triangular/quadrilateral mesh in pygmsh about pygmsh

[tady57]

This is my code:

import pygmsh
import numpy as np
import meshio
from math import pow
import string
import sys
import traceback


lcar=pow(10,22)
print(lcar)

Points=dict()
Splines=dict()
Line_loops=dict()
Ruled_surface=dict()
Points_with_lcar=dict()
Points_done=dict()
Points_with_lcar_done=dict()
Splines_done=dict()
Line_loops_done=dict()
Surfaces_done=dict()

def remove_char(s):
    if'Point' in s:
        s=s[6:]
        arr=[]
        helper=''
        counter=0
        for i in s:
            if i=='=':
                break
            else:
                counter=counter+1
       
        s=s[counter+1:]       
       
           
        if 'cl__1' in s:
            for i in s:
                if  not i==',' and not i.isdigit() and not i=='.'and not i=='-':
                    s=s.replace(i,'')
                else:
                    if i==',':
                        arr.append(float(helper))
                        helper=''
                    else:
                   
                        helper=helper+i
        else:
            for i in s:
                if not i==',' and not i.isdigit() and not i=='.' and not i=='}'and not i=='-':
                    s=s.replace(i,'')
                else:
                    if i==',' or i=='}':
                        arr.append(float(helper))
                        helper=''
                    else:
                   
                        helper=helper+i           
            s=s.replace('}','')   
       
        return arr   
    elif 'Spline' in s:
       
        s=s[7:]
        arr=[]
        helper=''
        counter=0
        for i in s:
            if i=='=':
                break
            else:
                counter=counter+1
       
        s=s[counter+1:]       
           
       
               
        for i in s:
            if i=='{'  or i=='=' or i==';' or i=='\n':
                s=s.replace(i,'')       
            else:   
                if i==',' or i=='}':
                    arr.append(helper)
                    helper=''   
                else:
                    helper=helper+i
        s=s.replace('}','')           
        return arr
   
    elif 'Line Loop' in s:
        s=s[10:]
        arr=[]
        helper=''
        counter=0
        for i in s:
            if i=='=':
                break
            else:
                counter=counter+1
       
        s=s[counter+1:]   
       
        for i in s:
            if i=='{'  or i=='=' or i==';' or i=='\n':
                s=s.replace(i,'')       
            else:   
                if i==',' or i=='}':
                    arr.append(int(helper)) #maybe this should be changed
                    helper=''   
                else:
                    helper=helper+i
        s=s.replace('}','')           
        return arr
    elif 'Surface' in s:
        s=s[8:]
        arr=[]
        helper=''
        counter=0
        for i in s:
            if i=='=':
                break
            else:
                counter=counter+1
       
        s=s[counter+1:]   
        for i in s:
            if i=='{'  or i=='}' or i=='\n' or i==';':
                s=s.replace(i,'')
            else:helper=helper+i
        arr.append(helper)
        return arr

code part2:

def find_id(s):
    string_helper=''
    if 'Point' in s:
            s=s[6:]
            for i in s:
               
                if not i==')':
                    string_helper=string_helper+i
                else:break
                                   
                   

    elif 'Spline' in s:
            s=s[7:]
            for i in s:
               
                if not i==')':
                    string_helper=string_helper+i
                else:break
    elif 'Line Loop' in s:
            s=s[10:]
            for i in s:
               
                if not i==')':
                    string_helper=string_helper+i
                else:break                       
   
    elif 'Surface' in s:
        s=s[8:]
        for i in s:
               
                if not i==')':
                    string_helper=string_helper+i
                else:break
    return string_helper

part3:

with open('proba.txt', 'r') as myfile:
   
    for line in myfile:
       
        text=line
       
        if 'Point'in text and text:   
            if 'cl__1' in text:
                text=remove_char(text)
                if text:
                    s=find_id(line)
                    Points_with_lcar[s]=text
            else:
                text=remove_char(text)
                if text:
                    s=find_id(line)
                    Points[s]=text
               
                   
        elif 'Spline' in text:   
            text=remove_char(text)
            if text:
                s=find_id(line)
                Splines[s]=text
        elif 'Line Loop' in text:
            text=remove_char(text)
            if text:
                s=find_id(line)
               
                Line_loops[s]=text
        elif 'Surface' in text:
            text=remove_char(text)
            if text:
                s=find_id(line)
               
                Ruled_surface[s]=text

part4:

myfile.close()  

geom = pygmsh.built_in.Geometry()

#adding points
for i in Points:
    Points_done[i]=geom.add_point(Points[i],0.1)
   
for i in Points_with_lcar:
    Points_with_lcar_done[i]=geom.add_point(Points_with_lcar[i],lcar)

#adding bsplines   
for i in Splines:
    helper=[]
    for k in Line_loops:
        for l in Line_loops[k]:
            i=int(i)
            if -i==l:
                i=str(i)
                Splines[i].reverse()
            else: i=str(i)
    for j in Splines[i]:
       
        j=j[1:] #small mistake but now it's fine
        if j in Points_done.keys():
            helper.append(Points_done[j])
           
       
        elif j in Points_with_lcar_done.keys():
            helper.append(Points_with_lcar_done[j])
       
    Splines_done[i]=geom.add_bspline(helper)   

#print(Splines_done.keys())

#adding line loops
for i in Line_loops:
    helper2=[]
    for j in Line_loops[i]:
        if j<0:
            j=j*-1       
            j=str(j)   
        else: j=str(j)
        helper2.append(Splines_done[j])
    Line_loops_done[i]=geom.add_line_loop(helper2)   


#adding surfaces
for i in Ruled_surface:
    #helper3=[]
    #print(i)
    #for j in Ruled_surface[i]:
    #    j=j[1:]
    #    helper3.append(Line_loops_done[j])
    Surfaces_done[i]=geom.add_surface(Line_loops_done[i])

points, cells, point_data, cell_data, field_data = pygmsh.generate_mesh(geom)

meshio.write('test7.vtu', points, cells, cell_data=cell_data)

[tady57]

I am sorry, it seems like I have some problems with putting the code, did I do something wrong - is the code to big?

[nschloe]

No idea, probably. Anyways it's too big for me to review. Best generate a minimal example that highlights your problem.

[tady57]

Ok, I will describe what I did and put part of the code that highlights my problem if that would be necessary. I went line by line from geo file and recognize points,splines, line loops or surfaces. After that I would extract data from that line and put it in dictionaries Points, Spline,...where key was id of point,spline or lineloop and values are coordinates or in case of Spline ,for example, values are ids of point which create that Spline. After that I went through all dictionary values and add points to geometry,add splines to geometry(with fuctions geom.add_point etc.) and than I called

points, cells, point_data, cell_data, field_data = pygmsh.generate_mesh(geom) meshio.write('test7.vtu', points, cells, cell_data=cell_data) .

I can see my structure in paraview with all points,splines,lineloops,...But I don't have the mesh.
How can I make mesh from here? And I copy-paste my previous questions:

Is it possible to make the quadrilateral mesh in pygmsh?How can I manipulate and remember only points on the surface of geometric character and the points which create triangular mesh? I will appreciate all links and examples you have on this too.

Thank you very much.

[nschloe]

For quad meshes see here: https://github.com/nschloe/pygmsh/blob/master/test/test_quads.py.

For the rest I cannot help you. You'll have to provide a minimal example that fails.

[tady57]

Ok, I will create perfect minimal example :)
Cheers

[tady57]

Hi , while I was doing minimal example I figured it out. The problem is that I have gmsh2.10 version and for this I have to have gmsh3.0 which I am unable to install on ubuntu. In my minimal example I didn't use Ruled surface and it works perfectly well and creates mesh. So does anyone know how to install gmsh3.0 on ubuntu's latest version?

[tady57]

I will put here my minimal example so that anyone who has similar problem(putting data from external geo.file inside of pygmsh python code) can see what I've done. This is data inside of my geo file:

Point(1)={0,0,0,1/10};
Point(2)={1,0,0,1/10};
Point(3)={1,1,0,1/10};
Point(4)={0,1,0,1/10};
Line(5)={1,2};
Line(6)={2,3};
Line(7)={3,4};
Line(8)={4,1};
Line Loop(9)={5,6,7,8};
Plane Surface(10)={9};

And this is my python code:

import pygmsh
import numpy as np
import meshio
import string
from tiz import r_char,f_id

Points=dict()
Points_done=dict()
Line_loops=dict()
Line_loops_done=dict()
Line=dict()
Line_done=dict()
Plane_surface=dict()


with open('nico.txt', 'r') as myfile:
	for line in myfile:
		text=line
       
		if 'Point'in text and text:   
			text=r_char(text)
			if text:
				s=f_id(line)
				Points[s]=text
		
		elif 'Line Loop' in text:
			
			text=r_char(text)
			if text:
				s=f_id(line)
				Line_loops[s]=text
        
		elif 'Line' in text:   
			text=r_char(text)
			if text:
				s=f_id(line)
				Line[s]=text
		
		elif 'Plane Surface' in text:
			text=r_char(text)
			if text:
				s=f_id(line)
				Plane_surface[s]=text
				
myfile.close() 
geom = pygmsh.built_in.Geometry()
#adding points
for i in Points:
    Points_done[i]=geom.add_point(Points[i],0.1)
    
#adding lines
for i in Line:
	helper=[]
	for j in Line[i]:
		j=str(j)
		helper.append(Points_done[j])
	Line_done[i]=geom.add_line(helper[0],helper[1])

#adding line loop
for i in Line_loops:
	helper=[]
	for j in Line_loops[i]:
		j=str(j)
		helper.append(Line_done[j])
	Line_loops_done[i]=geom.add_line_loop(helper)
	
#adding surface
for i in Plane_surface:
	for j in Plane_surface[i]:
		j=str(j)
		geom.add_plane_surface(Line_loops_done[j])		    

points, cells, point_data, cell_data, field_data = pygmsh.generate_mesh(geom)

meshio.write('nico.vtu', points, cells, cell_data=cell_data)

[tady57]

Sorry , the code is still to big to be inside of "insert code" space :(

[nschloe]

You can format block code with triple-backticks. I did that for you now. See https://help.github.com/articles/creating-and-highlighting-code-blocks/.

[tady57]

Ok, thank you. I will now know it-for the future conversation :)

Have a nice day

[gdmcbain]

As to getting Gmsh 3 on Ubuntu, try downloading the source code and compiling it. I haven't tried that lately under Ubuntu, but this is what I'm doing routinely these days under Debian which is quite similar. It should be fairly straightforward; otherwise ask on the Gmsh list if you get stuck.

[tady57]

Thank you , I've done that and it is working. 2018-01-17 20:11 GMT+01:00 Geordie McBain <[email protected]>:

…

As to getting Gmsh 3 on Ubuntu, try downloading the source code <http://gmsh.info/#Download> and compiling it. I haven't tried that lately under Ubuntu, but this is what I'm doing routinely these days under Debian which is quite similar. It should be fairly straightforward; otherwise ask on the Gmsh list if you get stuck. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#137 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AetjYNSnSEMVtp3TYUbjuyz6nRpIb-0Wks5tLkX_gaJpZM4Rf4FW> .

[nschloe]

I've got a backports PPA for Gmsh up and running for Ubuntu; check out https://launchpad.net/~nschloe/+archive/ubuntu/gmsh-backports.