Contact changes in shear-stabilized jammed packings

  • Simon Dagois-Bohy (Creator)
  • Silke Henkes (Creator)
  • Johannes Simon (Creator)
  • Brian P. Tighe (Creator)
  • Merlijn S. van Deen (Creator)
  • Martin van Hecke (Creator)
  • Zorana Zeravcic (Creator)
  • Bjoern Schelter (Data Manager)

Dataset

Description

This data set contains the result of small simple shear deformations applied to approximately 140,000 shear-stabilized jammed packings (see [...]), focusing on contact changes, as described in [1,2,3,4].

These packings contain N=16…4096
N=16…4096
particles with harmonic interactions, under a confining pressure p=10 −7 …10 −2
p=10−7…10−2
. Ensemble sizes range from 10 (N=4096) to 5000 (N=16).

In addition, a data file summarizing properties of the first contact change for each packing is provided.

Particle interactions

The simulation code minimizes the enthalpy

H=∑ k2 δ 2 ij +pL 2
H=∑k2δij2+pL2


where L² is the simulation box area, p the externally applied pressure, k=1 the spring constant and

δ ij ={R i +R j −|r ij → |0 if |r ij → |<R i +R j ,otherwise.
δij={Ri+Rj−|rij→|if |rij→|<Ri+Rj,0otherwise.




During shear, the boundary conditions are changed, and the system is relaxed to the new state. The simulation uses a bisection algorithm to efficiently step towards each subsequent contact change; see [3,4] for details.

Data files

The packings are stored in HDF5 data files. For each ensemble, we provide two files: one with and one without particle positions:
•N1024~P3162e-3_shear_noparticles.h5 includes all simulation data, but omits particle positions (see below for which data is included).
•For small data sets, N1024~P3162e-3_shear.h5 contains all simulations and all particle positions
•For large data sets, N1024~P3162e-3_shear_partial.h5 contains a subset of all simulations, but with all particle positions.
•Full particle positions for all simulations are available upon request to the authors. Please contact Martin van Hecke .

All files follow the same HDF5 layout:
•Example name: N1024~P3162e-3_shear.h5 and N1024~P3162e-3_shear_noparticles.h5 ◦Packings with N=1024
N=1024
particles
◦Pressure p=3.162⋅10 −3
p=3.162⋅10−3


•Packings are stored in a directory structure, e.g. /N1024/P3.1620e-03/0090/SR for the packing with id 0090. ◦​This directory contains a table 'data' indicating system parameters for each simulation step: ◾boundary conditions L1 and L2 (also as L, alpha, delta)
◾pressure P,
◾strain gamma,
◾stresses s_xy (simple shear), s_xx and s_yy,
◾number of contacts Ncontacts, contact number Z and number of rattlers #rattler
◾number of changed contacts for this contact change bisection Nchanges, N+ (created), N- (broken)
◾contact number Z
◾energy U, enthalpy H and their change in the last relaxation step (dU, dH)
◾step runtime t_run (seconds), #CG, #FIRE (number of conjugate gradient and FIRE iterations)
◾path to the packing corresponding to this state (does not always exist for each state for older simulations)

◦Each state is saved in /N1024/P3.1620e-03/0090/SR/0000 (initial), /N1024/P3.1620e-03/0090/SR/0001, ...etc. ◾States are not included in the _noparticles.h5 files
◾Some files omit intermediate positions, and only store positions just before and just after a contact change.
◾The format of these directories is the same as in https://dx.doi.org/10.5281/zenodo.59216.



Finally, we provide a summary file (shear_summary_cache.h5) which contains one table ('data') with properties of the first contact change of all packings. We provide the following columns:
•The variable postfix determines whether the value was calculated in the initial state (_base), just before the first contact change (_min) or just after the first contact change (_plus).


•General/simulation properties ◦Number of particles 'N'
◦Random seed ['num', 'PackingNumber_base']
◦External pressure 'P0_base'
◦Simulation step ['i_min', 'i_plus']

•Relaxation statistics ◦Last change in enthalpy during relaxation ['dH_base', 'dH_plus', 'dH_min']
◦Last change in energy during relaxation ['dU_base', 'dU_plus', 'dU_min']
◦Maximum gradient ['maxGrad_base', 'gg_min', 'gg_plus']
◦Initial simulation runtime ['runtime (s)_base']

•State properties ◦Number of rattlers 'N - Ncorrected_base'
◦Number of non-rattler particles ['Neff_min', 'Neff_plus']
◦Number of contacts ['Ncontacts_plus', 'Ncontacts_min']
◦Contact number z ['Z_base', 'Z_min', 'Z_plus']
◦Internal pressure ['P', 'P_base', 'P_min', 'P_plus']
◦Mean overlap δ ['mean_delta_base']
◦Packing fraction ['phi_base', 'phi_min', 'phi_plus']
◦Enthalpy ['H_base', 'H_plus', 'H_min']
◦Energy ['Uhelper_base', 'U_min', 'U_plus']
◦Simple shear parameter alpha ['alpha_base', 'alpha_min', 'alpha_plus']
◦Pure shear parameter delta ['delta_base', 'delta_plus', 'delta_min']
◦Square root of area ['L_base', 'L_min', 'L_plus']
◦Stresses on boundaries: ◾xx ['sxx_base', 's_xx_min', 's_xx_plus',]
◾yy [ 'syy_base', 's_yy_plus', 's_yy_min',]
◾xy ['sxy_base', 's_xy_plus', 's_xy_min']

◦Elastic moduli: ◾ ['c1_base', 'c1_min', 'c1_plus',
◾'c2_base', 'c2_min', 'c2_plus',
◾'c3_base', 'c3_min', 'c3_plus',
◾'c4_base', 'c4_plus', 'c4_min',
◾'c5_base', 'c5_plus', 'c5_min',
◾'c6_base', 'c6_min', 'c6_plus',
◾'Dac_base', 'Dac_plus', 'Dac_min',

◦AC component of G(θ) ['Gac_base', 'Gac_min', 'Gac_plus']
◦DC component of G(θ) ['Gdc_base', 'Gdc_min', 'Gdc_plus',]
◦AC component of U(θ) ['Uac_base', 'Uac_plus', 'Uac_min']
◦DC component of U(θ) ['Udc_base', 'Udc_plus', 'Udc_min']
◦Simple shear ['Galpha_base', 'Galpha_plus', 'Galpha_min' ]

•Contact change properties ◦Applied strain gamma ['gamma_plus', 'gamma_min'] ◾gamma_min is used as contact change strain

◦Number of created/broken contacts ['N+_plus', 'N+_min', 'N-_plus', 'N-_min']
◦Number of changed contacts (=N+ + N-) ['Nchanges_plus', 'Nchanges_min']
◦Making & breaking strain from upar and uperp: ◾simple linear (SL) solution: ['gmk_SL_base', 'gbk_SL_base']
◾full quadratic (FQ) solution: ['gmk_FQ_base' 'gbk_FQ_base']

◦G up to CC from fit σ=Gγ & error bar ['Glin', 'Glinerr']
◦G up to CC from fit σ=Gγ + λγ² & error bar ['Gquad', 'Gquaderr']
◦λ up to CC from fit σ=Gγ + λγ² & error bar ['lambdaquad', 'lambdaquaderr']
Date made available31 Jul 2031
PublisherZenodo

Cite this

Dagois-Bohy, S. (Creator), Henkes, S. (Creator), Simon, J. (Creator), Tighe, B. P. (Creator), van Deen, M. S. (Creator), van Hecke, M. (Creator), Zeravcic, Z. (Creator), Schelter, B. O. (Data Manager) (31 Jul 2031). Contact changes in shear-stabilized jammed packings. Zenodo. 10.5281/zenodo.59217