Merge branch 'hyschive:main' into wiki_sanitizer

hyschive · Dec 11, 2024 · a9fb64a · a9fb64a
2 parents 0a4d34d + 18cccac
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diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,8 @@
 .DS_Store
 
 *.o
+*.bin
+*~
 
 bin/**
 src/generate_make.sh
@@ -10,6 +12,5 @@ GAMER_CompareData
 GAMER_ExtractUniform
 GAMER_ExtractProfile
 .vscode
-*~
 src/Makefile
 src/Makefile.log
diff --git a/configs/eureka_gnu.config b/configs/eureka_gnu.config
@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/default
 GRACKLE_PATH
 GSL_PATH        /software/gsl/default
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/default
 
 # compilers
 CXX     g++

diff --git a/configs/eureka_intel.config b/configs/eureka_intel.config
@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/default
 GRACKLE_PATH
 GSL_PATH        /software/gsl/default
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/default
 
 # compilers
 CXX     icpc

diff --git a/configs/spock_intel.config b/configs/spock_intel.config
@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/1.10.6-intel-2023.1.0
 GRACKLE_PATH
 GSL_PATH        /software/gsl/2.6-intel-2023.1.0
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/22.11
 
 # compilers
 CXX     icpc

diff --git a/configs/template.config b/configs/template.config
@@ -9,6 +9,7 @@ HDF5_PATH       /path/to/hdf5
 GRACKLE_PATH    /path/to/grackle
 GSL_PATH        /path/to/gsl
 LIBYT_PATH      /path/to/libyt
+CUFFTDX_PATH    /path/to/cufftdx
 
 # 2. Compiler type
 CXX     icpc                    # Serial compiler

diff --git a/doc/wiki/ELBDM-Spectral-Interpolation.md b/doc/wiki/ELBDM-Spectral-Interpolation.md
@@ -5,7 +5,7 @@ This section provides an overview of the spectral interpolation method in GAMER
 
 ### Compilation and Runtime Settings
 - **Compile-Time Flag**: Ensure GAMER is compiled with `SUPPORT_SPECTRAL_INT` (or configured with `--spectral_interpolation`).
-- **Runtime Parameters**: Set `OPT__FLU_INT_SCHEME` and `OPT__REF_FLU_INT_SCHEME` to `8` for enabling spectral interpolation. Set `SPEC_INT_TABLE_PATH` to the directory containing `interpolation_tables` and `boundary2extension_tables`. Enable `SPEC_INT_XY_INSTEAD_DEPHA` to interpolate x = density^0.5\*cos( phase/SPEC_INT_WAVELENGTH_MAGNIFIER ), y = density^0.5\*sin( phase/SPEC_INT_WAVELENGTH_MAGNIFIER ) instead of density and phase, which has the advantage of being well-defined across vortices. `SPEC_INT_WAVELENGTH_MAGNIFIER` is the stretching factor of wavelength; setting it to unity gives x=real part and y=imaginary part.
+- **Runtime Parameters**: Set `OPT__FLU_INT_SCHEME` and `OPT__REF_FLU_INT_SCHEME` to `8` for enabling spectral interpolation. Set `SPEC_INT_TABLE_PATH` to the directory containing `interpolation_tables` and `boundary2extension_tables`. Enable `SPEC_INT_XY_INSTEAD_DEPHA` to interpolate real and imaginary parts instead of density and phase around vortices, which has the advantage of being well-defined across vortices. `SPEC_INT_VORTEX_THRESHOLD` sets the vortex detection threshold for `SPEC_INT_XY_INSTEAD_DEPHA`. If the laplacian of the phase field exceeds this threshold, we interpolate the real and imaginary parts. `SPEC_INT_GHOST_BOUNDARY` sets the ghost boundary size for spectral interpolation. A large ghost boundary increases interpolation accuracy but can negatively affect performance.
 
 ### Obtaining Interpolation Tables
 

diff --git a/doc/wiki/Home.md b/doc/wiki/Home.md
@@ -7,13 +7,14 @@ parallel scalability and supports a rich set of physics modules.
 
 ### Physics Modules
 * Hydrodynamics
-* [Magnetohydrodynamics](https://arxiv.org/abs/1804.03479)
-* [Special relativistic hydrodynamics](https://arxiv.org/abs/2012.11130)
+* [Magnetohydrodynamics](https://iopscience.iop.org/article/10.3847/1538-4365/aac49e/meta)
+* [Special relativistic hydrodynamics](https://academic.oup.com/mnras/article/504/3/3298/6224873)
 * Self-gravity and external gravity
 * Particles
 * Chemistry and radiative processes with [GRACKLE](http://grackle.readthedocs.io/en/latest/index.html)
 * General equation of state
 * [Cosmic rays with anisotropic diffusion](https://iopscience.iop.org/article/10.3847/1538-4357/ad50c5#apjad50c5app2)
+* Fuzzy (Wave) dark matter: [Nature Physics paper](http://www.nature.com/nphys/journal/v10/n7/covers/index.html), [code paper](https://arxiv.org/abs/2411.17288) 
 
 ### Other Features
 * Adaptive mesh refinement
@@ -28,10 +29,15 @@ parallel scalability and supports a rich set of physics modules.
 * Feedback interface
 
 ### Upcoming Physics and Features
-* [Wave dark matter (&psi;DM)](http://www.nature.com/nphys/journal/v10/n7/covers/index.html)
+* Anisotropic diffusion
+* Anisotropic/Braginskii viscosity
 
 ### Need Helps?
 * Project leader: Hsi-Yu Schive ([email protected])
 * Mailing list: [GAMER Google Group](https://groups.google.com/forum/#!forum/gamer-amr)
 * Live chat: [GAMER Slack](https://join.slack.com/t/gamer-project/shared_invite/enQtNTUwMDA5ODAwMTMzLTc3ZWY2MWE2YTlmMDI0MTQ4M2JjOTg2NmU4OWVkOGY1ZTI3MmY5NjUxOTk1ZjM5ZjNjOGViMGY3ZGExMDdiYzU)
-* Code papers: [GAMER-2](https://arxiv.org/abs/1712.07070) <a name="CODE_PAPER"></a>, [GAMER-MHD](http://iopscience.iop.org/article/10.3847/1538-4365/aac49e/meta) <a name="MHD_PAPER"></a> , [GAMER-SR](https://arxiv.org/abs/2012.11130) <a name="SR_PAPER"></a>
+* Code papers:
+[GAMER-2](https://academic.oup.com/mnras/article/481/4/4815/5106358) <a name="CODE_PAPER"></a>,
+[GAMER-MHD](http://iopscience.iop.org/article/10.3847/1538-4365/aac49e/meta) <a name="MHD_PAPER"></a> ,
+[GAMER-SR](https://academic.oup.com/mnras/article/504/3/3298/6224873) <a name="SR_PAPER"></a>,
+[GAMER-FDM](https://arxiv.org/abs/2411.17288) <a name="FDM_PAPER"></a>
diff --git a/doc/wiki/Installation:-External-Libraries.md b/doc/wiki/Installation:-External-Libraries.md
@@ -73,9 +73,9 @@ Follow the installation instructions in the
 [GRACKLE website](http://grackle.readthedocs.io/en/latest/index.html).
 Note that it must be configured with a
 consistent floating-point accuracy as GAMER using
-```
-make precision-{32,64}
-```
+
+    > make precision-{32,64}
+
 Specifically, configure GRACKLE with `make precision-64/32` when
 compiling GAMER with/without the option
 [[FLOAT8 | Installation: Simulation-Options#FLOAT8]], respectively.
@@ -84,9 +84,9 @@ In addition, when enabling OpenMP in GAMER (i.e., with the
 compile-time option [[OPENMP | Installation: Simulation-Options#OPENMP]]),
 GRACKLE must be configured with OpenMP
 support as well using
-```
-make omp-on
-```
+
+    > make omp-on
+
 ### HDF5
 GAMER uses [HDF5](https://support.hdfgroup.org/HDF5/) for storing snapshots.
 It is not necessary to enable either `--enable-cxx` or `--enable-parallel` when

diff --git a/example/input/Input__DumpTable b/example/input/Input__DumpTable
@@ -1,4 +1,4 @@
-#Dump ID             Dump Time
+#Dump_ID             Dump_Time
        0    0.0909090920000000
        1    0.0965026241318910
        2    0.1022642090403268

diff --git a/example/input/Input__Flag_Interference b/example/input/Input__Flag_Interference
@@ -0,0 +1,12 @@
+# Level          QP   Density   PhaseLap   OnlyAtExtrema
+      0        0.03         0        1.0               0
+      1        0.03         0        1.0               0
+      2        0.03         0        1.0               0
+      3        0.03         0        1.0               0
+      4        0.03         0        1.0               0
+      5        0.03         0        1.0               0
+      6        0.03         0        1.0               0
+      7        0.03         0        1.0               0
+      8        0.03         0        1.0               0
+      9        0.03         0        1.0               0
+     10        0.03         0        1.0               0
diff --git a/example/input/Input__Flag_Spectral b/example/input/Input__Flag_Spectral
@@ -0,0 +1,13 @@
+# Level   Refinement   Derefinement (derefinement currently not functional)
+      0          1.0             -1.0
+      1          1.0             -1.0
+      2          1.0             -1.0
+      3          1.0             -1.0
+      4          1.0             -1.0
+      5          1.0             -1.0
+      6          1.0             -1.0
+      7          1.0             -1.0
+      8          1.0             -1.0
+      9          1.0             -1.0
+     10          1.0             -1.0
+     11          1.0             -1.0
diff --git a/example/script/clean.sh b/example/script/clean.sh
@@ -3,4 +3,4 @@ rm -f Record__Note Record__Timing Record__TimeStep Record__PatchCount Record__Du
       Diag* BaseXYslice* BaseYZslice* BaseXZslice* BaseXline* BaseYline* BaseZline* BaseDiag* \
       PowerSpec_* Particle_* nohup.out Record__Performance Record__TimingMPI_* \
       Record__ParticleCount Record__User Patch_* Record__NCorrUnphy FailedPatchGroup* *.pyc Record__LoadBalance Record__Center \
-      GRACKLE_INFO Record__DivB
+      GRACKLE_INFO Record__DivB Record__Hybrid