Five Degree-of-Freedom Grain Boundary Interpolation

version 1.0.2 (50.7 MB) by Sterling Baird
Fast Gaussian Process Regression (GPR) interpolation of small and large grain boundary property datasets in a 5 degree-of-freedom sense.

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Updated Sat, 05 Feb 2022 00:18:34 +0000

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Five Degree-of-Freedom Grain Boundary Interpolation

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DOI arXiv arXiv

Code related to meshing, interpolation, and distance calculations of grain boundaries by representing 5DOF of grain boundaries as grain boundary octonions (GBOs) and mapping them into a Voronoi Fundamental Zone (VFZ). (https://github.com/sgbaird-5DOF/interp)

Figure adapted based on table of contents from DOI: 10.1016/j.commatsci.2021.110756 (a) 2D analogy of a Grain Boundary Octonion Voronoi Fundamental Zone (GBO-VFZ) with dark blue points within the VFZ, with the VFZ defined by the reference point (white) and Oh point group. (b) grain boundary energy (GBE) values plotted continuously between two arbitrary grain boundary octonions (i.e. changes in all 5DOF). (c) Hexagonally binned parity plot of GPR predictions colored by number of points per bin, log colorscale.

We go over dependencies, getting started instructions including installation, basic usage, distance calculations, plotting, and using custom datasets. Finally, we go over the file dependencies (no additional installation needed), short descriptions of various files in the repository, advanced installation, and citing information.

To quickly navigate the README table of contents, use the table of contents button at the top-left of the GitHub README window.

Dependencies

MATLAB Version

MATLAB R2019b or higher (mainly for the arguments ... end syntax checking at the beginning of functions, which is used extensively throughout).

R2007a - R2019a

I suggest removing the arguments ... end syntax for any functions that use this and replacing it with corresponding inputParser() and varargin code to deal with variable input arguments, default parameter values, and repeating arguments. Alternatively, you could remove the arguments ... end syntax lines for each function and update every place that the function is called so that all input arguments are specified. Open up an issue if you need more details on this. Other functions may need to be replaced if they aren't available in early MATLAB versions.

MATLAB Toolboxes

Files

See File dependencies for a list of files that interp5DOF.m depends on.

Getting Started

Quick Installation

The quickest way to install the code is downloading and unzipping the latest release or latest version, add all subfolders of interp to the path via addpath(genpath(".")), and make sure it's working by running interp5DOF_test. For additional details or development instructions, see advanced installation.

Basic Usage

See interp5DOF.m, which is a high-level function for Gaussian Process Regression (GPR), barycentric, nearest neighbor (NN), and inverse-distance weighting (IDW) interpolation. This involves importing/generating data and computing an interpolation.

interp5DOF.m can be called in other functions/scripts to produce interpolation results using 5DOF misorientation/boundary plane normal pairs (qm/nA) and grain boundary property values. It was written with loosely similar input/output structure to the MATLAB built-in function interpn() involving input points and values, query points and values, and options.

For a short description of the various functions included in this repository, see Contents.m or this section.

Simple Example Data

Separate from interp5DOF_test.m, the following is a fast, bare-bones example to show the basic input/output format of interp5DOF.m. See also get_cubo.m

cd code/
addpath(genpath("."))
npts = 100;
qm = get_cubo(npts); nA = normr(rand(npts,3)); %random (qm,nA) pairs
propList = 1:npts; %property values
qm2 = get_cubo(npts); nA2 = normr(rand(npts,3)); %random (qm,nA) pairs
method = 'gpr'; %interpolation method
[propOut,interpfn,mdl,mdlpars] = interp5DOF(qm,nA,propList,qm2,nA2,method)

Test functions

Most functions have a corresponding "test" function (e.g. hsphext_subdiv.m --> hsphext_subdiv_test.m, interp5DOF.m --> interp5DOF_test.m) which gives simple usage example(s). These are useful for debugging, visualizations, and understanding the functions without having to do a full run which could be time-consuming. This also allows for the non-test function code to be more succinct, as certain plotting routines can be moved to the test function instead. The various test functions generally run to completion within a few seconds, and the parameters can generally be changed freely (e.g. dimension, number of points). Some test functions have specific plotting routines for 1-sphere (2D) and 2-sphere (3D) cases since a 7-sphere is difficult to visualize and interpret (n-sphere). For example, see sphbary_test.m and toBPFZ_test.m.

Distance Calculations

If you only want to (manually) compute distances in the VFZ sense, first you need to map all GBs into a VFZ.

npts = 100;
o = get_ocubo(npts); %generate some random data
o = get_octpairs(o); %symmetrize (using default reference GBO), vecnorm(o(1,:)) == ~sqrt(2)
o = normr(o); % normalize

At this point, you can get the VFZ pairwise distance matrix via:

pd = pdist(o);
mat = squareform(pd);

The units will be the same as is given by eq.(1) from DOI: 10.1016/j.commatsci.2021.110756.

To convert to the traditional GBO distance, multiply <math-renderer class="js-inline-math" style="display: inline" data-static-url="https://github.githubassets.com/static" data-run-id="d2e8e3b923ac55da94c40c13a2c2912a">$d_E$</math-renderer> by a factor of 2.

Alternatively, pdist2() may be of interest if you want pairwise distances between two sets of points, or vecnorm() if you want to calculate distances between two lists of GBOs:

npts2 = 100;
o1 = get_ocubo(npts1);
o1 = get_octpairs(o1);
o1 = normr(o1);

o2 = get_ocubo(npts2);
o2 = get_octpairs(o2);
o2 = normr(o2)

d = vecnorm(o1-o2,2,2); %o1 and o2 need to be the same size

If you want the "true" minimum distances (i.e. essentially the same implementation as GB_octonion_code, but vectorized and parallelized), you may use GBdist4.m directly with two sets of GBOs.

d = GBdist4(o1,o2,dtype="norm");

It depends on the application, but if you want to compute large pairwise distance matrices that are nearly identical to the traditional GBO distances, I recommend using the ensembled VFZ distance via ensembleGBdist.m with K >= 10.

d = ensembleGBdist(o,o2,dtype="omega")

This will be much faster than using GBdist4.m. For reference, this corresponds to (from the main paper when K==10):

This is distinct from ensembleVFZO.m, which takes the average interpolated property from K different VFZs.

Open an issue if you have something you'd like to do or something you'd like to clarify, but can't figure out among the (many) options and functions in the interp repo. With a few details, there's a good chance I can offer some suggestions that will save a lot of time.

Plots

Most plots in the paper are produced in the script: plotting.m. First, you need to create a dummy folder:

mkdir interp/code/interp5DOF-paper/figures/

The larger file dependencies, gitID-0055bee_uuID-475a2dfd_paper-data6.mat and gpr46883_gitID-b473165_puuID-50ffdcf6_kim-rng11.mat can be downloaded at figshare and have the following citation:

@misc{baird_homer_fullwood_johnson_2021, title={Five Degree-of-Freedom Grain Boundary Interpolation}, url={https://figshare.com/articles/dataset/gitID-0055bee_uuID-475a2dfd_paper-data6_mat/14405924/3}, DOI={10.6084/m9.figshare.14405924.v3}, abstractNote={These are larger MATLAB .mat files required for reproducing plots from the sgbaird-5DOF/interp repository for grain boundary property interpolation. gitID-0055bee_uuID-475a2dfd_paper-data6.mat contains multiple trials of five degree-of-freedom interpolation model runs for various interpolation schemes. gpr46883_gitID-b473165_puuID-50ffdcf6_kim-rng11.mat contains a Gaussian Process Regression model trained on 46883 Fe simulation GBs.}, publisher={figshare}, author={Baird, Sterling and Homer, Eric R and Fullwood, David and Johnson, Oliver K.}, year={2021}, month={Apr} }

Data Preparation

Input GBs can take on the following forms:

  • misorientation (qm) / boundary plane normal (nA) pairs
  • octonions (o)

Prediction GBs have a 2 appended, as in qm2. The inputs are stacked vertically (i.e. 1st row corresponds to 1st GB, 2nd row to 2nd GB, etc.).

Data can be converted between forms/conventions using the various rotation functions available in the repository (modified versions of GB Octonion Code). See also:

  1. code/GBlab2oct.m
  2. code/TJ2oct.m
  3. code/eumA2oct.m
  4. code/five2oct.m
  5. code/om2oct.m

For an example of converting real literature data for Ni and Fe grain boundaries to octonions, see code/Kim2oct.m.

Active vs. Passive Rotation Convention

Active rotation is specified with an input parameter 'epsijk' == 1 and is the default used throughout the work. Passive rotation, in theory, can be specified via epsijk == -1 which should be propagated throughout the entire codebase via the top-level input, but this has not undergone the same extensive testing as the active rotation convention. To convert from the passive to the active rotation convention, I suggest converting the GB into octonion form and applying qinv.m to each grain boundary, that is:

o = [qinv(o(1:4,:) qinv(o(5:8,:))];

or simply

o = oflip(o);

parfor loops

Parfor loops are used by default where there is potential for significant speed-up. A parfor-compatible text progress bar is encoded into many of these. Adding disp() or fprintf() inside the parfor loop (aside from what's already inside the nested text progress bar function) may cause odd behavior on the command line output, but should not affect the integrity of the code execution. Because the parfor-compatible text progress bars need to be nested functions, in order to deal with the inability to add variables to static workspaces while debugging, you can either assign variables to "ans" (a special variable that is still accessible), output statements directly to the command line terminal (no variable assignment). Alternatively, you can comment the nested function, nUpdateProgress().

If the parallel computing toolbox is not installed, the parfor loops will execute as regular for loops. If the parallel computing toolbox is installed and you only want to use a single core, start a parallel pool with only one core before running any of the functions via parpool(1). The loop will still run internally as a parfor loop, however. A parfor loop with a single core and parallel computing toolbox should not run any slower than a regular for loop as long as they are contained within functions. A parfor loop executed within a script, however, is likely to result in significant slow-down.

To debug within a parfor loop, simply change it to a for loop while debugging and change it back afterwards. I added "parfor compatible" as a comment next to the parfor statements. Thus, you can use MATLAB find files (Ctrl+Shift+F) to search for the keyword "parfor compatible" (including quotes) in order to keep track of which parfor loops have been changed to for loops. If you make changes and an error arises, it is possible it will only give useful information at the top-level where the parfor started, hence the debugging suggestion above.

File dependencies

Take a look at parseReqFiles_test.m for generating a list of file dependencies for interp5DOF.m (below) or other files.

  1. GB5DOF.m
  2. GB5DOF_setup.m
  3. PGnames.mat
  4. PGsymops.mat
  5. GBfive2oct.m
  6. qinv_francis.m
  7. qmult.m
  8. GetPyramid.m
  9. ax2qu.m
  10. cu2ho.m
  11. cu2qu.m
  12. ho2ax.m
  13. ho2qu.m
  14. qu2om.m
  15. GBdist4.m
  16. GBlab2oct.m
  17. get_gitcommit.m
  18. get_uuid.m
  19. structhorzcat.m
  20. var_names.m
  21. addpathdir.m
  22. allcomb.m
  23. constructGBMatrices.m
  24. get_cubo.m
  25. get_errmetrics.m
  26. get_interp.m
  27. get_knn.m
  28. get_octpairs.m
  29. get_ocubo.m
  30. get_omega.m
  31. get_sympairs.m
  32. idw.m
  33. get_ppts.m
  34. get_pts.m
  35. interp_avg.m
  36. interp_bary.m
  37. interp_bary_fast.m
  38. interp_gpr.m
  39. interp_idw.m
  40. interp_nn.m
  41. intersect_facet.m
  42. mustBeSqrt2Norm.m
  43. mustContainFields.m
  44. normr.m
  45. numStabBary.m
  46. osymset.m
  47. osymsets.m
  48. proj_down.m
  49. proj_up.m
  50. projfacet2hyperplane.m
  51. projray2hyperplane.m
  52. projray2hypersphere.m
  53. gmat2q.m
  54. q2gmat.m
  55. qconj.m
  56. qinv_johnson.m
  57. qmultiply.m
  58. qnorm.m
  59. sphbary.m
  60. sphbary_setup.m
  61. sphconvhulln.m
  62. sqrt2norm.m
  63. zeta_min2.m

Contents.m (short descriptions)

Version as of Nov 3, 2020. See Contents.m for latest version.

File (.m) Description
addpathdir.m add folders of filenames using addpath() and dir()
allcomb.m All combinations (Cartesian Product)
axpolytope.m Indices of a polytope with vertices on every axis and every intersection of every plane formed by axes.
axpolytope_test.m generate vertices on the axes of a polytope in n-D
chebycenter.m Compute Chebyshev center of polytope Ax <= b.
constant_colorbar.m script to generate a colorbar with constant limits
constructGBMatrices.m Make Olmsted GB matrices for GB5DOF using labframe quaternion/normal inputs
correctdis.m convert to disorientation (for plotting)
cprnd.m Draw from the uniform distribution over a convex polytope.
datagen.m generate octonion data for various literature datasets (or
datagen_setup.m setup for generating octonion data (random or from literature)
datagen_test.m test generation of octonion data
degdelaunayn.m compute delaunay triangulation of d-1 hyperplane in d-dimensions
disorientation.m determines the unique misorientation between two adjacent
DisplayRequiredFunctions.m List required files and toolboxes. Displays them in the command window or console window (if deployed).
dynamicCellExample.m Dynamically creating a nested cell structure (unfinished/deprecated)
facet_subdiv.m Project a facet from n-dimensional space to a simplex in n-1
facet_subdiv_test.m SUBDIV_TEST e.g. subdivide a d-1 or d-2 simplex (e.g. triangle or line in 3D Cartesian coordinates) and plot
findgeometry.m FINDGEOMETRY: Output the misorientation FZ geometry of a point given a quaternion (e.g. 'OAB').
findgeometry_test.m test findgeometry for 'OAB', 'OBCE', 'OADE', etc. of misorientation FZ
fz_inserter.m Compute misorientations in the fundamental zone for two lists of orientations
GB5DOF.m computes the energy of an arbitrary boundary in FCC metals (BRK energy function)
GB5DOF_setup.m Compute 5DOF GB energy from BRK function
GB5DOF_setup_test.m GB5DOF_setup test
GBdist2.m troubleshooting for GBdist() (deprecated)
GBdist3.m troubleshooting for GBdist() (deprecated)
GBdist4.m modified version of GBdist function by CMU group. Keeps o1 constant.
GBdist4_r2018a.m arguments
GBdistdis.m modified version of GBdist() (deprecated)
GBdistEucl.m modified version of GBdist() for Euclidean distances (deprecated)
GBlab2oct.m convert lab coordinate grain boundareis to octonions
GBlab2oct_test.m Test from GB Octonion Tutorial script
GBoct2five.m (incorrect, derivation error, 2020-11-03) Inverse operation of GBfive2oct.m (GB_octonion_code), output "five" struct
GBoct2five_r2018a.m arguments
GBoct2five_test.m
GBoct2five_test2.m
GBpair.m (deprecated) Method 1: Find o3 that has the minimum summed distances, o1-->o3, and o2-->o3.
GBpair2.m deprecated
GBpair_r2018a.m arguments
GBpair_test.m test
gcfpos.m get current figure position and copy to clipboard
get_cubo.m get n quaternions from randomly or uniformly sampled cubochoric points
get_cubo_r2018a.m arguments
get_errmetrics.m get various error metrics for measured data relative to
get_failed.m find failed jobs (under construction)
get_failed_test.m test getfailed.m
get_fname.m Get a filename to load or save (deprecated, specific to old naming scheme)
get_interp.m Interpolate query point values based on spherical or planar barycentric coords in a mesh
get_octpairs.m Get a set of octonions that are symmetrized with respect to a fixed reference GB (rng seed == 10)
get_octpairs2.m deprecated version of get_octpairs()
get_octpairs_r2018a.m arguments
get_octpairs_test.m get_octpairs test
get_ocubo.m get octonions formed by pairs of quaternions from randomly or uniformly sampled cubochoric points.
get_ocubo_r2018a.m arguments
get_ocubo_test.m get_ocubo test
get_omega.m calculate octonion distance
get_omega_r2018a.m arguments
get_repsets.m Find sets of points with at least a degeneracy of n
get_repsets_test.m nonunique test
get_sympairs.m get all combinations (pairs) of operators for a point group
get_sympairs_r2018a.m arguments
hsphext_subdiv.m Hypersphere exterior hull subdivision.
hsphext_subdiv_test.m hypersphere exterior hull subdivision test
hypercube.m Calculate vertices and convex hull triangulation of a hypercube
hypercube_test.m hypercube test
hyperquadrant.m Generate n-dimensional Ellipsoid or Sphere
hypersphere.m Generate n-dimensional Ellipsoid or Sphere
hypersphere_subdiv.m Subdivide a "spherical" convex hull and collapse the triangulation.
hypersphere_subdiv_test.m
hypersphereSetup.m wrapper function for hypersphere.m, includes 'orthant' option
inBPFZ.m return logical of which boundary plane normals are in BP fundamental zone
InCubicFZ.m Test whether or not a set of rodrigues vectors is within the cubic misorientation fundamental zone.
inhull.m tests if a set of points are inside a convex hull
inhull_setup.m wrapper function for inhull (deprecated)
inmisFZ.m check which rodrigues vectors fall inside the misorientation fundamental zone via vert2con (FEX)
inmisFZ_test.m inmisFZ test
insertrows.m Insert rows into a matrix at specific locations
interp5DOF.m Convert misorientation and boundary plane normal 5DOF input
interp5DOF_setup.m setup for interpolating five-degree-of-freedom property
interp5DOF_test.m interp5DOF test
interpplot.m Create parity plot with 5DOF plots on side (deprecated)
intersect_facet.m Find intersection of ray with facet using barycentric coordinates.
intersect_facet_test.m intersect facet test
ismembc_test.m ismembc vs. ismember test
knninterp.m compute linear interpolation using hyperplane fitted to k-nearest neighbors
knninterp_test.m knninterp test
mesh5DOF.m generate "five" and "o" for a five degree-of-freedom fundamental zone (deprecated)
meshBP.m generate boundary plane (BP) fundamental zone mesh for a
meshBP_test.m test meshBP
meshFZ.m mesh the misorientation fundamental zone (issues with tetgen)
meshgen.m generate octonions randomly or from literature (deprecated)
meshgen_test.m
misFZcon.m get constraints for misorientation fundamental zone (misFZ)
misFZcon_test.m misFZcon test
mustBeSqrt2Norm.m check that first octonion in list has norm == sqrt(2) and each quaternion has norm == 1
mustContainFields.m check fieldnames(S) and make sure every checkname exists
myismember.m do an ismembertol by rows with set precision and tolerance
n2c.m t = num2cell(pts,1)
n2cplot.m convert rows of points to cells of points, convenient for plotting.
normr.m normalizes vectors row-by-row. Outputs zero vector if zero vector input (shadowed by Computer Vision Toolbox)
numStabBary.m a numerically stable barycentric approach in high dimensions
numStabBary_example.m
numSubplots.m Calculate how many rows and columns of sub-plots are needed to neatly display n subplots
Oh_pg.m Oh point group load/testing function
optimize_zeta.m Minimize the pairwise distance matrix of a set of GBs w.r.t. zeta (twist angle via U(1) symmetry)
optimize_zeta_r2018a.m arguments
optimize_zeta_test.m optimize_zeta test
optimize_zeta_test_r2018a.m optimize_zeta test
orthoplex.m Find indices and convex hull triangulation of an orthoplex
orthoplex_test.m orthoplex test
OSLERP_setup.m script to call OSLERP (deprecated)
OSLERP_setup2.m another script to call OSLERP (deprecated)
osymset.m get symmetrically equivalent octonions
osymset_r2018a.m arguments
osymsets.m Get symmetrically equivalent octonions (osymsets) for each octonion in a list of octonions
osymsets_r2018a.m arguments
parityplot.m Create a parity plot and pass options to (scatter() or hexscatter()) and refline().
parseReqFiles.m parse required files & products using fileseparator sep
parseReqFiles_test.m parseMyFiles_test
pd_sse.m get the error of a pairwise distance matrix relative to the true pairwise distance matrix
pd_sse_r2018a.m arguments
plot5DOF.m plotting five degree-of-freedom parameters in misorientation and boundary plane spaces
plotFZrodriguez.m define the FZ vertices
plotFZrodriguez_test.m PLOTFZRODRIGUEZ_TEST
plotFZrodriguez_vtx.m plotFZrodriguez with 'A','B','C','D','E','O' vertices
proj_down.m project down by removing null dimensions (i.e. a rotation and translation) via singular value decomposition
proj_down_r2018a.m arguments
proj_down_test.m
proj_up.m project up (restore null dimensions) using "USV" struct from proj_down.m
projfacet2hyperplane.m project facet vertices onto a hyperplane defined by nvec
projfacet2hyperplane_test.m project facet to hyperplane test
projray2hyperplane.m Project ray (pt) from unit hypersphere to tangent hyperplane at another point (nvec)
projray2hyperplane_test.m project ray to hyperplane test
projray2hypersphere.m project ray to hypersphere, compute barycentric coordinates, compute intersecting facet
projray2hypersphere_test.m project ray to hypersphere test
randOctParityData.m submit sets of jobs to supercomputer or run locally for interp5DOF()
readNODE.m Read vertex positions from .node file, .node files are used by Stellar and Triangle
rescale_test.m rescale test (test of built-in function)
rotationmat3D.m creates a rotation matrix based on axis and angle
RotMatrix.m N-dimensional Rotation matrix
roundp.m rounds values in x to n digits past the decimal sign.
run.m runRun MATLAB script
run2.m run test
sbatch_setup.m setup for SLURM sbatch submissions (deprecated)
simplex_subdiv.m Compute the subdivision cartesian coordinates of a simplex
slightRot.m rotate points slightly in every dimension
slightRot_test.m slight rotation matrix test
sphbary.m compute spherical barycentric coordinates of a facet or simplex [1]
sphbary_setup.m sphbary coords and intersections for points
sphbary_test.m spherical barycentric coordinates test
sphconvhulln.m Compute the "convex hull" on a spherical surface
sphconvhulln_test.m spherical convhulln test
sphere_stereograph.m compute the stereographic image of points on a sphere.
sphere_stereograph_inverse.m compute stereographic preimages of points.
sphere_stereograph_test.m sphere stereograph test
sphere_stereographic_inverse_testsphere.m
stereographic inverse test.m
sphtri_subdiv.m Subdivision scheme that segments the triangle formed by vertices of a spherical triangle
sphtri_subdiv_test.m
sqrt2norm.m take a set of octonions and give each row norm == sqrt(2) if (norm == 1) || (norm == sqrt(2))
sqrt2norm_r2018a.m arguments
symaxis.m Return the symmetry axes (if multiple) and the geometry given a quaternion
symaxis_test.m {
tblvertcat.m vertically catenate tables with different variables, filling in dummy values as needed
tblvertcat_test.m tblvertcat_test
testForGBFZSymmetryPlot.m
toBPFZ.m Rotate an arbitrary boundary plane normal for quaternion into standard boundary plane fundamental zone
tofiveFZ.m Take 5DOF data and rotate it into misorientation and boundary plane fundamental zones.
tricollapse.m collapse triangulation of points (i.e. a triangulation involving repeat points).
vecpair2rmat.m Compute a (non-unique) rotation matrix to go from v1 to v2.
vert2con.m convert a set of points to the set of inequality constraints
vert2lcon.m An extension of Michael Kleder's vert2con function, handles degeneracy
write_video.m write a set of images to a video named movname with some defaults
write_video_test.m
zeta_min2.m ZETA_MIN Alternative version of CMU group function zeta_min(), vectorized by Sterling Baird
zeta_min2_r2018a.m arguments
GBoct2mat.m convertion grain boundary octonions to orientation matrices (unfinished)
Kim2oct.m load Kim2011 dataset, convert to norm-symmetrized octonions
avgrepeats.m average values for duplicate points, remove all but one from degenerate set
avgrepeats_test.m avgrepeats test
bugtest.m checking a "bug" (turns out actually intended) with arguments..end syntax
el2po.m elevation angles to polar angles
el2po_test.m po2el_test
get_alen.m get arclength of sphere (acos of dot product)
get_charlbl.m get character labels, e.g. '(a)', '(b)', ... for figures.
get_five.m generate random cubochoric misorientation and random boundary plane normal pairs
get_knn.m k-nearest neighbor points, distances, mean, and std
get_walltimefn.m get a function handle for computing interp5DOF SLURM walltimes (e.g. 'gpr')
hexscatter.m A scatter-plot substitutegenerate a density plot using hexagonal patches.
idw.m inverse-distance weighting interpolation
idw_tovar.m Original inverse distance weight function by Andrew Tovar
multiparity.m create tiled parity plots using cell parity data
multixyplots.m create tiled xy-plots from variables in a table
nnhist.m nearest neighbor distance histogram
nnhist_test.m nnhist test
padcat.m concatenate vectors with different lengths by padding with NaN
paperfigure.m call figure in centimeters and with appropriate size
papertext.m do a text() command for the figure labels '(a)', '(b)', etc. for num == 1, 2, etc.
plotting.m plotting script for interp5DOF paper
po2el.m convert polar angles to elevation angles
qlab2qm.m Convert lab/sample frame quaternions of grain A and grain B and
qmA2nA.m QLAB2FIVE Convert lab/sample frame quaternions of grain A and grain B and
quivplot.m plot three quivers in the x-hat, y-hat, and z-hat directions
savefigpng.m save a figure and print the figure as 300 DPI .png
sphplot.m plot a simple sphere for visualization purposes
tblfilt.m filter a table based on a struct of parameters (deprecated, see built-in findgroups() and splitapply())
tblfilt_test.m parfilter_test
test_voronoisphere.m Script to test voronoisphere (modified from original (Bruno Luong) by Sterling Baird)
toBPFZ_test.m
vcell_solidangle.m Compute the solid angles of All voronoi cell
voronoisphere.m Compute the voronoi's diagram of points on the spheres S^2
xyplot.m make an errorbar xyplot using a table (tbl) and output (G) from findgroups()
xyplots.m plot multiple datasets on the same axes using a "master" table and findgroups()

Advanced Installation

Basic steps:

  • Step 0: download the code
  • Step 1: set interp/ as working directory
  • Step 2: add subfolders to path (addpath(genpath('.'))) and run interp5DOF_test.m to verify it works

Platform-specific directions

Windows

Step 0: Download the code
Download GitHub Desktop and Git Bash. For Git Bash, the default installation options should be fine. I prefer to use Atom as the text editor which has some slick integrations with git. Login to GitHub Desktop and make a dummy repository via Ctrl+N so that you can open Git Bash via GitHub Desktop. Then clone and/or fork https://github.com/sgbaird-5DOF/interp.git by opening the Git Bash command line (i.e. Menubar --> Repository --> "Open in Git Bash") or

Ctrl+`

then run the following command in the directory where you want the interp directory to appear:

git clone --recurse-submodules https://github.com/sgbaird-5DOF/interp.git

Alternatively, you can try cloning directly in GitHub Desktop or via the "Open in GitHub Desktop" button under image, but it will likely throw an error, and it may not correctly clone the MATslurm submodule by the time it reaches that error. MATslurm is a bare minimum requirement for running interp5DOF.m. Attempt at your own risk.

Step 1: open MATLAB and navigate to navigate to interp-5DOF/code/

matlab
cd interp-5DOF/code/

Step 2: Add subfolders to path and run interp5DOF_test.m

>> addpath(genpath('.'))

>> interp5DOF_test

Linux

Step 0: download the code

git --recurse-submodules https://github.com/sgbaird-5DOF/interp.git

Step 1: open MATLAB and navigate to navigate to interp-5DOF/code/
matlab

>> cd interp-5DOF/code/

Step 2: Add subfolders to path and run interp5DOF_test.m

>> addpath(genpath('.'))

>> interp5DOF_test

Troubleshooting

See cloning a repository and git submodules for more information or other options such as using GitHub Desktop (Windows, Linux, etc.) or downloading a .zip file. Forking, pull requests, and opening of issues are welcome/encouraged. Note that the .zip files will not contain submodules, which means that you'll need to download any submodules individually if you go that route (bare minimum would be the MATslurm repository). Instead of downloading a .zip file, I suggest instead downloading and using GitHub Desktop. If you run into issues with the repository, you can download a lightweight version of interp5DOF.m and its dependencies, unzip it, and read README.txt for instructions, but please open up an issue in the GitHub repo if you do run into trouble with the repo. That way, you can get the most recent updates and others can benefit from it.

Adding as Submodule

If you wish to add the interp repository as a submodule to your own repository, first navigate to where you would like the submodule to appear, and then run the following commands in git bash:

git submodule add https://github.com/sgbaird-5DOF/interp.git
git submodule update --init --recursive

Then commit/push your changes.

If you later need to remove the submodule from your repository (or need to start over), you will need to do the following:

  • Run git rm --cached <submodule name>
  • Delete the relevant lines from the .gitmodules file.
  • Delete the relevant section from .git/config.
  • Commit
  • Delete the now untracked submodule files.
  • Remove directory .git/modules/<submodule name> (Source)

Citing

  1. Baird, S. G.; Homer, E. R.; Fullwood, D. T.; Johnson, O. K. Five Degree-of-Freedom Property Interpolation of Arbitrary Grain Boundaries via Voronoi Fundamental Zone Framework. Computational Materials Science 2021, 200, 110756. https://doi.org/10.1016/j.commatsci.2021.110756.
  2. Baird, S. G.; Homer, E. R.; Fullwood, D. T.; Johnson, O. K. Towards a Quantitative Cartography of the Grain Boundary Energy Landscape: Paths and Correlations; preprint; Chemistry, 2021. https://doi.org/10.26434/chemrxiv-2021-ds0ml.
  3. GB_octonion_code
  4. Chesser, I., Francis, T., De Graef, M., & Holm, E. A. (2020). Learning the Grain Boundary Manifold: Tools for Visualizing and Fitting Grain Boundary Properties. Acta Materialia. https://doi.org/10.2139/ssrn.3460311
  5. Francis, T., Chesser, I., Singh, S., Holm, E. A., & De Graef, M. (2019). A geodesic octonion metric for grain boundaries. Acta Materialia, 166, 135–147. https://doi.org/10.1016/j.actamat.2018.12.034

Cite As

Sterling Baird (2022). Five Degree-of-Freedom Grain Boundary Interpolation (https://github.com/sgbaird-5DOF/interp/releases/tag/1.0.2), GitHub. Retrieved .

Baird, Sterling G., et al. “Five Degree-of-Freedom Property Interpolation of Arbitrary Grain Boundaries via Voronoi Fundamental Zone Framework.” Computational Materials Science, vol. 200, Elsevier BV, Dec. 2021, p. 110756, doi:10.1016/j.commatsci.2021.110756.

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MATLAB Release Compatibility
Created with R2019b
Compatible with R2019b and later releases
Platform Compatibility
Windows macOS Linux

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code

code/GB_octonion_code-master_CMU/Data/GB_ids

code/GB_octonion_code-master_CMU/TutorialCode

code/GB_octonion_code-master_CMU/TutorialCode/crystal_symmetry_ops

code/GB_octonion_code-master_CMU/TutorialCode/octonion_functions

code/GB_octonion_code-master_CMU/TutorialCode/rotation_conversions

code/MATslurm/code

code/interpfns

code/numeric-relation-operators

code/quaternions

code/spinningGIF

code/walltimefns

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.