CALiPPSO.jl: A Linear Programming Algorithm for Jamming Hard Spheres

---

Important!! Breaking changes introduced in v0.2.0 when changing the default optimizer or passing it arguments. See the corresponding section below.

This might cause the following error message if the main function is interrupted.

ERROR: The provided `optimizer_constructor` returned a non-empty optimizer.

In this section we give the instructions for solving it.

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This package is a pure Julia implementation of the CALiPPSO algorithm for generating jammed packings of hard spheres. The algorithm itself was introduced in this article by Artiaco, Díaz, Parisi, and Ricci-Tersenghi. As explained there, CALiPPSO consists of a Chain of Approximate Linear Programming for Packing Spherical Objects. It works in arbitrary dimensions, and for both monodisperse and polydisperse configurations, as shown below:

(Left: Monodisperse packing of 16k particles; coloured according to their number of contacts. Right: Polydisperse packing of 1024 disks, with radii from a log-normal distribution, and network of contacts drawn.

This package is licensed under the MIT license, so please feel free to use/modify/improve this code as better suits you. We only ask you to cite our work if you find it useful.

@article{CALiPPSO,
  title = {Hard-Sphere Jamming through the Lens of Linear Optimization},
  author = {Artiaco, Claudia and D{\'i}az Hern{\'a}ndez Rojas, Rafael and Parisi, Giorgio and {Ricci-Tersenghi}, Federico},
  year = {2022},
  month = nov,
  journal = {Physical Review E},
  volume = {106},
  number = {5},
  pages = {055310},
  publisher = {{American Physical Society}},
  doi = {10.1103/PhysRevE.106.055310},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.106.055310}
}

Documentation

You can read the full documentation of our code here.

Basic usage

Installation

From a Julia REPL, Jupyter notebook, etc. simply do

]add CALiPPSO

Or, if you prefer to import the Package manager (Pkg), do:

import Pkg
Pkg.add("CALiPPSO")

This will also automatically install the required dependencies; the main ones are JuMP.jl, StaticArrays.jl and GLPK.jl. The latter is needed because GLPK is the default solver of CALiPPSO. In any case, once CALiPPSO is added, you can simply import it into your current working space (i.e. the REPL, a Jupyter notebook, script, etc) as any other package, namely using CALiPPSO.

Below we show a minimal working example (MWE) and show how to change the solver used by CALiPPSO. See also the scripts in the Examples folder of this repo for more usage examples.

Minimal example

We tried to make this package as easy to use as possible and, indeed, it consists of a single main function: produce_jammed_configuration!(Xs0, r0, L=1.0). We also provide a function to generate a low density random initial condition so that you can use CALiPPSO right away. However, as we explain in our paper and in the relevant part of the documentation, our algorithm works best if the initial condition is already close to its jamming point. Thus, our code is not guaranteed to work with any such low density configurations. However, for small systems, even a low density configuration should be suitable for initializing CALiPPSO. So, for instance, to jammed a d=3 system of 512 hard-spheres of the same size, here is a MWE

using CALiPPSO  
precompile_main_function() #optional, but highly recommended. This will produce a colorful output that you can safely ignore
using Random
Random.seed!(123) # optional, but just for reproducibility sake of this MWE
# Choosing the seed of the Julia's RNG determines the random IC produces below with `generate_random_configuration`

const d, N, φ0, L = 3, 512, 0.3, 1.0
r0, Xs0 = generate_random_configuration(d, N, φ0, L) # if L is not passed, it's assumed that the systems is in a box of size 1

packing, info, Γ_vs_t, Smax_vs_t, isostatic_vs_t = produce_jammed_configuration!(Xs0, r0; 
            ℓ0=0.2*L, max_iters=500)

Therefore, the main arguments of produce_jammed_configuration! are the particles' initial position Xs0 and their initial radius, r0. For polydisperse systems r0 should be instead an array specifying the size of each particle. So far, our implementation of produce_jammed_configuration! assumes the system is contained in a periodic (hyper-) cube of size L. The value of L is inferred in the following way

1. If Xs0 is a $d\times N$ matrix specifying the position of each particle (i.e. each of the $N$ columns is the $d$-dimensional position vector of a particle). Then L should be passed as a third argument to produce_jammed_configuration!.
   • If left unspecified, but Xs0 is of type Matrix{Float64}, then it is assumed L=1.0.
2. If Xs0 is of type Vector{SVector{d, PeriodicNumber{Float64}}}, the elements of Xs0 are of PeriodicNumber type, and hen L is automatically inferred from them.
   • For instance, this is the case when Xs0 is generated by calling generate_random_configuration as in the example above.

The usage of the keyword arguments (ℓ0, max_iters, etc.) is explained in the dedicated section of the documentation, and in the docstring of the main function. Thus, simply try

?produce_jammed_configuration!

Output

The output of produce_jammed_configuration! is the following:

1. A jammed packing (provided convergence was attained) stored as a MonoPacking struct (or PolyPacking for systems with polydispersity). This object contains an array of all the particles, and for each of them, the list of contact vectors, magnitudes of contact forces, and list of neighbours.
2. Information about the termination status of CALiPPSO, the time and amount of memory allocated during the full process, list of times of each LP optimization, etc. (see the docstring of convergence_info for a complete list).
3. The list of values of $\sqrt{\Gamma^\star}$ obtained after each optimization.
4. The list of values of $\max_{i,\mu} \ {s_{i,\mu}^\star }_{i=1,\dots,N}^{\mu=1,\dots,d}$ obtained after each optimization.
5. An analogous list that specifies (with boolean variables) if isostaticity holds at the corresponding iteration.

Changing the solver

We used the fantastic JuMP.jl package for model creation within our algorithm. Thus, you should be able to use any of the available solvers (that are suited for Linear Optimization). Our implementation already includes working code for the following solvers: Gurobi.jl, HiGHS.jl, GLPK.jl. We also tested it using Mosek.jl, Clp.jl, Hypatia.jl, and COSMO.jl. But we were not able to obtain good configurations due to lack of precision. So if you know how to help please let us know!

We strongly advice using Gurobi.jl (a Julia wrapper of the Gurobi Solver) because it's the solver we tested the most when developing our package.

Thus, choosing a different solver (e.g. Gurobi), the MWE from above will look like

using CALiPPSO 
using Random
Random.seed!(123) # optional, but just for reproducibility sake of this MWE
# Choosing the seed of the Julia's RNG determines the random IC produces below with `generate_random_configuration`

using Gurobi
const grb_env = Gurobi.Env()
const grb_opt = Gurobi.Optimizer(grb_env)
const grb_attributes = Dict("OutputFlag" => 0, "FeasibilityTol" => 1e-9, "OptimalityTol" => 1e-9, "Method" => 3, "Threads" => CALiPPSO.max_threads)

precompile_main_function(grb_opt, grb_attributes) #optional, but highly recommended. This will produce a colorful output that you can safely ignore

const d, N, φ0, L = 3, 512, 0.3, 1.0
r0, Xs0 = generate_random_configuration(d, N, φ0, L) # if L is not passed, it's assumed that the systems is in a box of size 1

packing, info, Γ_vs_t, Smax_vs_t, isostatic_vs_t = produce_jammed_configuration!(Xs0, r0; 
        ℓ0=0.2*L, max_iters=500, optimizer=grb_opt, solver_attributes=grb_attributes)

Note that different solvers usually require different choices of attributes to tune their accuracy and performance. Refer to the documentation for more options and advanced usage.

Changes with previous versions

Note that in versions v0.1.x this was not the way to choose which optimizer to use for solving the LP instances. From v0.2.0 onwards the user can declare the optimizer (i.e. grb_opt above), with all the needed arguments (i.e. grb_env above) and pass them as a single argument to produce_jammed_configuration!. This led to a cleaner implementation, since it is truly solver agnostic.

However, it also introduced a potential problem. Every time optimize! is called, the optimizer is associated to a given instance of a (LP) model. If, for any reason, produce_jammed_configuration! is interrupted or its main loop exits it is very likely that if this function is called again (or any time a model is created with the same optimizer) an error like this will occur:

ERROR: The provided `optimizer_constructor` returned a non-empty optimizer.

This is caused by the way an optimizer gets linked to a model, once optmize! is called in JuMP. In any case, to solve it, simply do

CALiPPSO.empty!(<your chosen solver>)

So for instance, CALiPPSO.empty!(grb_opt) in the example above. Or, if you are using the default optimizer, do CALiPPSO.empty!(CALiPPSO.default_optimizer).

Other examples

You can find other examples of how CALiPPSO is used in dimensions d=3,4,5, and other features in the Examples section of the documentation. We refer to the Examples folder of this repo for the scripts of some other usage cases.

Advanced usage

For other features, advanced usage, and more details of how produce_jammed_configuration! works please refer to the documentation.

ToDo's

1. Add documentation of functions for polydisperse packings (although they are very similar to their monodisperse counterpart).
2. Implement functions for closed boundary conditions.
3. Register CALiPPSO in Julia's packages registry. ✔️

Acknowledgements

This work was supported by the Simons Collaboration on Cracking the Glass Problem, Grant No. 454949 (G.P.); and by the European Research Council (ERC) under the European Union’s Horizon 2020 Grant No. 101001902 (C.A.) and No. 694925 (G.P.).