installation:-Option-List#--particle]]
 - Available options
-   - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
+  - [[Miscellaneous Options | Installation:-Option-List#miscellaneous-options]]
 
 
 # Default setup
@@ -24,9 +24,9 @@
 
 # Note
 - Evolve a rotating vortex pair in 2D
-   - Wave function `psi(R,phi) = background - A*J1( sqrt(2*Eta*Omega)*R )*exp( i*(phi-Omega*t+Phase0) )`,
-     where `A` is a constant on the order of background, `Eta=ELBDM_MASS/PLANCK_CONSTANT`,
-     `phi` is azimuthal angle, `R` is radius, `Omega` is angular frequency, and `Phase0` is a phase constant
+  - Wave function `psi(R,phi) = background - A*J1( sqrt(2*Eta*Omega)*R )*exp( i*(phi-Omega*t+Phase0) )`,
+    where `A` is a constant on the order of background, `Eta=ELBDM_MASS/PLANCK_CONSTANT`,
+    `phi` is azimuthal angle, `R` is radius, `Omega` is angular frequency, and `Phase0` is a phase constant
 - Ref: [Tzihong Chiueh et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 115101](https://doi.org/10.1088/0953-4075/44/11/115101),
   Vortex turbulence in linear Schrödinger wave mechanics
 
diff --git a/doc/wiki/Test-Problems-related/Test-Problems:-Zeldovich.md b/doc/wiki/Test-Problems-related/Test-Problems:-Zeldovich.md
index 03cdce8a4..02ba9fa0c 100644
--- a/doc/wiki/Test-Problems-related/Test-Problems:-Zeldovich.md
+++ b/doc/wiki/Test-Problems-related/Test-Problems:-Zeldovich.md
@@ -8,78 +8,78 @@
 
 # `configure.py` options
 - Must enable
-   - [[--model | Installation:-Option-List#--model]]=`HYDRO`
-   - [[--gravity | Installation:-Option-List#--gravity]]
-   - [[--comoving | Installation:-Option-List#--comoving]]
-   - [[--particle | Installation:-Option-List#--particle]]
-   - [[--gsl | Installation:-Option-List#--gsl]]
-   - [[--fftw | Installation:-Option-List#--fftw]]=`FFTW2`/`FFTW3`
-   - [[--dual | Installation:-Option-List#--dual]]=`DE_ENPY`
+  - [[--model | Installation:-Option-List#--model]]=`HYDRO`
+  - [[--gravity | Installation:-Option-List#--gravity]]
+  - [[--comoving | Installation:-Option-List#--comoving]]
+  - [[--particle | Installation:-Option-List#--particle]]
+  - [[--gsl | Installation:-Option-List#--gsl]]
+  - [[--fftw | Installation:-Option-List#--fftw]]=`FFTW2`/`FFTW3`
+  - [[--dual | Installation:-Option-List#--dual]]=`DE_ENPY`
 - 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                  | Note |
-   |---             |---                     |--- |
-   | A_INIT         | 0.00990099009900990099 | z_i = 100 |
-   | OMEGA_M0       | 1.0                    | matter-only Universe |
-   | HUBBLE0        | 0.6732117              |  |
+  | Parameter name | Value                  | Note |
+  |---             |---                     |--- |
+  | A_INIT         | 0.00990099009900990099 | z_i = 100 |
+  | OMEGA_M0       | 1.0                    | matter-only Universe |
+  | HUBBLE0        | 0.6732117              |  |
 
 - Simulation
-   | Parameter name     | value       | Note |
-   |---                 |---          |--- |
-   | BOX_SIZE           |  80         | Mpc/h |
-   | NX0_TOT_X/Y/Z      |  128/32/32  |  |
-   | OPT__BC_*          |  1          |  |
-   | MAX_LEVEL          |  0          |  |
-   | GPU_NSTREAM        | -1          |  |
-   | OPT__FLAG_RHO      |  1          |  |
-   | OPT__OUTPUT_PART   |  4          |  |
-   | OPT__OUTPUT_BASEPS |  0          |  |
-   | OUTPUT_PART_X/Y/Z  |  0.0        |  |
+  | Parameter name     | Value       | Note |
+  |---                 |---          |--- |
+  | BOX_SIZE           |  80         | Mpc/h |
+  | NX0_TOT_X/Y/Z      |  128/32/32  |  |
+  | OPT__BC_*          |  1          |  |
+  | MAX_LEVEL          |  0          |  |
+  | GPU_NSTREAM        | -1          |  |
+  | OPT__FLAG_RHO      |  1          |  |
+  | OPT__OUTPUT_PART   |  4          |  |
+  | OPT__OUTPUT_BASEPS |  0          |  |
+  | OUTPUT_PART_X/Y/Z  |  0.0        |  |
 
 - Particle
-   | Parameter name  | value |
-   |---              |---    |
-   | PAR_NPAR        | -1    |
-   | PAR_INIT        | 1     |
-   | PAR_IC_FORMAT   | 1     |
-   | PAR_IC_MASS     | -1.0  |
-   | PAR_IC_TYPE     | -1    |
+  | Parameter name  | Value |
+  |---              |---    |
+  | PAR_NPAR        | -1    |
+  | PAR_INIT        | 1     |
+  | PAR_IC_FORMAT   | 1     |
+  | PAR_IC_MASS     | -1.0  |
+  | PAR_IC_TYPE     | -1    |
 
 - For "gas-only" setup
-   - `Input__Parameter`
-      | Parameter name     | value        |
-      |---                 |---           |
-      | GAMMA              | 1.6666666667 |
-      | MOLECULAR_WEIGHT   | 0.6          |
-      | DUAL_ENERGY_SWITCH | 3.0e-2       |
-      | OPT__FREEZE_FLUID  | 0            |
-      | OPT__OUTPUT_USER   | 1            |
-   - `Input__TestProb`
-      | Parameter name  | value |
-      |---              |---    |
-      | Gas_Par_Setup   | 1     |
-      | n_Pert_Wave_Len | 1     |
-      | zc_Collapse     | 1.0   |
-      | GasTemp_Init    | 100   |
+  - `Input__Parameter`
+    | Parameter name     | Value        |
+    |---                 |---           |
+    | GAMMA              | 1.6666666667 |
+    | MOLECULAR_WEIGHT   | 0.6          |
+    | DUAL_ENERGY_SWITCH | 3.0e-2       |
+    | OPT__FREEZE_FLUID  | 0            |
+    | OPT__OUTPUT_USER   | 1            |
+  - `Input__TestProb`
+    | Parameter name  | Value |
+    |---              |---    |
+    | Gas_Par_Setup   | 1     |
+    | n_Pert_Wave_Len | 1     |
+    | zc_Collapse     | 1.0   |
+    | GasTemp_Init    | 100   |
 
 - For "particle-only" setup
-   - `Input__Parameter`
-      | Parameter name    | value |
-      |---                |---    |
-      | OPT__FREEZE_FLUID | 1     |
-      | OPT__OUTPUT_USER  | 0     |
-   - `Input__TestProb`
-      | Parameter name  | value |
-      |---              |---    |
-      | Gas_Par_Setup   | 2     |
-      | n_Pert_Wave_Len | 1     |
-      | zc_Collapse     | 1.0   |
-      | NPar_X          | 64    |
+  - `Input__Parameter`
+    | Parameter name    | Value |
+    |---                |---    |
+    | OPT__FREEZE_FLUID | 1     |
+    | OPT__OUTPUT_USER  | 0     |
+  - `Input__TestProb`
+    | Parameter name  | Value |
+    |---              |---    |
+    | Gas_Par_Setup   | 2     |
+    | n_Pert_Wave_Len | 1     |
+    | zc_Collapse     | 1.0   |
+    | NPar_X          | 64    |
 
 
 # Note
@@ -104,8 +104,8 @@
   can be properly resolved.
 
 - The analysis script `./plots/analysis_plot_Zeldovich.py` works for both gas-/particle-only setups. Note
-   that the parameters under "# user-specified parameters" in the script NEED to match those adopted in
-   `Input__TestProb`, especially the value of `Gas_Par_Setup`.
+  that the parameters under "# user-specified parameters" in the script NEED to match those adopted in
+  `Input__TestProb`, especially the value of `Gas_Par_Setup`.
 
 - For references, see Sec. 9.2 of [Springel, MNRAS 401 791 (2010)](https://doi.org/10.1111/j.1365-2966.2009.15715.x)
   and Sec. 3 of [Heitmann et al., ApJS 160 28 (2005)](https://dx.doi.org/10.1086/432646).