DOI: 10.5061/dryad.dbrv15ffr
title: Data from: Orientational order in confined systems of self-driven spinners

description: We investigated large systems of self-driven spinners confined over a
 substrate through direct numerical simulation of 3D hydrodynamics. Our
 results demonstrated that these systems generate unique flows from which
 spatial and orientational order emerges. We showed that a transition in
 particle orientation accompanies the appearance of crystallinity as the
 packing fraction is increased. Further exploration revealed a rich,
 tunable state space, offering insights into the biophysics of natural
 microswimmers with rotational motion as well as into the design of
 synthetic spinner systems. This is a dataset of the simulations performed
 to generate the figures in the corresponding paper. The directories are
 organized by figure and subfigure. Raw simulation data are in the KAPSEL
 UDF format; please refer to the KAPSEL-DNS website and user manual for
 further details on this format. In addition, postprocessing and analysis
 scripts to read raw data, perform postprocessing calculations, and
 generate figures are supplied.
description: ## 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 *S*~2~. * `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 Re~0~ = 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 Re~0~ = 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](https://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.