DOI: 10.5281/zenodo.15858471
title: Simulation Files for "ReaxFF Parameter Set for Boron Clusters and Icosahedral Boron Crystals: Comparison with Density Functional Theory and Machine-Learning Potentials"

description: Ahmadisharaf et al.**********************************

This data set for the manuscript entitled "Improved ReaxFF Parameter Set for Small Boron Clusters and Icosahedral Boron Crystals" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software LAMMPS, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text. They include all developed force field parameter files in this study (in ReaxFF format), LAMMPS configuration files (*.in), ReaxFF control files (*.control), LAMMPS log files (*.log), and LAMMPS output including restart files (in binary LAMMPS format) and trajectories in dcd format (downsampled to 12.5 or 25 ps per frame). We also included the PDB and PSF files, which are useful for visualization with VMD. Analysis is performed by Python and shell scripts (Bash-compatible) that call VMD Tcl scripts or Python scripts. These scripts and their output are also included.

The simulations were performed with LAMMPS (29 Oct 2020). The ReaxFF input parameters must be changed for newer versions of LAMMPS (see Figures/Figure3/simu/npt3600_small_boron_nff2_lammps-29Aug2024.in):

14c14< pair_style    reax/c ${name}.control checkqeq yes safezone 1.2 mincap 180 ---> pair_style    reaxff template2024.control checkqeq yes safezone 1.2 mincap 180 21c21< fix             1 all qeq/reax 1 0.0 10.0 1e-6 ffield.B-O-Ni.qeq---> fix             1 all qeq/reax 1 0.0 10.0 1e-6 reaxff

The icosahedrality analysis is performed by the Python script "Figure3/analysis/cal_icosa_angle_penta_planarity.py".

The suffixes "liu" correspond to the 2017 published ReaxFF parameters of boron, we called it Original ReaxFF in the main text. https://doi.org/10.1021/acsnano.6b06736

The directory contents are as follows.----------------------------------------------------------------------------------------------------------------------------ForceFields----------------------------------------------------------------------------------------------------------------------------All three ReaxFF versions developed in this study, as well as the ReaxFF parameters published previously by Liu et al. 2017 (referred to as Original in the main text).----------------------------------------------------------------------------------------------------------------------------Figures 1--8----------------------------------------------------------------------------------------------------------------------------Figure1: B80_t1buckyball, B80_c1coreshell, and B80_pouch represent, respectively, the B80 buckyball announced by Gonzalez-Szwacki et al. (2009), the B80 coreshell introduced by Li et al. (2012), and the B80 Pouch structure identified in this study.--------------------------------------------------------------Figure2: Beta and Alpha rhombohedral boron structures included in the initial training set. The icosahedrality script was tested on these structures as a benchmark.--------------------------------------------------------------Figure3: Structures from Li et al., Hayami et al., and Pham et al. used in the test set. Includes resulting structures after DFT relaxation.--------------------------------------------------------------Figure4: Simulations of crystal growth from molten beta-boron (small system) at 1600 K with all three developed ReaxFF parameteres and previously published that is explained earlier (Liu 2017). The analysis of icosahedrality clusters is performed by the python script "Figure3/analysis/cal_icosa_angle_penta_planarity". --------------------------------------------------------------Figure5: Simulations of crystal growth from molten beta-boron (big system) at 1600 and 1300 K with Version 3 ReaxFF and 1600 K with Version 2 ReaxFF. The analysis of icosahedrality clusters is performed by the python script "Figure4/analysis/cal_icosa_angle_penta_planarity". --------------------------------------------------------------Figure6: Simulation of the seed effect on crystal growth, and recognition and counting of the icosahedral boron motifs at 1600 K. The related simulations files and outputs for 1600 K (restrain seed) is located in Figure 3 directory.--------------------------------------------------------------Figure7: Simulation of the temperature effect on crystal growth, and recognition and counting of the icosahedral boron motifs at 1300, 1400, 1500, and 1600 K. The related simulations files and outputs for 1600 K is located in Figure 3 directory. Simulation of the pressure effect on crystal growth, and recognition and counting of the icosahedral boron motifs at 1 atm, 10, and 24 GPa. The related simulations files and outputs for 1600 K (1 atmospheric pressure) is located in Figure 3 directory.--------------------------------------------------------------Figure8: Solubility of boron in molten liquid nickel at 1750 and 2000 K, and counting the solvated boron atoms in the center of the molten nickel.  The Python script (B_solubility_in_Ni.py) is available in Figure8/analysis.

----------------------------------------------------------------------------------------------------------------------------Tables 1--4----------------------------------------------------------------------------------------------------------------------------Table1: Energy minimization for the three B80 structures used in the training set along with the De et al. B80 core-shell for all ReaxFF versions developed here, as well as the Liu et al. B/N/Ni force field. The LAMMPS log files contain the energy values used to compute Table 1.--------------------------------------------------------------Table2: Calculation of RMSD values for B80 training set and De et al. B80 core-shell structures.--------------------------------------------------------------Table3: DFT relaxation for the B80 training set and De et al. B80 core-shell structures. Input files for MACE and Matlantis energy minimization.--------------------------------------------------------------Table 4: B8–B103 Structures from Li et al., Hayami et al., and Pham et al. used in the test set. Includes resulting structures after DFT relaxation.

----------------------------------------------------------------------------------------------------------------------------Icosahedrality----------------------------------------------------------------------------------------------------------------------------The more friendly user version of the icosaherality script and a few examples included.