Crack-tip deformation transitions and fracture mechanisms in glassy polymers revealed by particle-continuum coupling simulations

This dataset contains public data for the publication "Crack-tip deformation transitions and fracture mechanisms in glassy polymers revealed by particle-continuum coupling simulations" [1].These files include code, initial files, and parameters for 1) pure molecular dynamics (MD) simulations, 2) constitutive modeling, and 3) particle-continuum coupling simulations, respectively saved in the following folders:    01_MD_PBC/    02_constitutive_model/    03_MD-FE_coupling/1. pure MD simulations (in folder "01_MD_PBC")    The aim of pure MD simulations is to identify the constitutive model used in coupled simulations. Coarse-grained polystyrene (CGPS) with force field parameters identified by the Müller-Plathe group at TU Darmstadt [2] is used as an example. The initial configuration is generated by the Ibisco code [3], which is not included in this dataset. The MD simulations are performed using LAMMPS [4], version 20211027.    This folder has 4 subfolders: While "00_systems" contains the force field filed and lammps scripts, the other folders correspond to the simulations steps.        (1) file creation. In each subfolder of "01_initialization_MD_PBC_b4quil", the MD configuration before equilibration can be generated by the command "./generate_MD_pbc.sh".        (2) Thermal processing. This can be performed in folder "02_thermal_processing_FracNp", including NPT equilibrium at a high temperature, NVT equilibrium at this temperature, and cooling, which can be stepwise implemented by the commend "sbatch job_PBC_equil.sh" on slurm-based HPC or "./job_PBC_equil.sh" locally. Here, the path to lammps executable file must be set correctly.        (3) Deformation simulations. In folder "10_deform_MD_PBC_FracNp", deformation simulations of the equilibrated MD systems can be performed in each subfolder through the command "sbatch job_deform_PBC.sh"2. constitutive modeling (in folder "02_constitutive_model")    This contains two steps:        (1) data processing in folder "00_pure_MD_data", which saves the raw MD data in its subfolder "MD_data_processed" through "main_data_processing_FracNp_MD.m" using Matlab, and        (2) simulations of the constitutive model "main_constitutive_model.m", plotting stress-strain curves.3. coupled simulations and data processing (in folder "03_MD-FE_coupling")    Subfolder "00_source_coupling" contains source code for particle-continuum simulations adapted from the Capriccio 2.0 [5] with modifications mainly for implementation of the identified constitutive model.    Subfolder "10_system_CGPS_3D" includes files for different steps of coupled simulations:        (1) subfolder "00_system_convert_pbs2hbc". Converting PBC to hybrid boundary conditions (HBC) and creating pre-cracks in the MD domain. This can be performed through            (a) run "./01_generate_MD_sbc_delete_short_chains.sh" in folder "10_converting_pbc2sbc" to convert PBC to HBC.            (b) conduct particle-continuum coupling simulations in folder "03_MD-FE_coupling/10_system_CGPS_3D/21_sim_cpl_equil/individual_simulations" in HPC using command "sbatch ../../../00_source_coupling/Capriccio_v2/Capriccio_FEMD_main_HPC.sh". More detailed documentation can be found in [5]. Copy the equilibrated file to "03_MD-FE_coupling/10_system_CGPS_3D/00_system_convert_pbs2hbc/10_converting_pbc2sbc/02_output_data_equil_cpl/".            (c) run "./02_dump_anchor_points.sh" to generate initial file for anchor point positions of the equilibrated MD systems.            (d) run "./03_generate_MD_cracks.sh" to create pre-cracks. The generated files are located in folder "03_MD-FE_coupling/10_system_CGPS_3D/00_system_convert_pbs2hbc/10_converting_pbc2sbc/03_output_data_crack/". These files will be used as input files of the MD domain in coupled fracture simulations.        (2) subfolder "10_FE_meshing". Creating mesh file for the continuum domain using Abaqus following subsequent steps:            (a) open Abaqus CAE            (b) open file "FE_mesh_SSP_CGPS_nano_frac2.py" in Abaqus using "File - Run Scripts". Here, the anchor_path and filepath in the file "FE_mesh_SSP_CGPS_nano_frac2.py" should be set correctly.              (c) set boundary conditions            (d) Write Input            (e) Switch CRLF format to LF. Several mesh files for uniaxial deformation and fracture simulations are provided in folder "03_MD-FE_coupling/10_system_CGPS_3D/10_FE_meshing/mesh_file/"        (3) subfolder "21_sim_cpl_equil". For quilibration of the MD domain in coupled systems.        (4) subfolder "22_sim_cpl_frac".            (a) For coupled fracture simulations, containing two examples with raw data: "cpl_frac_Nl4_fixz_r10_dFE0002_Haward_Np400_sys1_T60_kAP800_Eb0" and "cpl_frac_Nl4_fixz_r10_dFE0002_Haward_Np400_sys1_T60_kAP800_Eb0". Run "sbatch ../../../00_source_coupling/Capriccio_v2/Capriccio_FEMD_main_HPC.sh" in corresponding subfolder for coupled simulations (more details to run this simulation can be found in [5]).            (b) All initial MD configurations are provided in subfolder "input_files/" (different chain length and temperatures.) This can be using by modifying the parameter file "Capriccio.prm" in folder "input_parameters/".        (5) subfolder "30_data_processing". Postprocessing raw data using matlab.            (a) processing raw data: save_01_raw_to_stress_avg.m; save_02_raw_to_bond_angle_avg.m;            (b) evaluating results: plot_01_curves_avg.m; plot_02_configuration_MD.m; plot_03_statistical_results.m            (c) Remark 1: Running save_03_raw_to_Z1.m requires installing Z1+ code [6] and implementing "Z1_analysis_SSP.py" in each individual coupled simulation.            (d) Remart 2: The quantities of atomic Dmin2 and atomic volume are calculated using Ovito [7].            (e) Remark 3: The curve figures are converted to .tex file through matlab2tikz with source code in "03_MD-FE_coupling/10_system_CGPS_3D/30_data_processing/utilities/matlab2tikz/" (BSD License).[1] W. Zhao, P. Steinmann. Crack-tip deformation transitions and fracture mechanisms in glassy polymers revealed by particle-continuum coupling simulations. Journal of the Mechanics and Physics of Solids, 2026, 106595. DOI: doi.org/10.1016/j.jmps.2026.106595[2] H.-J. Qian, P. Carbone, X. Chen, H. A. Karimi-Varzaneh, C. C. Liew, F. Müller-Plathe. Temperature-transferable coarse-grained potentials for ethylbenzene, polystyrene, and their mixtures. Macromolecules, 2008, 41 (24), 9919–9929.[3] H. A. Karimi-Varzaneh, H.-J. Qian, X. Chen, P. Carbone, F. Müller-Plathe. IBIsCO: A molecular dynamics simulation package for coarse-grained simulation. Journal of Computational Chemistry, 2011, 32 (7), 1475-1487.[4] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in’t Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 2022, 271, 108171.[5] S. Pfaller, M. Ries, W. Zhao, C. Bauer, F. Weber, L. Laubert, L. CAPRICCIO - Tool to run concurrent Finite Element-Molecular Dynamics Simulations (2.0.0). Zenodo, 2024. doi.org/10.5281/zenodo.10423466[6] M. Kröger, J. D. Dietz, R. S. Hoy, C. Luap. The Z1+ package: Shortest multiple disconnected path for the analysis of entanglements in macromolecular systems. Computer Physics Communications, 2023, 283, 108567.[7] A. Stukowski. Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool. Modelling and Simulation in Materials Science and Engineering, 2009, 18, 015012.