Frozen atom analysis in "Cooperative atomic motion during shear deformation in metallic glass"

## Frozen atom analysis This page has been prepared for the peer review of the manuscript titled **"Cooperative Atomic Motion During Shear Deformation in Metallic Glass"** submitted to **Nature Communications.** It provides access to the short Python script implementing the core algorithm of the manuscript—**frozen atom analysis**—allowing reviewers or readers to examine the algorithm and perform test runs as part of the review process. ### Contents * code/frozen_atom_analysis.py Python script to run the frozen atom analysis * data/1e09_002/xy_m/m445 Subdirectories including LAMMPS dump files to reproduce the histogram in figure 1c of the manuscript * results/displacement_histogram.png Histogram shown in Figure 1c of the manuscript * results/displacement_norms.csv CSV file including D_f parameter for each atom ### Usage * **Reproducible run** * **Check the figure in results/displacement_histogram.png**. This should be the same as Figure 1c in the manuscript (https://arxiv.org/pdf/2503.14903). The atomic group with small $D_\text{f}$ is the STZ core detected in the frozen atom analysis. ### To prepare input files This code requires LAMMPS dump files that record atomic configurations before and after relaxation, in order to calculate the $D_\text{f}$ parameter in the manuscript. Since preparing a complete input file set can be time-consuming, an example dataset is provided in the directory `data/1e09_002/xy_m/m445` for convenience. The procedure for generating these input files is outlined below (for further details, please refer to the manuscript): 1. Perform an AQS (Athermal Quasi-Static) shear deformation simulation using LAMMPS. Examine the resulting stress–strain curve, and extract atomic configurations just before each stress drop event. In this example, we use a particular event labeled `m445`. 2. For each atom in the configuration, create a separate directory named after its atom ID. See `data/1e09_002/xy_m/m445` for an example, and proceed to the next step. 3. Using the configuration from step 1, perform a LAMMPS relaxation calculation in each directory. In each calculation, the atom corresponding to the directory name (i.e., the atom ID) is frozen. A sample LAMMPS input file for this purpose is provided as `misc/frozen.inp`. 4. After completing the above preparation for each event, run `frozen_atom_analysis.py`. This script analyzes the resulting atomic displacements and computes the $D_\text{f} parameter. ### Reference and citing https://arxiv.org/pdf/2503.14903 ### Author Yoshinori Shiihara, Toyota Technological Institute ### Contact shiihara[at]toyota-ti.ac.jp