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Readme.md

TOPOLOGICAL CLUSTER CLASSIFICATION

This package contains the source code of the Topological Cluster Classification method described in A. Malins, S. R. Williams, J. Eggers, and C. P. Royall, J. Chem. Phys. 139, 234506 (2013). We request that you cite this article when using the TCC. The bundle, provided without support, may be downloaded here.

Compilation

From a bash shell, move to the TCCpackage folder and type

make -C src

This will produce the executable ./TCC.

Usage

The code performs the analysis of a trajectory file composed by a series of frames in xyz format.
To do so, two main parameter files inputparameters.in and d0_init.params need to be provided. For non cubic boxes, a geometry input file d0_box.txt is also needed in input.

All these scripts can be conveniently generated with the use of the graphical interface Prepare_Input.py, which also illustates the possible additional options. A standard python installation is needed (including Tkinter). To execute the script, just type

python Prepare_Input.py

inside the TCCpackage folder.

Once the scripts are generated and bounded to a suitable configuration or trajectory file (see ExampleTrajectory.xyz), just execute

./TCC

This will provide a series of output files, corresponding to the selections made in the inputparameters.in file.

Input script parameters

This list provides a description of the relevant input parameters in the graphical interface:

Trajectory

  • File name: The trajectory file name.
  • Box type: The shape of the box: it can be a regulare cube (Cubic), a rectangular parallelepiped (Non-cubic), and a generalised parallelepiped (Triclinic).
  • Number of particles: The total number of particles per frame.
  • Number of A particles: Considering a binary mixture of A and B particles, this enty corresponds to the number of particles of species A. If only one species is present in the model, this number is equal to the total number of particles.
  • Lx, Ly, Lz: Box lateral sizes.
  • Tilt: For Triclinic boxes, the geometric tilt of the box (compare with LAMMPS's definition).
  • Number of frames: The number of frames to be analysed in the trajectory.
  • Start frame: The initial frame in the sequence of analysed frames.
  • Frame sampling frequency: The steps between consecutively analysed frames.
  • Alpha relaxation time: The duration (in simulation time units) of the alpha relaxation time.

Bonds

  • Voronoi: Activate (deactivate) the Voronoi bond detection algorithm. If deactivated, simple (cut-off-based) bond detection is used.
  • PBC: Activate (deactivate) the usage of Periodic Boundary Conditions.
  • rcutAA, rcutAB, rcutBB: Cut-off distances for the AA, AB and BB bonds.
  • Maximum number of bonds: For memory reasons, bound the maximum number of detected neighbours.
  • Fc parameter: Modified Voronoi Method (see J. Chem. Phys. 139, 234506 (2013)). For the Wahnstrom binary mixture 0.82 is indicated while for the Kob-Andersen mixture 1 (standard Voronoi) is the suitable value.
  • Binning: When (and if) computing the bond lengths histograms, this value is used for the binning.

Optional output

The default output provides a *.static_clust file containing the statistics for the several clusters. Additional output can be set in this section:

  • Bonds file: A *.bonds file containing the list of bonds IDs and lengths for every single particle.
  • All clusters: For every cluster type, provide a table containing all the clusters, one per row. This takes large HD space.
  • xmol cluster files: For every cluster, provide an list of N entries distinguishing cluster particles (C-D) from non-cluster ones (A-B).
  • Population per frame: Provide the statistics of th cluster population for every frame.
  • 13A centres: Centres of the icosahedral structures.
  • Bond length distributions: Histograms for the several bond longths.
  • Coordination distribution: Histograms for the number of neighbours.
  • Cluster compositions: Repartition of A and B particles in the clusters.
  • Coslovich Voronoi-face analysis: Identify structures on the basis of the number of edges on the Voronoi faces.