Making further changes to an existing file #1022

Ava-22-neper · 2025-10-10T13:15:24Z

Ava-22-neper
Oct 10, 2025

Dear all,

I previously generated a tessellation and now, I want to make some changes in it. For example, I want to add more cuts or fill in previous cuts with some new grains. Do you have any recommendations how I can reload it and make further changes in it?
I tried the following command with "loadtess" but got the error: Dom is void (you probably used `-loadtess'.)

neper -T -loadtess Location2-9.tess -domain "cube(1,1,1)" -transform "cut(sphere(1,
0,0,0.2))" -o Location2-1

Answered by rquey

Oct 13, 2025

-loadtess and -transform are mutually exclusive. There are 2 solutions:

run again the tessellation command and add the transformation option.
use -morphooptiini "file(file.tess)" (with the proper number of grains, domain definition, etc.), which will also regenerate the tessellation. This is faster.

Here is an example:

$ neper -T -n 100 -morpho gg                              
                                                                      
========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.                                                                         
Info   : Version 4.10.2-308-de…

View full answer

rquey · 2025-10-13T09:25:00Z

rquey
Oct 13, 2025
Maintainer

-loadtess and -transform are mutually exclusive. There are 2 solutions:

run again the tessellation command and add the transformation option.
use -morphooptiini "file(file.tess)" (with the proper number of grains, domain definition, etc.), which will also regenerate the tessellation. This is faster.

Here is an example:

$ neper -T -n 100 -morpho gg                              
                                                                      
========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.                                                                         
Info   : Version 4.10.2-308-devel                                     
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 15 threads.                                                                                                             
Info   : <https://neper.info>                                                                                                               
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.                                                                            
Info   : Loading initialization file `/home/rquey/.neperrc'...                                                                              
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:                                                                                                  
Info   : [ini file] (none)                                            
Info   : [com line] -n 100 -morpho gg
Info   : ---------------------------------------------------------------                                                                    
Info   : Reading input data...                                        
Info   : Creating domain...                                           
Info   : Creating tessellation...                                     
Info   :   - Setting seeds... 100%                                    
Info   :   - Running tessellation...                                                                                                        
Info   :     > Initial solution: f   =2.806198409
Info   :     > Iteration    75255: fmin=0.849399326 f=0.849399326
Info   :     > Final solution  : f   =0.849399326 (755 iterations)    
Warning:     > Stopping on Ctrl+C invocation.                                                                                               
Info   : Generating crystal orientations...     
Info   : Writing results...                                           
Info   :     [o] Writing file `n100-id1.tess'...                                                                                            
Info   :     [o] Wrote file `n100-id1.tess'.                          
Info   : Elapsed time: 1.894 secs.                                                                                                          
========================================================================

$ neper -T -loadtess n100-id1.tess -transform "cut(sphere(0,0,0,0.5))" -o n100-id1-cut0

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -loadtess n100-id1.tess -transform
         cut(sphere(0,0,0,0.5)) -o n100-id1-cut0
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Importing tessellation...
Info   :     [i] Parsing file `n100-id1.tess'...
Info   :     [i] Parsed file `n100-id1.tess'.
Info   : Transforming tessellation...
Info   :   - Cutting (experimental)...
Error  :     > Dom is void (you probably used `-loadtess'.)
Aborted (core dumped)

$ neper -T -n 100 -morpho gg -transform "cut(sphere(0,0,0,0.5))" -o n100-id1-cut

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 100 -morpho gg -transform cut(sphere(0,0,0,0.5))
         -o n100-id1-cut
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds... 100%
Info   :   - Running tessellation...
Info   :     > Initial solution: f   =2.806198409
Info   :     > Iteration  78471: fmin=0.001956303 f=0.001956304  
Info   :     > Final solution  : f   =0.001956303 (78471 iterations)
Info   :     > Reached `eps' criterion.
Info   : Generating crystal orientations...
Info   : Transforming tessellation...
Info   :   - Cutting (experimental)...
Info   :     > sphere(0,0,0,0.5)... 
Info   : Writing results...
Info   :     [o] Writing file `n100-id1-cut.tess'...
Info   :     [o] Wrote file `n100-id1-cut.tess'.
Info   : Elapsed time: 71.691 secs. 
========================================================================

$ neper -T -n 100 -morphooptiini "file(n100-id1.tess)" -transform "cut(sphere(0,0,0,0.5))" -o n100-id1-cut2

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 100 -morphooptiini file(n100-id1.tess) -transform
         cut(sphere(0,0,0,0.5)) -o n100-id1-cut2
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds... 
Info   :   - Running tessellation...
Info   : Generating crystal orientations...
Info   : Transforming tessellation...
Info   :   - Cutting (experimental)...
Info   :     > sphere(0,0,0,0.5)... 
Info   : Writing results...
Info   :     [o] Writing file `n100-id1-cut2.tess'...
Info   :     [o] Wrote file `n100-id1-cut2.tess'.
Info   : Elapsed time: 0.085 secs.
========================================================================

$ neper -V n100-id1.tess -print img1

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] n100-id1.tess -print img1
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Loading tessellation...
Info   :     [i] Parsing file `n100-id1.tess'...
Info   :     [i] Parsed file `n100-id1.tess'.
Info   : Printing image...
Info   :   - Printing tessellation...
Info   :   - Generating png file (1200x900 pixels)...
Info   :     [o] Writing file `img1.png'...
Info   :     [o] Wrote file `img1.png'.
Info   : Printing scale...
Info   : Elapsed time: 1.020 secs.
========================================================================

$ neper -V n100-id1-cut.tess -print img2                  

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] n100-id1-cut.tess -print img2
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Loading tessellation...
Info   :     [i] Parsing file `n100-id1-cut.tess'...
Info   :     [i] Parsed file `n100-id1-cut.tess'.
Info   : Printing image...
Info   :   - Printing tessellation...
Info   :   - Generating png file (1200x900 pixels)...
Info   :     [o] Writing file `img2.png'...
Info   :     [o] Wrote file `img2.png'.
Info   : Printing scale...
Info   : Elapsed time: 0.955 secs.
========================================================================

 $ neper -V n100-id1-cut2.tess -print img3                 

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.2-308-devel
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 12 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] n100-id1-cut2.tess -print img3
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Loading tessellation...
Info   :     [i] Parsing file `n100-id1-cut2.tess'...
Info   :     [i] Parsed file `n100-id1-cut2.tess'.
Info   : Printing image...
Info   :   - Printing tessellation...
Info   :   - Generating png file (1200x900 pixels)...
Info   :     [o] Writing file `img3.png'...
Info   :     [o] Wrote file `img3.png'.
Info   : Printing scale...
Info   : Elapsed time: 0.982 secs.
========================================================================

img1:

img2:

img3:

1 reply

Ava-22-neper Oct 13, 2025
Author

Hi Professor,

Thank you very much for your answer. It was really helpful.

Ava-22-neper · 2025-10-13T11:44:04Z

Ava-22-neper
Oct 13, 2025
Author

Sorry now another issue comes up! I want to add an additional cut. However, repeating the command with -morphooptiini "file(file.tess)" I get an error: Segmentation Fault!

I think this is because after cutting the first part the number of grains reduced. Thus, I cannot use the same -n 100 for that. Are there any commands to know the number of grains in a tessellation?

2 replies

rquey Oct 13, 2025
Maintainer

You should apply the cuts all at once.

Ava-22-neper Oct 13, 2025
Author

Thank you very much for your reply. It would be great if a feature can be added to the software that can provide users with this capability to edit the tessellations.

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