Comments (4)
Error : . Could not process '-n from_morpho'.
This comes from the fact that -n from_morpho
determines n
from -morpho
and not -morphooptiini
. Just provide the number of seeds in -n
...
number of common seeds = 4 != 3
seeds = 7 -5 27 4
This comes from the fact that the seeds are regularly arranged on a grid, leading to a degenerate configuration where more than 4 cells intersect at a vertex. (This only happens for the discrete events where seeds are regularly arranged. This will never happen when there is some level of randomness in the seed coordinates.)
A workaround is to "randomize" the seed coordinates:
gsl-randist 1 32 flat 0 0.00001 > x
gsl-randist 2 32 flat 0 0.00001 > y
gsl-randist 3 32 flat 0 0.00001 > z
paste POSCAR-00002 x y z | awk '{print $1+$4,$2+$5,$3+$6}' > pos
and then
neper -T -n 32 -morphooptiini "coo:file(pos)" -o n32 -per 1
neper -V n32.tess -datacellcol id -datacelltrs 0.5 -dataedgerad 0.001 -cameracoo 8:6:4 -print n32
Still, a possible issue is that the cells will contain tiny edges and faces coming from the randomized seed coordinates, which you can see like this:
neper -T -n 32 -morphooptiini "coo:file(pos)" -o n32 -per 1 -statedge length -statface area
head n32.stedge
head n32.stface
This could be fixed using regularization (-reg 1
), but it is not available yet for periodic tessellations.
Some regular tessellations are directly supported by Neper: cubes and truncated octahedra. If I'm correct, you are aiming for truncated dodecahedra here, which are not included.
from neper.
Thanks a lot for the quick answer.
Yes, basically I am trying to create the Wigner-Seitz-cells in an fcc crystal (rhombic dodecahedron)
The tesselation does indeed work after adding some randomness, however after
neper -T -n 32 -morphooptiini "coo:file(POSCAR-00002)" -o n32 -per 1
meshing with
neper -M n32.tess -format 'inp'
fails:
Info : Loading input data...
Info : - Loading tessellation...
Info : [i] Parsing file n32.tess'... Info : [i] Parsed file
n32.tess'.
Info : Meshing...
Info : - Preparing... (cl = 0.1575) 100%
Info : - 0D meshing... 100%
Info : - 1D meshing... 100%
Info : - 2D meshing... 100% (0|0.2/99%| 1%| 0%)
Info : - Fixing 2D-mesh pinches...
Info : - 3D meshing... 3% (0|0/ 0%|100%| 0%)Error : > Meshing of poly 1 (1) failed
I've tried playing around with the meshing algorithm, but so far without success.
I also tried to change the element size with -cl, but this ends with a core dump.
It works when I use hex elements, which is probably sufficient for what I need, but if you have any hints how I could create the tet mesh, that would of course be great.
Thanks again
from neper.
Meshing struggles with the tiny edges and faces. You can increase the "randomization" distance:
gsl-randist 1 32 flat 0 0.01 > x
gsl-randist 2 32 flat 0 0.01 > y
gsl-randist 3 32 flat 0 0.01 > z
paste POSCAR-00002 x y z | awk '{print $1+$4,$2+$5,$3+$6}' > pos
and then
neper -T -n 32 -morphooptiini "coo:file(pos)" -o n32 -per 1
neper -M n32.tess -pl 10000 -rcl 0.5 -for msh,inp
neper -V n32.tess,n32.msh -dataelsetcol id -dataelt1drad 0.0025 -dataelt3dedgerad 0.001 -showelt1d all -cameracoo 8:6:4 -print n32m
You will notice that the geometry differs slightly from theory.
from neper.
Thanks again, that's very helpful.
from neper.
Related Issues (20)
- Missing Parenthesis Error in File - net_mtess_flatten_cell1.c:41:89: HOT 1
- initial 2d tesselation iteration segfaults with large number of cells HOT 2
- Is it possible to control the area fraction and distribution of grains ? HOT 1
- Bug when prescribing initial centroid coords HOT 3
- incorrect msh4 format generated from neper HOT 8
- missing physical tags description in the Entities section in msh4 file HOT 3
- A bug occurred when generating tessellation using coordinate files. HOT 2
- all $PhysicalNames not reflected in $Entities
- error:Cannot convert to ".inp" format.
- Quiery about the Error: - simulation.tess and simulation.msh do not match (2D).
- Query about the error "simulation.tess and simulation.msh do not match (2D)."
- Undeclared Function HOT 1
- Meshing Tests Fail (Mac M1) HOT 2
- Error slicing tessellation HOT 1
- Build failures on 32 bit systems HOT 2
- Can't read .msh file in -M module
- neper -T bug
- Mesh inclusion
- 2D cube cut
- Periodic Tessellation error
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from neper.