Simulation outputs and softwares for "Simulations of Electron Interaction with Ionospheric Alfvén Resonator in the Jovian Aurora" paper

The alfjup contains the full-wave code that simulates the formation of an Ionospheric Alfvéne Resonator, using the same code as Lysak et al. (2021), https://doi.org/10.1029/2021JA029886. The main change is that the output files are now written in HDF format. xyzb.dat is a data file that contains the x,y,z coordinates and the magnetic field strength along the central field line of the IAR simulations. rhozbxyz.dat is a data file that contains the rho, z coordinates and the x,y,z components of the magnetic field along the central field line of the IAR simulations. The MATLAB scripts that read the output files and generate the figures with the output data are listed below. constants.m is a MATLAB script that contains some constants. calc_dAflux.m is a MATLAB function that calculates the cross-section at a position with z coordinate z0, given the rho coordinate of the injection with dR and dML. dR and dML are the length perpendicular to the magnetic field and the magnetic latitude extent. This fuction is used in some of the routines that plot the Figures in the manuscript. magfield_rho0.m is a MATLAB function that calculates the rho, and z components of the magnetic field with the ratio of the magnetic field at a position with rho0 coordinate on the central field line and the magnetic field at the ionosphere. movie_s1.m, this makes the Movie S1 of the Supplemental Materials. The rdir should be the same as the directory that contains the output fields of the alfjup. In our case, it is /scratch.global/weshetu/run105/, and it should be modified in alfjup/write_fields.f90. plot_figure_1a_1b.m plots Figures 1a and 1b of the manuscript. It needs trj_25keV.dat. This file is output from a test particle. It contains eight columns of data, including the tag number, time, x, y, z, energy, pitch angle, and parallel electric field, along the particle trajectory for a run with an initial energy of 25 keV. plot_figure_1c_1d.m plots Figures 1c and 1d of the manuscript. It needs trj_5keV.dat. This file is the same format as trj_25keV.dat for an initial energy of 5 keV. plot_figure_2.m plots Figure 2 of the manuscript. It needs trj_phase.dat, output from a test particle run of the same format as trj_25keV.dat, for particles started at different phases of the wave. plot_figure_3.m plots Figure 3 of the manuscript. It requires runE25keV_isotropic_test.dat, a seven-column data file containing tag number, time, x, y, z, energy, and pitch angle as particles cross a crossection perpendicular to the magnetic field, positioned at an altitude of approximately 0.6 RJ (1.6 RJ Jovicentric distance). This run was done without the electromagnetic field of the Alfvén wave. plot_figure_4_5_movie_s2.m plots Figures 4 and 5 of the manuscript as well as Movie S2 of the Supplementary Materials. It needs runE250keV_1.dat, which is the same format as runE25keV_isotropic_test.dat, simulated with the Alfvén wave field. The test particles were initiated around the field line where the parallel electric field is maximum. The Movie S2 is made with a cadence of 0.1 seconds. plot_figure_6.m plots Figure 6 of the manuscript. It uses the runE250keV_1.dat data. The time cadence of the flux calculation is set at 1 second. plot_figure_7.m plots Figure 7 of the manuscript, which is the average flux seen by a moving satellite around an altitude of 0.6 RJ. It uses the run_satellite250keV.dat data, which is the same format as runE250keV_1.dat. The spatial distribution of the test particle was designed so that it maps along the trajectory of the virtual satellite. plot_figure_8.m plots Figure 8 of the manuscript. It needs run_powerlaw.dat, which is the same format as runE250keV_1.dat. The run is with an initial flux that follows the power law index of -2. plot_figure_9_movie_s5.m plots Figure 9 of the manuscript and makes Movie S5 of the Supplementary Materials. It needs runE250keV_1.dat and runE250keV_2.dat. Both files are in the same format; runE250keV_2.dat contains run results on field lines away from the central field line, corresponding to the red line in Movie S1. movie_s6.m makes Movie S6 of the Supplementary Materials. It needs runE250ke_arc.dat, which is the same format as runE250keV_2.dat. The flux are calculate at an altitude of 0.6 RJ. plot_figure_s1.m plots Figure S1 of the Supplementary Materials and makes movie for the case of an initial energy of 25 keV. It needs run E25keV_1.dat, which is in the same format as runE250keV_2.dat. plot_figure_s2.m plots Figure S1 of the Supplementary Materials and makes movie for the case of an initial energy of 5 keV. It needs run E5keV.dat, which is in the same format as runE250keV_2.dat. plot_figure_10a_b.m plots Figures 10a and 10b. It needs trj_100eV.dat, which contains an 8-column file in the same format as trj_25keV.dat for an electron with an initial energy of 100 eV moving upward from the ionosphere. plot_figure_10c_d.m plots Figures 10c and 10d. It requires trj_1keV.dat, in the same format as trj_100eV.dat, for an initial electron energy of 1 keV. plot_figure_11.m plots Figures 11a-c of the manuscript. It needs run_noiar.dat, a run without the electromagnetic field of the IAR. The data contains tag number, time, x, y, z, energy, and pitch angle dumped at several specified times. The data was further reduced to save memory by only saving data around specific positions. plot_figure_12.m plots Figure 12 of the manuscript. It needs runTe100eV_2.dat, which contains data with the same format as run_noiar.dat for a run with an initial electron temperature of 100 eV and the electromagnetic field. The results of the distribution are at an altitude of 0.6 RJ. plot_figure_13.m plots Figure 13 of the manuscript. It needs runTe100eV_2.dat. The results of the distribution are at an altitude of 2.6 RJ. plot_figure_14.m plots Figure 14 of the manuscript. It needs runTe100eV_2.dat. The results of the distribution are at an altitude of 2.6 RJ at different phases of the wave. plot_figure_15.m plots Figure 15 of the manuscript. It needs runTe100eV_2.dat. The results of the distribution are at an altitude of 1.1 RJ at different phases of the wave. plot_figure_16a_b.m plots Figures 16a and 16b of the manuscript. It needs runTe1keV.dat, a run with an initial electron temperature of 1k eV. The results are at an altitude of 2.6 RJ. plot_figure_16c_d.m plots Figures 16c and 16d of the manuscript. It needs runTe1keV.dat, a run with an initial electron temperature of 1k eV. The results are at an altitude of 5.7 RJ.