Version 2024-02-15 - T.J.J.M. van Overveld

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#  General information  #
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Title:
  From hydrodynamics to dipolar colloids: modeling complex interactions and self-organization with generalized potentials

Authors:
  T.J.J.M. van Overveld, W.G. Ellenbroek, J.M. Meijer, H.J.H. Clercx, M. Duran-Matute

Corresponding author:
  M. Duran-Matute (m.duran.matute@tue.nl) 
  Fluids and Flows group and J.M. Burgers Center for Fluid Dynamics
  Department of Applied Physics, Eindhoven University of Technology
  P.O. Box 513, 5600 MB Eindhoven
  The Netherlands


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#  File structure and usage  #
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Data/
  Experiments/
    X.png               [Experiment snapshots]
    Ar_over_D.txt       [Ar/D values corresponding to the snapshots]
  
  IBM Simulations/
    IX/ & JX/           [I = Staggered configuration, J = Straight configuration]
      pchar00XX.out     [Particle data, with 17 columns corresponding to Time Step | Time | X Y Z Position | X Y Z Velocity | X Y Z Angular Velocity | X Y Z Hydrodynamic Force | X Y Z Collision Force]     
    HXY/                [Two fixed chains, X={1,2,3} corresponding to Ar/D={0.5,1,2}, Y={a,b,c,d,e,f} corresponding to different chain spacings {1,2,3,0.5,0,staggered}]
      pchar00XX.out     [Particle data, see above]     
    fymean_X.npy        [Period averaged particle data, I = Staggered configuration, J = Straight configuration]
    Mean_norm_forces.npy [Period averaged particle data from HXX directories]

  MC Simulations/
    1D/
      Sweep/            [Phase space data]
        phiXX_TXX.npy   [Simulation output for specified density and temperature]
      1DMCAnalysis.npy  [Averaged and combined 1D Monte Carlo data]
      Single/pair.npy   [For Fig.7]
      Siren/Mermaid/Well_X.npy [1D MC data for the specified potential, X denoted the density]
    
    2D/
      pos_NXXkbTXXX.npy [2D MC output for the specified number of particles N and temperature kbT] 

Figures/
  Figure_X.pdf  [Figure X from the manuscript]
  PC_X.png      [Figures of configurations, used in Fig.2]

Processing/
  Functions.ipynb           [Contains regularly used functions]
  IBM_Preprocessing.ipynb   [Input: IBM Simulations/XXX/pchar00XX.out, Output: fymean_X.npy, Mean_norm_forces.npy]
  MC_1D_preprocessing.ipynb [Input: Sweep/phiXX_TXX.npy, Output: 1DMCAnalysis.npy]
  Figure_X.ipynb            [Generate Figure X from the manuscript]