Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

31 May 2018

      you have to add the print statement before you enter the if statements.

Marco

On May 31, 2018, at 10:25 AM, [email protected]<mailto:[email protected]> wrote:

c-----------------------------------------------------------------------
      subroutine usrdat
      include 'SIZE'
      include 'TOTAL'

      do i=1,nelt
        do j=1,2*ndim
          if(bc(5,j,i,1).eq.1) then
            cbc(j,i,1)='O  '
            write (6,1) j,i,nelt,ndim,bc(5,j,i,1)
1           format(i4,i4,i4,i4,7f20.8)
          elseif(bc(5,j,i,1).eq.2) then
            cbc(j,i,1)='W  '
            write (6,2) j,i,nelt,ndim,bc(5,j,i,1)
2           format(i4,i4,i4,i4,7f20.8)
          elseif(bc(5,j,i,1).eq.3) then
            cbc(j,i,1)='W  '
            write (6,3) j,i,nelt,ndim,bc(5,j,i,1)
3           format(i4,i4,i4,i4,7f20.8)
          elseif(bc(5,j,i,1).eq.4) then
            cbc(j,i,1)='W  '
            write (6,4) j,i,nelt,ndim,bc(5,j,i,1)
4           format(i4,i4,i4,i4,7f20.8)
          elseif(bc(5,j,i,1).eq.5) then
            cbc(j,i,1)='V  '
            write (6,5) j,i,nelt,ndim,bc(5,j,i,1)
5           format(i4,i4,i4,i4,7f20.8)
          elseif(bc(5,j,i,1).eq.6) then
            cbc(j,i,1)='W  '
            write (6,6) j,i,nelt,ndim,bc(5,j,i,1)
6           format(i4,i4,i4,i4,7f20.8)
          else
            cbc(j,i,1)='E  '
            write (6,7) j,i,nelt,ndim,bc(5,j,i,1)
7           format(i4,i4,i4,i4,7f20.8)

          endif
        enddo
      enddo

      call gen_rea(0)
      call exit
      return
      end
c-----------------------------------------------------------------------

i used this and only bold lines of code are executed at every time step and a small piece of the results is shown below

   1 9991000   3          0.00000000
   2 9991000   3          0.00000000
   3 9991000   3          0.00000000
   4 9991000   3          0.00000000
   5 9991000   3          0.00000000
   6 9991000   3          0.00000000

Thank you

Sijo

________________________________
De: "nek5000-users" <[email protected]<mailto:[email protected]>>
À: "nek5000-users" <[email protected]<mailto:[email protected]>>
Envoyé: Jeudi 31 Mai 2018 16:12:12
Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

You should output values of i, j, next, ndim and bc(5,j,i,1) for sanity check.

Marco

On May 31, 2018, at 10:07 AM, [email protected]<mailto:[email protected]> wrote:

When I checked the loop I can see that only the bold letter codes are executing in all the iteration.

      subroutine usrdat
      include 'SIZE'
      include 'TOTAL'

      do i=1,nelt
        do j=1,2*ndim
          if(bc(5,j,i,1).eq.1) then
            cbc(j,i,1)='O  '
          elseif(bc(5,j,i,1).eq.2) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.3) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.4) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.5) then
            cbc(j,i,1)='V  '
          elseif(bc(5,j,i,1).eq.6) then
            cbc(j,i,1)='W  '
          else
            cbc(j,i,1)='E  '
          endif
        enddo
      enddo

      call gen_rea(0)
      call exit
      return
      end

Thanks
Sijo

________________________________
De: "nek5000-users" <[email protected]<mailto:[email protected]>>
À: "nek5000-users" <[email protected]<mailto:[email protected]>>
Envoyé: Jeudi 31 Mai 2018 15:54:04
Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

It probably means that the boundary conditions are not correctly set in usrdat(). Can you add a write statement in each line of the do loop to check wether boundary conditions are properly set when running?

Also add ‘call exist’ after setting the boundary conditions that way Nek5000 will automatically exit.

Marco

On May 31, 2018, at 9:51 AM, [email protected]<mailto:[email protected]> wrote:

Yes. I see the problem now.

it shows there is 1000 elements but all the co ordinates are  zero. In fact there is nothing and all the boundary conditions are E.

Could you please tell me where i am probably wrong?  It was showing correct number of elemnts and the range of domain. Even when i was using exo2nek it was showing the correct numbers. And genmap worked as well.

Regards
Sijo

________________________________
De: "nek5000-users" <[email protected]<mailto:[email protected]>>
À: "nek5000-users" <[email protected]<mailto:[email protected]>>
Envoyé: Jeudi 31 Mai 2018 15:43:20
Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

Can you add ‘call gen_rea(0)’ after setting the boundary conditions in usrdat()? It will generate a *.rea file with all boundary conditions.

Marco

On May 31, 2018, at 9:37 AM, [email protected]<mailto:[email protected]> wrote:

I generated again it didnt work.
I will explain what I did so far.

I made a cube fluid mesh in ICEM.

Then I gave B.Cs to the cube as follows : outlet = Sideset no : 1,   inlet = Sideset no : 5 , Wall_up = Sideset no:4  ,Wall_down = Sideset no:3 , P_Wall_Right =Side_set 6, P_wall_left = Sideset no: 2
After that I exported the mesh from ICEM to exodus.exo format file.

Then using exo2nek tool from NEK5000, I converted the above file to exodus.re2 file. (Then I tried to convert into rea file but thrown some errors).
Then I mapped the file into exodus.ma2 file.

Then from example Turbulent channel I took a .par file to give parameters.

Now I also given the B.Cs through the .usr file.
 as follows:

c-----------------------------------------------------------------------
      subroutine usrdat
      include 'SIZE'
      include 'TOTAL'

      do i=1,nelt
        do j=1,2*ndim
          if(bc(5,j,i,1).eq.1) then
            cbc(j,i,1)='O  '
          elseif(bc(5,j,i,1).eq.2) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.3) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.4) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.5) then
            cbc(j,i,1)='V  '
          elseif(bc(5,j,i,1).eq.6) then
            cbc(j,i,1)='W  '
          else
            cbc(j,i,1)='E  '
          endif
        enddo
      enddo

      return
      end
c-----------------------------------------------------------------------

Then in my folder I have .ma2,.re2,.par,.usr files to run this case and when i run the case I get an error shown before.

Could you please tell me, if therer is anything wrong?

Thank you
________________________________
De: "nek5000-users" <[email protected]<mailto:[email protected]>>
À: "nek5000-users" <[email protected]<mailto:[email protected]>>
Envoyé: Jeudi 31 Mai 2018 15:22:49
Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

Did you generate a new map file after changing the BCs?

This matters when switching periodic bcs on or off...

Paul

________________________________
From: Nek5000-users <[email protected]<mailto:[email protected]>> on behalf of [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>>
Sent: Thursday, May 31, 2018 8:12:55 AM
To: [email protected]<mailto:[email protected]>
Subject: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

I do not think this method supports periodic boundary conditions. You will have to replace the periodic boundary conditions with wall boundary conditions and see it is runs.

Marco

On May 31, 2018, at 9:11 AM, [email protected]<mailto:[email protected]> wrote:

Hi Marco,

I tried and it compiled . But before starting the time step it failed.
Its a very simple case, the water flowing throgh a cube. So I have inlet, outlet, walls on upside and bottom and periodic conditions on side walls.
I get this error:

Matrix:   0 aa         6       6       6
  0 aa     8.33333E+01  -4.87842E+01   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00
  0 aa    -4.87842E+01   8.66667E+01  -4.87842E+01   7.11752E+00  -1.66667E+00   0.00000E+00
  0 aa     0.00000E+00  -4.87842E+01   8.33333E+01  -4.16667E+01   7.11752E+00   0.00000E+00
  0 aa     0.00000E+00   7.11752E+00  -4.16667E+01   8.33333E+01  -4.87842E+01   0.00000E+00
  0 aa     0.00000E+00  -1.66667E+00   7.11752E+00  -4.87842E+01      Infinity     -Infinity
  0 aa     0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00     -Infinity      Infinity

Matrix:   0 bb         6       6       6
  0 bb     4.16667E-02   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00
  0 bb     0.00000E+00   1.66667E-02   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00
  0 bb     0.00000E+00   0.00000E+00   4.16667E-02   0.00000E+00   0.00000E+00   0.00000E+00
  0 bb     0.00000E+00   0.00000E+00   0.00000E+00   4.16667E-02   0.00000E+00   0.00000E+00
  0 bb     0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   8.33333E-03   0.00000E+00
  0 bb     0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00

Matrix:   0 Aeig       6       6       6
  0 Aeig   8.33333E+01  -4.87842E+01   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00
  0 Aeig  -4.87842E+01   8.66667E+01  -4.87842E+01   7.11752E+00  -1.66667E+00   0.00000E+00
  0 Aeig   0.00000E+00  -4.87842E+01   8.33333E+01  -4.16667E+01   7.11752E+00   0.00000E+00
  0 Aeig   0.00000E+00   7.11752E+00  -4.16667E+01   8.33333E+01  -4.87842E+01   0.00000E+00
  0 Aeig   0.00000E+00  -1.66667E+00   7.11752E+00  -4.87842E+01      Infinity     -Infinity
  0 Aeig   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00     -Infinity      Infinity

Matrix:   0 Deig       1       6       6
  0 Deig   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00   0.00000E+00
 Error in generalev, info=          12           6          -6

an error occured: dying ...

Could you please tell me why?

Thank you

Sijo GEORGE
________________________________
De: "nek5000-users" <[email protected]<mailto:[email protected]>>
À: "nek5000-users" <[email protected]<mailto:[email protected]>>
Envoyé: Jeudi 31 Mai 2018 14:52:40
Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

I specify the boundary conditions in the usrdat subroutine using the following piece of code

      do i=1,nelt
        do j=1,2*ndim
          if(bc(5,j,i,1).eq.1) then
            cbc(j,i,1)='mv  '
          elseif(bc(5,j,i,1).eq.2) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.3) then
            cbc(j,i,1)='W  '
          elseif(bc(5,j,i,1).eq.4) then
            cbc(j,i,1)='W  '
          else
            cbc(j,i,1)='E  '
          endif
        enddo
      enddo

Marco

On May 31, 2018, at 8:50 AM, [email protected]<mailto:[email protected]> wrote:

Hi Neks,

I did the conversion of a mesh from ICEM to exodus file then to re2 file.

But I am bit confused on the boundary conditions. Because from ICEM before I export to exodus I give the B.Cs as side set numbers and after the conversion to re2 I wont be able to put the boundary conditions in NEK format.

So could you please tell me how you put the BC in NEK5000 format to a mesh file with exodus format.

Thank you
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]<mailto:[email protected]>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file

nek5000-users＠lists.mcs.anl.gov