Mesh generator#

Quick start

Install

Quick Start#

If you want to perform simulations on craft and R3iCe using the same initial microstructure, you can use the NT_3D.sh or NT_2D5.sh functions to generate microstructure files from the same Voronoi microstructure generated with neper.

Geometry#

The geometry of the sample is a cuboid with dimensions that depend on the aspect ratio \(\lambda = \frac{z}{x}\). Specifically, the dimensions are given by:

\[ [x, y, z] = \left[ \frac{\sqrt{\lambda}}{\lambda}, 2 \max\left(\frac{\sqrt{\lambda}}{\lambda}, \sqrt{\lambda}\right), \sqrt{\lambda} \right] \]

This ensures that the surface area \(n_y\) is equal to 1.

Generate Voronoi microstructure#

3D#

# number of grains in the microstructure
nb_g=100
# aspect ratio x/z
ar=0.1
# file name
fn=n100_ar10

# generate the microstructure
NT_3D.sh $nb_g $ar $fn

2D-1/2#

# number of grains in the microstructure
nb_g=250
# file name
fn=n250_2d5

# generate the microstructure
NT_2D5.sh $nb_g $ar $fn

Output#

Three output are given in folder n100_ar10/:

  1. n100_ar10_craft.vtk for craft simulation. It can be visualized using paraview

    paraview n100_ar10/n100_ar10_craft.vtk

  2. n100_ar10_gmsh.msh. It can be visualized using gmsh:

    gmsh n100_ar10/n100_ar10_gsmh.msh

  3. n100_ar10_rheolef.geo that correspond to the n100_ar10_gmsh.msh but compatible with R3iCe library and with the code R3iCe

Generate mesh file from AITA measurement#

Note

AITA measurement are raster measurement of orientation. Therefore the code can be adapted is you have an other type of raster measurement (EBSD, picture,…). Feel free to dig into the code to do it or contact me if you need help.

Warning

During the generation of mesh from AITA measurement the grain are labelled \(Gi\). But during the meshing some small grains can disappear. There the orientation file *.rhori should be edited and the lines containing the orientations of the missing grains removed. Overwise an error will appear when running CTI program.

Generate 3d mesh#

Export file using xarrayaita#

Here is an example of python script to run in order to obtain craft input file and neper compatible file .tesr.

import xarrayaita.loadData_aita as lda
import xarrayaita.aita as xa
import numpy as np

adr_dat='/data/Manips/Columnar_Ice/CI02/DataBrut/AITA/CI02_aita.dat'
adr_micro='/data/Manips/Columnar_Ice/CI02/DataBrut/AITA/CI02_micro.bmp'

ds=lda.aita5col(adr_dat,adr_micro)

pos=[[1.4,75],[8,89.6]]
ds=ds.aita.crop(pos)
ds=ds.aita.rot180()

ds.aita.craft('CI02_3d',res=0.5,m3d=10,tesr=True)
Generate mesh from .tesr file#

Run

mesh_size = 0.3
output=CI02_3d
input_tesr=CI02_3d_micro.tesr

NT_AITA.sh $input_tesr $output $mesh_size
Output#

Two output are given in folder CI02/:

  1. CI02_gmsh.msh. It can be visualized using gmsh:

    gmsh CI02/CI02_gmsh.msh

  2. CI02_rheolef.geo that correspond to the CI02_gmsh.msh but compatible with rheolef library and with the code rheolef_cti

From the python script you also have the input file compatible with craft :

 - `CI02_3d_micro.vtk`. It can be visualized using `paraview` 
    
    ```shell 
    paraview CI02_3d_micro.vtk
    ```

You also have .phase file containing euler angle of extracted from the AITA measurement. This file is compatible with craft but need to be adapted for R3iCe.

To do this use ori_craft2rh.py script

ori_craft2rh.py -i CI02_3d.phase -o CI02

You obtain CI02.rhori compatible with R3iCe.

Generate 2d mesh#

Export file using xarrayaita#

Here is an example of python script to run in order to obtain craft input file and neper compatible file .tesr.

import xarrayaita.loadData_aita as lda
import xarrayaita.aita as xa
import numpy as np

adr_dat='/data/Manips/Columnar_Ice/CI02/DataBrut/AITA/CI02_aita.dat'
adr_micro='/data/Manips/Columnar_Ice/CI02/DataBrut/AITA/CI02_micro.bmp'

ds=lda.aita5col(adr_dat,adr_micro)

pos=[[1.4,75],[8,89.6]]
ds=ds.aita.crop(pos)
ds=ds.aita.rot180()

ds.aita.craft('CI02_2d',res=0.2,tesr=True)
Generate mesh from .tesr file#

Run

mesh_size = 0.3
output=CI02_2d
input_tesr=CI02_2d_micro.tesr

NT_AITA_2d.sh $input_tesr $output $mesh_size
Output#

Two output are given in folder CI02/:

  1. CI02_gmsh.msh. It can be visualized using gmsh:

    gmsh CI02/CI02_gmsh.msh

  2. CI02_rheolef.geo that correspond to the CI02_gmsh.msh but compatible with rheolef library and with the code R3iCe

From the python script you also have the input file compatible with craft :

 - `CI02_2d_micro.vtk`. It can be visualized using `paraview` 
    
    ```shell 
    paraview CI02_2d_micro.vtk
    ```

You also have .phase file containing euler angle of extracted from the AITA measurement. This file is compatible with craft but need to be adapted for R3iCe.

To do this use ori_craft2rh.py script

ori_craft2rh.py -i CI02_3d.phase -o CI02

You obtain CI02.rhori compatible with R3iCe.

Note

The *.rhori file contains two bunge euler angles \(\phi_1\) and \(\phi\) but when using R3iCe only \(\phi_1\) will be taken into account using a 2d mesh. The 3d orientation is projected in the plane \(xOy\) :

\[c=(cos(\phi_1),sin(\phi_1)) \]