7.6. Nyx

Installation

1. Dependencies: MPI and "parallel hdf5"

2. Install ARMex

git clone https://github.com/AMReX-Codes/amrex.git
mkdir amrex/build && cd amrex/build
cmake .. -DAMReX_HDF5=ON -DAMReX_PARTICLES=ON -DAMReX_PIC=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$HOME/amrex/install
make -j 8
make install

2. Install Nyx

git clone https://github.com/AMReX-astro/Nyx.git
cd Nyx
mkdir build && cd build
cmake .. -DCMAKE_PREFIX_PATH=$HOME/amrex/install/ -DAMReX_DIR=$HOME/amrex/install/Tools/CMake/ -DNyx_SINGLE_PRECISION_PARTICLES=OFF -DNyx_OMP=OFF
make -j 8

Usage

The Nyx executable reads run-time information from an “inputs” file which you designate on the command line. Most executable directories have an "inputs" file. Nyx has several different executables. Here I only show how to run the LyA example.

Configure the "inputs" file under LyA directory

1. By default, Nyx doesn't output HDF5 files. To enable Nyx to write HDF5 files, adding nyx.write_hdf5 = 1 to the "inputs" file. For example:

# ------------------  INPUTS TO MAIN PROGRAM  -------------------
max_step = 200

nyx.ppm_type         = 1
nyx.use_colglaz      = 0
nyx.corner_coupling  = 1
nyx.write_hdf5       = 1  # add this line
nyx.strang_split     = 0
nyx.sdc_split        = 1
nyx.add_ext_src      = 0
nyx.heat_cool_type   = 11

2. Set the nyx.initial_z and nyx.final_z, z corresponds to time, but it is negative. nyx.initial_z is larger than nyx.final_z. For example:

nyx.initial_z = 190.0
nyx.final_z = 170.0

3. Nyx needs to initialize binary particles. I want it to read from a binary file. By default, there is a binary file 64sssss_20mpc.nyx in LyA directory. Here are some related parameters:

# >>>>>>>>>>>>>  PARTICLE INIT OPTIONS <<<<<<<<<<<<<<<<
nyx.particle_init_type = BinaryFile
nyx.binary_particle_file = 64sssss_20mpc.nyx
particles.nparts_per_read = 2097152

Note: If 64sssss_20mpc.nyx is located in a different directory, you need to use the absolute path of the file.

3. Nyx will generate two kinds of files: “plotfiles” and “checkpoint” files. The "plotfiles" are used for visualization and the "checkpoint" files for restarting the code. The "plotfiles" are written in AMReX plotfile binary format by default. You can tell Nyx to output HDF5 file by adding nyx.write_hdf5 = 1

3.1 Set "plotfiles" related parameters

# PLOTFILES
amr.plot_files_output = 1 
amr.plot_file       = /mnt/ssd/jye20/LyA_test/plt
amr.plot_int        = -1
nyx.plot_z_values   = 188.0 184.0 182.0

amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
#amr.derive_plot_vars = particle_mass_density particle_count

amr.plot_files_output: This is set to 1 to enable plot files. If you don't want to output plot files, set it to 0.

amr.plot_file: This is the base name for the plotfile, e.g. plt. If you set it to be /mnt/ssd/jye20/LyA_test/plt, /mnt/ssd/jye20/LyA_test is the output directory.

nyx.plot_z_values: Specify a list of z values for which Nyx will save a snapshot.

amr.plot_vars: Specify the name of state variables to include in plotfiles

amr.derive_plot_vars: Specify name of derived variables to include in plotfiles

3.2 Set checkpoint file parameters

# CHECKPOINT FILES
amr.checkpoint_files_output = 1
amr.check_file        = /mnt/ssd/jye20/LyA_test/chk
amr.check_int         = 100
amr.checkpoint_nfiles = 64

4. Resolution related parameters

amr.n_cell           =  64  64  64
amr.max_grid_size    = 32

Reference: Nyx document

Run the Nyx Application

1. Enter into the LyA executable directory

./nyx_LyA ./inputs