Some bug in neper regarding "planecut" and "crop" #1037
Description
Describe the bug
Both "planecut" and "crop" command from "-transform" appears to be unable to provide cut for crystal structure with large number of cells
*Minimal working example
For planecut:
$ neper -T -id 42 -dim 3 -domain cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor euler-bunge -o test -statcell id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(5) -morphooptistop iter=10 -transform planecut(0.0,0.0,0.0,1.0) -n from_morpho
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.10.2-22
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 32 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/tranh/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -id 42 -dim 3 -domain
cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor
euler-bunge -o
test -statcell
id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(5)
-morphooptistop iter=10 -transform planecut(0.0,0.0,0.0,1.0) -n
from_morpho
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : . Number of cells: 86
Info : - Setting seeds... 100%
Info : - Running tessellation...
Info : > Initial solution: f =2.579489156
Info : > Iteration 10: fmin=2.579083127 f=2.579083127
Info : > Final solution: f =2.579083127
Info : > Final solution : f =2.579083127 (11 iterations)
Info : > Reached `itermax' criterion.
Info : Generating crystal orientations...
Info : Transforming tessellation...
Info : - Cutting by plane...
Info : Writing results...
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.tess'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.tess'.
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.geo'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.geo'.
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.ori'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.ori'.
Info : Writing statistics...
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.stcell'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.stcell'.
Info : Elapsed time: 7.628 secs.
========================================================================
For crop:
neper -T -id 42 -dim 3 -domain cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor euler-bunge -o test -statcell id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(5) -morphooptistop iter=10 -transform crop(cube(-10.1,10.1,-10.1,10.1,-1,1)) -n from_morpho
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.10.2-22
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 32 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/tranh/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -id 42 -dim 3 -domain
cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor
euler-bunge -o
test -statcell
id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(5)
-morphooptistop iter=10 -transform
crop(cube(-10.1,10.1,-10.1,10.1,-1,1)) -n from_morpho
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : . Number of cells: 86
Info : - Setting seeds... 100%
Info : - Running tessellation...
Info : > Initial solution: f =2.579489156
Info : > Iteration 10: fmin=2.579083127 f=2.579083127
Info : > Final solution: f =2.579083127
Info : > Final solution : f =2.579083127 (11 iterations)
Info : > Reached `itermax' criterion.
Info : Generating crystal orientations...
Info : Transforming tessellation...
Info : - Cropping...
Error : You have discovered a bug in Neper! Please file an issue at
https://github.com/rquey/neper/issues. Thank you.
However, if I simply reduce number of cells, planecut and crop works correctly (I have confirm this visually)
neper -T -id 42 -dim 3 -domain cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor euler-bunge -o test -statcell id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(7) -morphooptistop iter=10 -transform planecut(0.0,0.0,0.0,1.0) -n from_morpho
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.10.2-22
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 32 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/tranh/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -id 42 -dim 3 -domain
cube(20.0,20.0,20.0):translate(-10.0,-10.0,-10.0) -oridescriptor
euler-bunge -o
test -statcell
id,vol,w,x,y,z,radeq -format tess,geo,ori -morpho gg(7)
-morphooptistop iter=10 -transform planecut(0.0,0.0,0.0,1.0) -n
from_morpho
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : . Number of cells: 31
Info : - Setting seeds... 100%
Info : - Running tessellation...
Info : > Initial solution: f =11.518479061
Info : > Iteration 10: fmin=11.437968869 f=11.437968869
Info : > Final solution: f =11.437968869
Info : > Final solution : f =11.437968869 (11 iterations)
Info : > Reached `itermax' criterion.
Info : Generating crystal orientations...
Info : Transforming tessellation...
Info : - Cutting by plane...
Info : Writing results...
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.tess'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.tess'.
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.geo'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.geo'.
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.ori'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.ori'.
Info : Writing statistics...
Info : [o] Writing file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.stcell'...
Info : [o] Wrote file `/home/tranh/projects/cpfe_aps/hedm_study/test/voronoi.stcell'.
Info : Elapsed time: 3.979 secs.
========================================================================