<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>Yes. The same results.<br></div><div><br data-mce-bogus="1"></div><div>Could you please tell me why there is a 5 on the bc(5,j,i,1)?<br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div>And the value of bc(5,j,i,1) was zero for all the iteration.<br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div>Thank you<br data-mce-bogus="1"></div><div><br></div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"nek5000-users" <nek5000-users@lists.mcs.anl.gov><br><b>À: </b>"nek5000-users" <nek5000-users@lists.mcs.anl.gov><br><b>Envoyé: </b>Jeudi 31 Mai 2018 16:28:59<br><b>Objet: </b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br></div><div><br></div><div data-marker="__QUOTED_TEXT__">you have to add the print statement before you enter the if statements.<div class=""><br class="">
</div>
<div class="">Marco<br class="">
<div><br class="">
<blockquote class="">
<div class="">On May 31, 2018, at 10:25 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">
nek5000-users@lists.mcs.anl.gov</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class="">
<div class="">c-----------------------------------------------------------------------<br class="">
subroutine usrdat<br class="">
include 'SIZE'<br class="">
include 'TOTAL'<br class="">
<br class="">
do i=1,nelt<br class="">
do j=1,2*ndim<br class="">
if(bc(5,j,i,1).eq.1) then<br class="">
cbc(j,i,1)='O '<br class="">
write (6,1) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
1 format(i4,i4,i4,i4,7f20.8)<br class="">
elseif(bc(5,j,i,1).eq.2) then<br class="">
cbc(j,i,1)='W '<br class="">
write (6,2) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
2 format(i4,i4,i4,i4,7f20.8) <br class="">
elseif(bc(5,j,i,1).eq.3) then<br class="">
cbc(j,i,1)='W '<br class="">
write (6,3) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
3 format(i4,i4,i4,i4,7f20.8) <br class="">
elseif(bc(5,j,i,1).eq.4) then<br class="">
cbc(j,i,1)='W '<br class="">
write (6,4) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
4 format(i4,i4,i4,i4,7f20.8) <br class="">
elseif(bc(5,j,i,1).eq.5) then<br class="">
cbc(j,i,1)='V '<br class="">
write (6,5) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
5 format(i4,i4,i4,i4,7f20.8) <br class="">
elseif(bc(5,j,i,1).eq.6) then<br class="">
cbc(j,i,1)='W '<br class="">
write (6,6) j,i,nelt,ndim,bc(5,j,i,1)<br class="">
6 format(i4,i4,i4,i4,7f20.8) <br class="">
else<br class="">
<strong class=""> cbc(j,i,1)='E '</strong><br class="">
<strong class=""> write (6,7) j,i,nelt,ndim,bc(5,j,i,1)</strong><br class="">
<strong class="">7 format(i4,i4,i4,i4,7f20.8) </strong><br class="">
<br class="">
endif<br class="">
enddo<br class="">
enddo<br class="">
<br class="">
call gen_rea(0)<br class="">
call exit<br class="">
return<br class="">
end<br class="">
c-----------------------------------------------------------------------</div>
<div class=""><br class="">
</div>
<div class="">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<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> 1 9991000 3 0.00000000<br class="">
2 9991000 3 0.00000000<br class="">
3 9991000 3 0.00000000<br class="">
4 9991000 3 0.00000000<br class="">
5 9991000 3 0.00000000<br class="">
6 9991000 3 0.00000000<br class="">
<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Thank you<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Sijo<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<hr id="zwchr" class="">
<div class=""><b class="">De: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">À: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Envoyé: </b>Jeudi 31 Mai 2018 16:12:12<br class="">
<b class="">Objet: </b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">You should output values of i, j, next, ndim and bc(5,j,i,1) for sanity check.
<div class=""><br class="">
</div>
<div class="">Marco<br class="">
<div class=""><br class="">
<blockquote class="">
<div class="">On May 31, 2018, at 10:07 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">
nek5000-users@lists.mcs.anl.gov</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class="">
<div class=""> </div>
<div class="">When I checked the loop I can see that only the bold letter codes are executing in all the iteration.<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> subroutine usrdat<br class="">
include 'SIZE'<br class="">
include 'TOTAL'<br class="">
<br class="">
do i=1,nelt<br class="">
do j=1,2*ndim<br class="">
if(bc(5,j,i,1).eq.1) then<br class="">
cbc(j,i,1)='O '<br class="">
elseif(bc(5,j,i,1).eq.2) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.3) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.4) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.5) then<br class="">
cbc(j,i,1)='V '<br class="">
elseif(bc(5,j,i,1).eq.6) then<br class="">
cbc(j,i,1)='W '<br class="">
else<br class="">
<strong class=""> cbc(j,i,1)='E '</strong><br class="">
<strong class=""> endif</strong><br class="">
<strong class=""> enddo</strong><br class="">
<strong class=""> enddo</strong><br class="">
<br class="">
call gen_rea(0)</div>
<div class=""> call exit<br class="">
return<br class="">
end<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Thanks<br class="">
</div>
<div class="">Sijo<br class="">
</div>
<div class=""><br class="">
</div>
<hr id="zwchr" class="">
<div class=""><b class="">De: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">À: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Envoyé: </b>Jeudi 31 Mai 2018 15:54:04<br class="">
<b class="">Objet: </b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br class="">
</div>
<br class="">
<div class="">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?
<div class=""><br class="">
</div>
<div class="">Also add ‘call exist’ after setting the boundary conditions that way Nek5000 will automatically exit.<br class="">
<div class=""><br class="">
</div>
<div class="">Marco<br class="">
<div class=""><br class="">
<blockquote class="">
<div class="">On May 31, 2018, at 9:51 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">
nek5000-users@lists.mcs.anl.gov</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class="">
<div class="">Yes. I see the problem now.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Regards<br class="">
</div>
<div class="">Sijo<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<hr id="zwchr" class="">
<div class=""><b class="">De: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">À: </b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Envoyé: </b>Jeudi 31 Mai 2018 15:43:20<br class="">
<b class="">Objet: </b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Can you add ‘call gen_rea(0)’ after setting the boundary conditions in usrdat()? It will generate a *.rea file with all boundary conditions.
<div class=""><br class="">
</div>
<div class="">Marco<br class="">
<div class=""><br class="">
<blockquote class="">
<div class="">On May 31, 2018, at 9:37 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">
nek5000-users@lists.mcs.anl.gov</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: arial, helvetica, sans-serif; font-size: 12pt;" class="">
<div class=""><br class="Apple-interchange-newline">
I generated again it didnt work.<br class="">
</div>
<div class="">I will explain what I did so far.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I made a cube fluid mesh in ICEM.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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<br class="">
</div>
<div class="">After that I exported the mesh from ICEM to exodus.exo format file.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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).<br class="">
</div>
<div class="">Then I mapped the file into exodus.ma2 file.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Then from example Turbulent channel I took a .par file to give parameters.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Now I also given the B.Cs through the .usr file.<br class="">
</div>
<div class=""> as follows:<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">c-----------------------------------------------------------------------<br class="">
subroutine usrdat<br class="">
include 'SIZE'<br class="">
include 'TOTAL'<br class="">
<br class="">
<br class="">
do i=1,nelt<br class="">
do j=1,2*ndim<br class="">
if(bc(5,j,i,1).eq.1) then<br class="">
cbc(j,i,1)='O '<br class="">
elseif(bc(5,j,i,1).eq.2) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.3) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.4) then<br class="">
cbc(j,i,1)='W '<br class="">
elseif(bc(5,j,i,1).eq.5) then<br class="">
cbc(j,i,1)='V '<br class="">
elseif(bc(5,j,i,1).eq.6) then<br class="">
cbc(j,i,1)='W '<br class="">
else<br class="">
cbc(j,i,1)='E '<br class="">
endif<br class="">
enddo<br class="">
enddo<br class="">
<br class="">
<br class="">
return<br class="">
end<br class="">
c-----------------------------------------------------------------------<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Could you please tell me, if therer is anything wrong?<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Thank you<br class="">
</div>
<hr id="zwchr" class="">
<div class=""><b class="">De:<span class="Apple-converted-space"> </span></b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">À:<span class="Apple-converted-space"> </span></b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Envoyé:<span class="Apple-converted-space"> </span></b>Jeudi 31 Mai 2018 15:22:49<br class="">
<b class="">Objet:<span class="Apple-converted-space"> </span></b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Did you generate a new map file after changing the BCs?</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">This matters when switching periodic bcs on or off...</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Paul</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
</div>
<hr style="display: inline-block; width: 1439.609375px;" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Nek5000-users <<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" class="" target="_blank">nek5000-users-bounces@lists.mcs.anl.gov</a>>
on behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">
nek5000-users@lists.mcs.anl.gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 31, 2018 8:12:55 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file</span>
<div class=""> </div>
</div>
<div class="" style="word-wrap: break-word; line-break: after-white-space;">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.
<div class=""><br class="">
</div>
<div class="">Marco<br class="">
<div class=""><br class="">
<blockquote class="">
<div class="">On May 31, 2018, at 9:11 AM,<span class="Apple-converted-space"> </span><a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a><span class="Apple-converted-space"> </span>wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="">
<div class="" style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">
<div class=""><br class="">
</div>
<div class="">Hi Marco,<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I tried and it compiled . But before starting the time step it failed.<span class="Apple-converted-space"> </span><br class="">
</div>
<div class="">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.<br class="">
</div>
<div class="">I get this error:<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Matrix: 0 aa 6 6 6<br class="">
0 aa 8.33333E+01 -4.87842E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
0 aa -4.87842E+01 8.66667E+01 -4.87842E+01 7.11752E+00 -1.66667E+00 0.00000E+00<br class="">
0 aa 0.00000E+00 -4.87842E+01 8.33333E+01 -4.16667E+01 7.11752E+00 0.00000E+00<br class="">
0 aa 0.00000E+00 7.11752E+00 -4.16667E+01 8.33333E+01 -4.87842E+01 0.00000E+00<br class="">
0 aa 0.00000E+00 -1.66667E+00 7.11752E+00 -4.87842E+01 Infinity -Infinity<br class="">
0 aa 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -Infinity Infinity<br class="">
<br class="">
Matrix: 0 bb 6 6 6<br class="">
0 bb 4.16667E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
0 bb 0.00000E+00 1.66667E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
0 bb 0.00000E+00 0.00000E+00 4.16667E-02 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 4.16667E-02 0.00000E+00 0.00000E+00<br class="">
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 8.33333E-03 0.00000E+00<br class="">
0 bb 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
<br class="">
Matrix: 0 Aeig 6 6 6<br class="">
0 Aeig 8.33333E+01 -4.87842E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
0 Aeig -4.87842E+01 8.66667E+01 -4.87842E+01 7.11752E+00 -1.66667E+00 0.00000E+00<br class="">
0 Aeig 0.00000E+00 -4.87842E+01 8.33333E+01 -4.16667E+01 7.11752E+00 0.00000E+00<br class="">
0 Aeig 0.00000E+00 7.11752E+00 -4.16667E+01 8.33333E+01 -4.87842E+01 0.00000E+00<br class="">
0 Aeig 0.00000E+00 -1.66667E+00 7.11752E+00 -4.87842E+01 Infinity -Infinity<br class="">
0 Aeig 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 -Infinity Infinity<br class="">
<br class="">
Matrix: 0 Deig 1 6 6<br class="">
0 Deig 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00<br class="">
Error in generalev, info= 12 6 -6<br class="">
<span class="Apple-converted-space"> </span><br class="">
an error occured: dying ...<br class="">
<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Could you please tell me why?<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Thank you<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Sijo GEORGE<br class="">
</div>
<hr id="x_zwchr" class="">
<div class=""><b class="">De:<span class="Apple-converted-space"> </span></b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">À:<span class="Apple-converted-space"> </span></b>"nek5000-users" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a>><br class="">
<b class="">Envoyé:<span class="Apple-converted-space"> </span></b>Jeudi 31 Mai 2018 14:52:40<br class="">
<b class="">Objet:<span class="Apple-converted-space"> </span></b>Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file<br class="">
</div>
<br class="">
<div class="">I specify the boundary conditions in the usrdat subroutine using the following piece of code
<div class=""><br class="">
</div>
<div class="">
<div class=""> do i=1,nelt</div>
<div class=""> do j=1,2*ndim</div>
<div class=""> if(bc(5,j,i,1).eq.1) then</div>
<div class=""> cbc(j,i,1)='mv '</div>
<div class=""> elseif(bc(5,j,i,1).eq.2) then</div>
<div class=""> cbc(j,i,1)='W '</div>
<div class=""> elseif(bc(5,j,i,1).eq.3) then</div>
<div class=""> cbc(j,i,1)='W '</div>
<div class=""> elseif(bc(5,j,i,1).eq.4) then</div>
<div class=""> cbc(j,i,1)='W '</div>
<div class=""> else</div>
<div class=""> cbc(j,i,1)='E '</div>
<div class=""> endif</div>
<div class=""> enddo</div>
<div class=""> enddo</div>
</div>
<div class=""><br class="">
</div>
<div class="">Marco</div>
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<blockquote class="">
<div class="">On May 31, 2018, at 8:50 AM,<span class="Apple-converted-space"> </span><a href="mailto:nek5000-users@lists.mcs.anl.gov" class="" target="_blank">nek5000-users@lists.mcs.anl.gov</a><span class="Apple-converted-space"> </span>wrote:</div>
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<div class="">Hi Neks,<br class="">
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<div class="">I did the conversion of a mesh from ICEM to exodus file then to re2 file. </div>
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<div class="">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.</div>
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<div class="">So could you please tell me how you put the BC in NEK5000 format to a mesh file with exodus format.<br class="">
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<div class="">Thank you<br class="">
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