lorenzo-rovigatti/patchy_eta_files

Code, examples and data accompanying the "Diffusion, viscosity and linear rheology of valence-limited disordered fluids" paper

Summary

This repository contains code, examples and data accompanying the "Diffusion, viscosity and linear rheology of valence-limited disordered fluids" paper.

The simulation code

All simulations have been run with oxDNA. The repository contains a snapshot dated 19/03/2024, which can be compiled with the following commands:

cd oxDNA
mkdir build
cd build
cmake ..
make install -j6
make rovigatti -j6

At the end of the compilation stage, the oxDNA executable will be placed in the build/bin folder. Check the oxDNA docs for additional information.

Note that the patchy interaction used in the paper is implemented as an oxDNA plugin, which means that input files should be updated to contain the correct plugin_search_path values.

Simulation options

All the simulation options are specified in the input file that oxDNA takes as an argument. The most important options (specified as key = value) are:

• T is the temperature at which the simulation will be run
• dt is the integration time step
• DPS_lambda is the $\lambda$ value: use $\lambda = 1$ and $\lambda = 10$ to simulate systems with and without swap, respectively.
• thermostat sets the way the simulation will be coupled to a thermostat. Use thermostat = no to run NVE simulations.

File formats

The configuration file has the same format as oxDNA, while the topology format is unique to these simulations and should have the following layout:

N N_species
N_1 N_patches_1 patch_type_a,patch_type_b,...
N_2 N_patches_2 patch_type_c,patch_type_d,...

where the first line contains the total number of particles and the number of particle species. Each following line pertains to a particle species and contains 3 fields: the number of particles of that species, its number of patches and then a comma-separated list of patch types. Note that the particle data stored in configurations is listed according to the order specified here.

As an example, the topology of a system made of 200 tetravalent particles and 800 divalent particles, all having patches of the same type would read

1000 2
200 4 0,0,0,0
800 2 0,0

The model also needs a file that contains an "interaction matrix" specifying the strength of patch-patch interactions. If not otherwise specified, by default the strength is 0. In the paper only same-type patches appear, and the interaction matrix file has always the following content:

patchy_eps[0][0] = 1.0

Examples

The examples folder contains all the files required to run simulations of two of the systems investigated in the paper: a pure $M = 4$ system (examples/M4) and a binary mixture made of 200 trivalent and 800 divalent particles (examples/M_2.2_M32). Each leaf subfolder contains the following files:

• input is the oxDNA input file.
• topology.dat is the topology file.
• interaction_matrix.dat specifies the interaction matrix.

You will first have to generate an initial configuration by using oxDNA's confGenerator, which takes an input file and a density value (in units of the inverse of the bead diameter cubed, $\sigma^{-3}$) as arguments, like this:

PATH/TO/OXDNA/build/bin/confGenerator input 0.6

A simulation can then be run by using the oxDNA executable, as follows:

PATH/TO/OXDNA/build/bin/oxDNA input

Nota Bene: if you copy the files somewhere else you'll also have to update the plugin_search_path values specified in the input files.

Data

The data folder contains most of the raw data used to draw the figures in the paper. The data is organised in the following hierarchy of folders: SYSTEM/LAMBDA/DENSITY/TEMPERATURE/SAMPLE, where

1. SYSTEM refers to the investigated system: M_2_NVE, M_3_NVE and M_4_NVE are the pure systems, the rest are binary mixtures specified by the average valence and the valence of the particles they are composed of. For instance, M_2.4_M32_NVE is a system of average valence 2.4 composed of trivalent and divalent particles.
2. LAMBDA can be either LAMBDA_1.0 or LAMBDA_10.0 and refers to systems with and without swap, respectively.
3. DENSITY is always equal to 0.6.
4. TEMPERATURE is the temperature at which the simulations were initially equilibrated.
5. SAMPLE has a name like TRY_Y, with all folders containing data generated with independent simulations of the same state point.

The folders store .dat files whose name should be self-explanatory. All files with prefix arr_ are quantities expressed as a function of $1 / T$. Files prefixed with avg_ are obtained by analysing time series obtained by averaging over all the samples data (e.g. first average all mean-squared displacements and then compute $D$), while files without it are obtained by first analysing the single time series and then taking averaging over the results (e.g. compute $D$ for each sample and then take the average). The two sets of results are very similar to each other.

Contact the authors if you have any questions about the data.