Directory Structure

spinners_pingali_luijten_dataset.tar.gz is the compressed directory. Upon extraction, nested directories for the data corresponding to each figure and subfigure are available:

├── Fig1
│   ├── Fig1a
│   ├── Fig1b
│   └── Fig1c
├── Fig2
│   ├── Fig2a
│   │   ├── crs_preprocessor
│   │   ├── set_1
│   │   ├── set_2
│   │   ├── set_3
│   │   ├── set_4
│   │   └── set_5
│   ├── Fig2b
│   └── Fig2c
├── Fig3
├── Fig4
│   ├── Fig4a
│   │   ├── crs_preprocessor
│   │   ├── set_1
│   │   ├── set_2
│   │   ├── set_3
│   │   ├── set_4
│   │   └── set_5
│   ├── Fig4b
│   ├── Fig4c
│   ├── Fig4d
│   ├── Fig4e
│   ├── Fig4f
├── FigS1
└── Re_0_calc

Overview of Repository Contents

Figure 1

Fluid streamlines showing flow generated by spinning particles driven by intrinsic torque.

Directories contain input, trajectory output, and restart files in the KAPSEL UDF format, and fluid velocity fields in the HDF5 format (in subdirectory output):

• Fig1a: Single spinner
• Fig1b: Two spinners with parallel axes of rotation
• Fig1c: Two spinners with antiparallel axes of rotation

Figure 2

Transition in spinner orientations.

Directories contain input and restart files in the KAPSEL UDF format.

Fig2a

Overall packing fraction φ vs nematic order parameter S₂.

• crs_preprocessor: contains python script and associated template to generate simulation input files
• set_1 - set_5: replicate datasets for the various parameter combinations specified in input.udf within each subdirectory
• CRS_3_7_postprocessing.m: MATLAB script to parse UDF output files
• CRS_3_7_nematic_analysis.m: MATLAB script to perform analysis and generate plot for figure
• CRS_3_7_sm_video_2.m: MATLAB script to produce supplemental video 2
• CRS_3_7_sm_video_3.m: MATLAB script to produce supplemental video 3

Fig2b

Example system at low φ = 0.29 and Re₀ = 34.8 and associated g(r).
Specific UDF directory corresponding to this system, including input, trajectory output, and restart files in the KAPSEL UDF format.

Fig2c

Example system at high φ = 0.81 and Re₀ = 13.3. Specific UDF directory corresponding to this system, including input, trajectory output, and restart files in the KAPSEL UDF format.

Figure 3

Dynamics of polycrystalline grain growth. Specific UDF directory corresponding to this system, including input, trajectory output, and restart files in the KAPSEL UDF format.

• CRS_3_7_dynamic_analysis.m: MATLAB script to parse UDF output files, generate simulation snapshots, and plot kinetic energies

Figure 4

State diagrams of spinner structures.

Directories contain input and restart files in the KAPSEL UDF format.

Fig4a

• crs_preprocessor: contains python script and associated template to generate simulation input files
• set_1 - set_5: replicate datasets for the various parameter combinations specified in input.udf within each subdirectory
• CRS_3_9_postprocessing.m: MATLAB script to parse UDF output files
• CRS_3_9_nematic_analysis.m: MATLAB script to calculate nematic order parameter data
• CRS_3_9_nematic_diagrams.m: MATLAB script to generate state diagram plot

Fig4b

Example system displaying disordered structure with rotation axes aligned with the z axis. Specific UDF directory corresponding to this system.

Fig4c

Example system displaying frustrated hexatic structure with axes aligned with the z axis. Specific UDF directory corresponding to this system.

Fig4d

Example system displaying hexagonal polycrystalline structure with axes in the x–y plane. Specific UDF directory corresponding to this system.

Fig4e

Example system displaying islands of hexagonal crystals. Specific UDF directory corresponding to this system.

Fig4f

Example system displaying spatially and orientationally disordered structure. Specific UDF directory corresponding to this system.

Figure S1

Large domain simulation. Directories contain input and restart files in the KAPSEL UDF format.

Re_0_calc

Simulations run for calculating Reynolds number of isolated particle in fluids of different viscosities. Directories contain input and restart files in the KAPSEL UDF format.

UDF Format and Variables

The KAPSEL simulation code uses the UDF format for input and output data. Please refer to the KAPSEL-DNS website and user manual for further details on the structure of a UDF file as well as an extensive description of various input/output variables and their units.

Codes and Analysis

HDF5 files were parsed using ParaView. output.udf ASCII trajectory files were parsed using MATLAB.

However, due to storage constraints, trajectory files cannot be provided for every simulation. Trajectory files can be regenerated by rerunning the simulations. Initial configurations are provided in input.udf. Alternatively, final frames can be extracted from restart.udf. In this case, postprocessing scripts will need to be adapted to read from restart.udf instead of output.udf.

If MATLAB is not available, .m files can be read with an ASCII text editor and .mat files can be read with h5py/GNU Octave/R.matlab to replicate the script logic in an open-source environment.

Python Scripts

Certain python scripts are included to assist with setup and analysis:

• crs_preprocessor.py: Generates replicate sets of initial random configurations and simulation parameters, formatted as an input.udf. Requires LAMMPS MD software to be installed (freely available at lammps.org). Requires numpy.
• rdf_analysis.ipynb: Calculates and plots radial distribution function. Requires numpy, matplotlib, and scipy.
• UDFManager.py, UDFWrapper.py, particleshow.py, plot.py, udf2xyz.py: the KAPSEL package supplies the UDFManager python module and some associated post-processing codes. These were not used for analysis of the dataset (which was largely performed in MATLAB) but are included for completeness.