Dataset for "Anomalous phonon dispersion near yielding in athermal crystals"

This repository includes raw data and simulation codes for the paper "Anomalous phonon dispersion near yielding in athermal crystals." OverviewWe perform numerical calculations using Python and discrete element method (DEM) simulations with LAMMPS. The repository folder, repository.zip, includes the following code and data, as shown in the tree structure below. .|-- directory_structure.txt|-- fig2: this directory includes code and data for Fig.2| |-- 20260127_argon_stress_strain_data: this directory includes DEM code and data. "argon" is just the name of my workstation.| | |-- base_begin_simu.sh: change parameters in directory base_origin, and execute DEM simulations.| | |-- base_origin: original file of DEM simulation codes| | |-- base_plot.plt: this code is not used for the main manuscript.| | |-- data_h5e-02_e5e-1_f0e+0_rate1e-5.txt| | |-- data_h5e-02_e5e-1_f0e+0_rate1e-6.txt| | |-- data_h5e-02_e5e-1_f0e+0_rate1e-7.txt| | `-- data_h5e-02_e5e-1_f0e+0_rate1e-8.txt| |-- base_begin_theory.sh: change parameters of base_theory.py, and execute python code.| |-- base_plot.plt: make Fig.2 using data files named "data_*"| |-- base_theory.py: calculates stress tensor, minimum eigenvalue, and eigenvector.| |-- data_evals_min_h5e-02.txt| |-- data_stress_h5e-02.txt| `-- data_x_y_u_v_h5e-02.txt`-- fig3-5: this directory includes code and data for Fig.3-5 |-- base_begin_theory.sh: change parameters of base_theory.py, and execute the python code |-- base_plot.plt: make Fig. 3-5 using data files in directory "runs" |-- base_theory.py: calculates the data of dispersions and VDOS used in Fig.3-5. `-- runs: data for Fig.3-5. The data is plotted using gnuplot code base_plot.plt. |-- 20260210-stress-eval-disp2d-vdos-angle-disp1d-h5e-02 |-- 20260211-vdos-h5e-02 |-- 20260216-angle-h5e-02 |-- 20260216-disp1d-h5e-02 |-- 20260216-disp1d-h5e-03 |-- 20260216-disp1d-h5e-04 `-- 20260224-disp1d-h1e-01