DOI: 10.5281/zenodo.6868243
title: On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers: dataset

description: <strong>Abstract:</strong><br> (from [1])<br> In the context of fracture simulations of polymers, the molecular mechanisms in the vicinity of the<br> crack tip are of particular interest. Nevertheless, to keep the computational cost to a minimum, a<br> coarser resolution must be used in the remaining regions of the numerical sample. For the specific<br> case of amorphous polymers, the Capriccio method bridges the gap between the length and time scales<br> involved at the different levels of resolution by concurrently coupling molecular dynamics (MD) with<br> the finite element method (FEM). Within the scope of the Capriccio approach, the coupling to the<br> molecular MD region introduces non-periodic, so-called stochastic boundary conditions (SBC). In<br> similarity to typical simulations under periodic boundary conditions (PBC), the SBC MD simulations<br> must reach an equilibrium state before mechanical loads are exerted on the coupled systems. In this<br> contribution, we hence extensively study the equilibration properties of non-periodic MD samples<br> using the Capriccio method. We demonstrate that the relaxation behavior of an MD-FE coupled<br> MD domain utilizing non-periodic boundary conditions is rather insensitive to the specific coupling<br> parameters of the method chosen to implement the boundary conditions. The behavior of an exemplary<br> system equilibrated with the parameter set considered as optimal is further studied under uniaxial<br> tension and we observe some peculiarities in view of creep and relaxation phenomena. This raises<br> important questions to be addressed in the further development of the Capriccio method.<br> <br> <strong>Contact:</strong><br> Felix Weber<br> Institute of Applied Mechanics<br> Friedrich-Alexander-Universität Erlangen-Nürnberg<br> Egerlandstr. 5<br> 91058 Erlangen<br> Germany<br> <br> <strong>Context:</strong><br> This dataset contains the results presented in [1] and related data. <strong>Content:</strong><br> Throughout this data set, Lammps [2] real units are used. The following folders contain the results obtained under periodic boundary conditions:<br> - biax_PBC: biaxial loading <br> - equil_PBC: equilibration<br> - ut_PBC: uniaxial tension<br> Each simulation directory contains:<br> - input.prm: input parameters of the specific simulation (read by the input file)<br> - job.out: simulation log file<br> - meta.info: meta data of the specific simulation run<br> - Lammps input file (*.in) of the specific simulation<br> - Lammps data file (*.data, molecular style) of the investigated sample<br> - LAMMPS_out: resulting Lammps data and restart (*.rst) files and simulation results (Lammps thermo_out) in <br> tabulated form, an overview of the columns is given in the respective folders The following folders contain the results obtained under stochastic boundary conditions using the Capriccio method [3]:<br> - best: equilibration with the parameter set considered to be most suitable for the MD-FE coupled equilibration<br> - biax: biaxial loading<br> - bridging: equilibration with different adaptivity levels of the bridging domain<br> - descr_obs: equilibration with a Lagrangian frame for the description of the observation region<br> - dpd: equilibration with different thicknesses of the dissipative particle dynamics (DPD) region<br> - friccoeff: equilibration with different friction coefficients applied in the dissipative particle dynamics region<br> - fur: equilibration with different numbers of fur beads <br> - gausspoints: equilibration with different numbers of quadrature points per direction <br> - min: equilibration applying an initial, static energy minimization<br> - nodes: equilibration with a higher number of finite element nodes<br> - shifted: equilibration with particle systems obtained at different positions and points in time within the periodic master system<br> - smdcub: equilibration with different remaining stiffness ratios for the cubic modified weighting factor<br> - smdlin: equilibration with different remaining stiffness ratios for the linear modified weighting factor<br> - timestepsize: equilibration with different molecular dynamics time step sizes<br> - ut: uniaxial tension<br> - ut_friccoeff: uniaxial tension with different friction coefficients applied in the dissipative particle dynamics region<br> - weighting: equilibration with different energy weighting functions<br> - youngsmod: equilibration with different Young's moduli<br> Each simulation directory contains:<br> - input_files: Abaqus [4] input file (*.inp) and Lammps data file (*.data, molecular style) of the investigated sample<br> - MD_data: Results evaluated in the molecular dynamics region. MD_data contains the following subfolders: <br> anchorforces (dumped force components on the anchor points (AP) in kcal/mol, files anchorforce_[load step]_[MD-FE iteration].AF), <br> data (resulting Lammps data files *.[load step].[MD-FE iteration].data), Density (dumped mass density in the observation region in kg/m^3), <br> Energy (dumped total (kinetic + potential), angle, bond, and pair energies in kcal/(mol*Angstrom)), Strain (integral strains in the<br> observation region in x-, y-, and z-direction calculated by means of the Matlab [5] script calc_OBSstrain.m),<br> Stress (stresses in the observation region in MPa), and Temperature (temperature in the observation region in K)<br> - job.out: simulation log file<br> - meta.info: meta data of the specific Lammps simulation<br> Information on the subfolders is given in the respective folders. <strong>References:</strong><br> [1] F. Weber, M. Ries, C. Bauer, C. R. Wick, S. Pfaller, "On equilibrating non-periodic molecular dynamics samples for coupled<br> particle-continuum simulations of amorphous polymers", Forces in Mechanics, 2023, 10, 100159.<br> [2] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, <br> S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton, "LAMMPS - a flexible simulation tool <br> for particle-based materials modeling at the atomic, meso, and continuum scales", Computer Physics Communications, 2022, 271, 108171.<br> [3] S. Pfaller, M. Rahimi, G. Possart, P. Steinmann, F. Müller-Plathe, M. C. Böhm, "An Arlequin-based method to couple molecular dynamics <br> and finite element simulations of amorphous polymers and nanocomposites", Computer Methods in Applied Mechanics and Engineering, <br> 2013, 260, 109-129. <br> [4] Dassault Systèmes, "Abaqus documentation", URL: https://abaqus-docs.mit.edu/2017/English/SIMACAEEXCRefMap/simaexc-c-docproc.htm.<br> [5] The MathWorks, Inc, "MATLAB. The Language of Technical Computing", URL: https://de.mathworks.com/help/matlab/. <strong>Funding:</strong><br> This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) -<br> 377472739/GRK 2423/1-2019. The authors are very grateful for this support. Sebastian Pfaller is furthermore<br> funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 396414850 (Individual<br> Research Grant ’Identifikation von Interphaseneigenschaften in Nanokompositen’).