From nek5000-users at lists.mcs.anl.gov Thu May 3 11:47:44 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 May 2018 17:47:44 +0100 Subject: [Nek5000-users] ffx ffy ffz from current run Message-ID: Hi Nek users, How can I get the ffx ffy and ffz from the simulation with flowrate fixed, where ffx ffy and ffz are in usr file? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 3 12:36:06 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 May 2018 17:36:06 +0000 Subject: [Nek5000-users] ffx ffy ffz from current run Message-ID: Hi Jian, Not exactly sure what you mean, but if you are using p54, p55 to set your flowrate, then you can use your logfile to get what the corresponding forcing should be using ffx/ffy/ffz. As per drive2.f, if you are using param(54),param(55), then in logfile you can grep for ?volflow?, and ?scale? represents the ffx/ffy/ffz. if (nio.eq.0) write(6,1) istep,chv(icvflow) $ ,scale,delta_flow,current_flow,flow_rate 1 format(i11,' volflow ',a1,11x,1p4e13.4) c Note, this scale factor corresponds to FFX, provided FFX has c not also been specified in userf. If ffx is also specified c in userf then the true FFX is given by ffx_userf + scale. Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 3 18:03:18 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 May 2018 23:03:18 +0000 Subject: [Nek5000-users] ffx ffy ffz from current run In-Reply-To: References: Message-ID: Dear Zhai, Assuming you have a periodic domain in direction "d" (d=1,2,3 or x,y,z), and that you have ffx=ffy=ffz=0 in your .usr file, then grep volf logfile will show a list of time step, time, and "ffd" + other columns. Column 3 will be "ffd" where ffd is the force in the direction "d" and d = |p54|. p54 = +/- 1 ==> d=x direction +/- 2 ==> y direction +/- 3 ==> z direction If p54 < 0, then p55 determines the mean velocity in direction d If p54 > 0, then p55 determines the volumetric flux in direction d (Note that p55 < 0 would be the flow is in the reverse direction.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, May 3, 2018 11:47:44 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] ffx ffy ffz from current run Hi Nek users, How can I get the ffx ffy and ffz from the simulation with flowrate fixed, where ffx ffy and ffz are in usr file? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri May 4 01:39:25 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 May 2018 06:39:25 +0000 Subject: [Nek5000-users] Postprocessing: Append data to output file Message-ID: Hi, I am postprocessing output files in order to compute the vorticity. So far I have followed the instructions in https://lists.mcs.anl.gov/pipermail/nek5000-users/2010-March/000171.html, where it is explained how to output the vorticity components as velocity components. I however would like to make a simultaneous visualization of the vorticity field, the velocity field and some of the scalar fields. If postprocessing a file "mycase0.f000XX" - is it then possible to append the vorticity to this file? If this is not possible, how would I to in order to write the velocity and the vorticity in the same file? The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but I have 3 scalars in addition to the temperature. How can I write a file containing both the vorticity and the four scalar fields? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri May 4 04:30:41 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 May 2018 11:30:41 +0200 Subject: [Nek5000-users] Postprocessing: Append data to output file In-Reply-To: References: Message-ID: Assuming you are using par, define a scalar: [SCALAR01] # vorticity solver = none Then, just store the vorticity in t(1,1,1,1,iscal +1) where iscal is your passive scalar index (in this example 1). On 4 May 2018, at 08:39, "nek5000-users at lists.mcs.anl.gov " > wrote: Hi, I am postprocessing output files in order to compute the vorticity. So far I have followed the instructions in https://lists.mcs.anl.gov/pipermail/nek5000-users/2010-March/000171.html, where it is explained how to output the vorticity components as velocity components. I however would like to make a simultaneous visualization of the vorticity field, the velocity field and some of the scalar fields. If postprocessing a file "mycase0.f000XX" - is it then possible to append the vorticity to this file? If this is not possible, how would I to in order to write the velocity and the vorticity in the same file? The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but I have 3 scalars in addition to the temperature. How can I write a file containing both the vorticity and the four scalar fields? Best, Johan _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat May 5 10:25:36 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 5 May 2018 16:25:36 +0100 Subject: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 3 In-Reply-To: References: Message-ID: Hello Paul and Ketan, I really appreciate your reply. Do you mean the third column which is 1.56E-02, is the ffz force if para(54) and para(55) are 0? To be honest, I tried a case that 1.56E-02 was used as ffz in the usr file while setting para(54) and (55) are 0. The case was set to start from where keeping flowrate stopped which have the right mean velocities. But the mean streamwise velocity decreased a lot. So I am wondering how much ffz should be. 1 0.1617415E+03 1.56161E-02 1.22442E-07 7.85399E-01 7.85399E-01 volflow Z 2 0.1617415E+03 1.56215E-02 9.51058E-08 7.85399E-01 7.85399E-01 volflow Z 3 0.1617415E+03 1.56186E-02 9.08498E-08 7.85399E-01 7.85399E-01 volflow Z 4 0.1617415E+03 1.56207E-02 1.09035E-07 7.85399E-01 7.85399E-01 volflow Z 5 0.1617416E+03 1.56204E-02 1.30839E-07 7.85399E-01 7.85399E-01 volflow Z 6 0.1617416E+03 1.56200E-02 1.57003E-07 7.85399E-01 7.85399E-01 volflow Z 7 0.1617416E+03 1.56198E-02 1.88400E-07 7.85399E-01 7.85399E-01 volflow Z 8 0.1617417E+03 1.56196E-02 2.26078E-07 7.85399E-01 7.85399E-01 volflow Z Kind regards, Jian On 4 May 2018 at 18:00, wrote: > Send Nek5000-users mailing list submissions to > nek5000-users at lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request at lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner at lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Re: ffx ffy ffz from current run (nek5000-users at lists.mcs.anl.gov) > 2. Re: ffx ffy ffz from current run (nek5000-users at lists.mcs.anl.gov) > 3. Postprocessing: Append data to output file > (nek5000-users at lists.mcs.anl.gov) > 4. Re: Postprocessing: Append data to output file > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 May 2018 17:36:06 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] ffx ffy ffz from current run > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Jian, > > Not exactly sure what you mean, but if you are using p54, p55 to set your > flowrate, then you can use your logfile to get what the corresponding > forcing should be using ffx/ffy/ffz. > > As per drive2.f, if you are using param(54),param(55), then in logfile you > can grep for ?volflow?, and ?scale? represents the ffx/ffy/ffz. > > > if (nio.eq.0) write(6,1) istep,chv(icvflow) > $ ,scale,delta_flow,current_flow,flow_rate > 1 format(i11,' volflow ',a1,11x,1p4e13.4) > > c Note, this scale factor corresponds to FFX, provided FFX has > c not also been specified in userf. If ffx is also specified > c in userf then the true FFX is given by ffx_userf + scale. > > > Ketan > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180503/19d76cf4/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Thu, 3 May 2018 23:03:18 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] ffx ffy ffz from current run > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Dear Zhai, > > > Assuming you have a periodic domain in direction "d" (d=1,2,3 or x,y,z), > and > > that you have ffx=ffy=ffz=0 in your .usr file, then > > > grep volf logfile > > > will show a list of time step, time, and "ffd" + other columns. > > > Column 3 will be "ffd" > > > where ffd is the force in the direction "d" and d = |p54|. > > > p54 = +/- 1 ==> d=x direction > > +/- 2 ==> y direction > > +/- 3 ==> z direction > > > If p54 < 0, then p55 determines the mean velocity in direction d > > > If p54 > 0, then p55 determines the volumetric flux in direction d > > > (Note that p55 < 0 would be the flow is in the reverse direction.) > > > hth, > > > Paul > > > ________________________________ > From: Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 3, 2018 11:47:44 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] ffx ffy ffz from current run > > Hi Nek users, > > How can I get the ffx ffy and ffz from the simulation with flowrate fixed, > where ffx ffy and ffz are in usr file? > > Kind regards, > > Zhai > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180503/ecd674f3/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Fri, 4 May 2018 06:39:25 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Postprocessing: Append data to output file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > > I am postprocessing output files in order to compute the vorticity. > > So far I have followed the instructions in https://lists.mcs.anl.gov/ > pipermail/nek5000-users/2010-March/000171.html, > > where it is explained how to output the vorticity components as velocity > components. > > > I however would like to make a simultaneous visualization of the vorticity > field, the velocity field and some of the scalar fields. > > If postprocessing a file "mycase0.f000XX" - is it then possible to append > the vorticity to this file? > > If this is not possible, how would I to in order to write the velocity and > the vorticity in the same file? > > > The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but > I have 3 scalars in addition to the temperature. > > How can I write a file containing both the vorticity and the four scalar > fields? > > > Best, > > > Johan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180504/c8b262ce/attachment-0001.html> > > ------------------------------ > > Message: 4 > Date: Fri, 4 May 2018 11:30:41 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Postprocessing: Append data to output > file > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Assuming you are using par, define a scalar: > > [SCALAR01] # vorticity > solver = none > > Then, just store the vorticity in t(1,1,1,1,iscal +1) where iscal is your > passive scalar index (in this example 1). > > On 4 May 2018, at 08:39, "nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov> " > wrote: > > Hi, > > > > I am postprocessing output files in order to compute the vorticity. > > So far I have followed the instructions in https://lists.mcs.anl.gov/ > pipermail/nek5000-users/2010-March/000171.html, > > where it is explained how to output the vorticity components as velocity > components. > > > > I however would like to make a simultaneous visualization of the vorticity > field, the velocity field and some of the scalar fields. > > If postprocessing a file "mycase0.f000XX" - is it then possible to append > the vorticity to this file? > > If this is not possible, how would I to in order to write the velocity and > the vorticity in the same file? > > > > The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but > I have 3 scalars in addition to the temperature. > > How can I write a file containing both the vorticity and the four scalar > fields? > > > > Best, > > > > Johan > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180504/e0c1a83b/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > End of Nek5000-users Digest, Vol 111, Issue 3 > ********************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat May 5 22:47:04 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 6 May 2018 03:47:04 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 3 In-Reply-To: References: , Message-ID: Dear Jian, Did you look a long time average of the scale factor? It does fluctuate over time when the flow is turbulent. Perhaps you got it at the wrong time, or perhaps there is something about your configuration that we're not understanding (though I have no idea of what that could possibly be at this point). Are you running with variable viscosity or anything like that? This approach normally provides the correct ffz value. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Saturday, May 5, 2018 10:25:36 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 3 Hello Paul and Ketan, I really appreciate your reply. Do you mean the third column which is 1.56E-02, is the ffz force if para(54) and para(55) are 0? To be honest, I tried a case that 1.56E-02 was used as ffz in the usr file while setting para(54) and (55) are 0. The case was set to start from where keeping flowrate stopped which have the right mean velocities. But the mean streamwise velocity decreased a lot. So I am wondering how much ffz should be. 1 0.1617415E+03 1.56161E-02 1.22442E-07 7.85399E-01 7.85399E-01 volflow Z 2 0.1617415E+03 1.56215E-02 9.51058E-08 7.85399E-01 7.85399E-01 volflow Z 3 0.1617415E+03 1.56186E-02 9.08498E-08 7.85399E-01 7.85399E-01 volflow Z 4 0.1617415E+03 1.56207E-02 1.09035E-07 7.85399E-01 7.85399E-01 volflow Z 5 0.1617416E+03 1.56204E-02 1.30839E-07 7.85399E-01 7.85399E-01 volflow Z 6 0.1617416E+03 1.56200E-02 1.57003E-07 7.85399E-01 7.85399E-01 volflow Z 7 0.1617416E+03 1.56198E-02 1.88400E-07 7.85399E-01 7.85399E-01 volflow Z 8 0.1617417E+03 1.56196E-02 2.26078E-07 7.85399E-01 7.85399E-01 volflow Z Kind regards, Jian On 4 May 2018 at 18:00, > wrote: Send Nek5000-users mailing list submissions to nek5000-users at lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request at lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner at lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Re: ffx ffy ffz from current run (nek5000-users at lists.mcs.anl.gov) 2. Re: ffx ffy ffz from current run (nek5000-users at lists.mcs.anl.gov) 3. Postprocessing: Append data to output file (nek5000-users at lists.mcs.anl.gov) 4. Re: Postprocessing: Append data to output file (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 3 May 2018 17:36:06 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" > Subject: Re: [Nek5000-users] ffx ffy ffz from current run Message-ID: > Content-Type: text/plain; charset="utf-8" Hi Jian, Not exactly sure what you mean, but if you are using p54, p55 to set your flowrate, then you can use your logfile to get what the corresponding forcing should be using ffx/ffy/ffz. As per drive2.f, if you are using param(54),param(55), then in logfile you can grep for ?volflow?, and ?scale? represents the ffx/ffy/ffz. if (nio.eq.0) write(6,1) istep,chv(icvflow) $ ,scale,delta_flow,current_flow,flow_rate 1 format(i11,' volflow ',a1,11x,1p4e13.4) c Note, this scale factor corresponds to FFX, provided FFX has c not also been specified in userf. If ffx is also specified c in userf then the true FFX is given by ffx_userf + scale. Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Thu, 3 May 2018 23:03:18 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" > Subject: Re: [Nek5000-users] ffx ffy ffz from current run Message-ID: > Content-Type: text/plain; charset="us-ascii" Dear Zhai, Assuming you have a periodic domain in direction "d" (d=1,2,3 or x,y,z), and that you have ffx=ffy=ffz=0 in your .usr file, then grep volf logfile will show a list of time step, time, and "ffd" + other columns. Column 3 will be "ffd" where ffd is the force in the direction "d" and d = |p54|. p54 = +/- 1 ==> d=x direction +/- 2 ==> y direction +/- 3 ==> z direction If p54 < 0, then p55 determines the mean velocity in direction d If p54 > 0, then p55 determines the volumetric flux in direction d (Note that p55 < 0 would be the flow is in the reverse direction.) hth, Paul ________________________________ From: Nek5000-users > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 3, 2018 11:47:44 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] ffx ffy ffz from current run Hi Nek users, How can I get the ffx ffy and ffz from the simulation with flowrate fixed, where ffx ffy and ffz are in usr file? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Fri, 4 May 2018 06:39:25 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" > Subject: [Nek5000-users] Postprocessing: Append data to output file Message-ID: > Content-Type: text/plain; charset="iso-8859-1" Hi, I am postprocessing output files in order to compute the vorticity. So far I have followed the instructions in https://lists.mcs.anl.gov/pipermail/nek5000-users/2010-March/000171.html, where it is explained how to output the vorticity components as velocity components. I however would like to make a simultaneous visualization of the vorticity field, the velocity field and some of the scalar fields. If postprocessing a file "mycase0.f000XX" - is it then possible to append the vorticity to this file? If this is not possible, how would I to in order to write the velocity and the vorticity in the same file? The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but I have 3 scalars in addition to the temperature. How can I write a file containing both the vorticity and the four scalar fields? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 4 Date: Fri, 4 May 2018 11:30:41 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Postprocessing: Append data to output file Message-ID: > Content-Type: text/plain; charset="utf-8" Assuming you are using par, define a scalar: [SCALAR01] # vorticity solver = none Then, just store the vorticity in t(1,1,1,1,iscal +1) where iscal is your passive scalar index (in this example 1). On 4 May 2018, at 08:39, "nek5000-users at lists.mcs.anl.gov > " > > wrote: Hi, I am postprocessing output files in order to compute the vorticity. So far I have followed the instructions in https://lists.mcs.anl.gov/pipermail/nek5000-users/2010-March/000171.html, where it is explained how to output the vorticity components as velocity components. I however would like to make a simultaneous visualization of the vorticity field, the velocity field and some of the scalar fields. If postprocessing a file "mycase0.f000XX" - is it then possible to append the vorticity to this file? If this is not possible, how would I to in order to write the velocity and the vorticity in the same file? The interface of the subroutine outpost is outpost(vx,vy,vz,pr,t,nam), but I have 3 scalars in addition to the temperature. How can I write a file containing both the vorticity and the four scalar fields? Best, Johan _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ------------------------------ End of Nek5000-users Digest, Vol 111, Issue 3 ********************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun May 6 03:36:57 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 6 May 2018 09:36:57 +0100 Subject: [Nek5000-users] *****SPAM*****Re: ffx ffy ffz from current run In-Reply-To: References: Message-ID: Good morning Paul, What I am doing is the single-phase pipe flow currently. I've done a correct one by keeping the flowrate in z direction. But what I am trying to do is setting one simulation by fixing ffz rather than flow rate. Can you please have look at my rea file and usr file? I don't know how to do actually. Kind regar??ds, Jian ? pipe.rea ?? pipe.usr ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 8 03:46:38 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 08 May 2018 16:46:38 +0800 Subject: [Nek5000-users] Compiling Problems in "Running your very first simulation" Message-ID: Hello, The title of my thread is the same as for an already existing thread (26-Sept-2017) because: I receive very similar warning messages when compiling nek5000 (./maketools all). Lots of warnings! >From your answer on that thread it seems that you do not worry at all for the warning messages. Should we really not care about them? How to know which warnings are not of concern and which other are? Can you post your own .log file to see which warning messages are considered normal for you? Or how do you check everything went fine for the compilation? Anyway, I will start running the examples in order to learn about the usage of the code. And I guess any abnormality would appear there. Many thanks, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 57128 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue May 8 06:31:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 8 May 2018 13:31:30 +0200 Subject: [Nek5000-users] Compiling Problems in "Running your very first simulation" Message-ID: Yes, you can ignore the compiler warnings! In case you want to double-check your local installation run the short tests. For more information please consult Nek5000/short_tests/README.md -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Tuesday 8th May 2018 13:17 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Compiling Problems in "Running your very first simulation" > > Hello, > The title of my thread is the same as for an already existing thread (26-Sept-2017) because: > I receive very similar warning messages when compiling nek5000 (./maketools all). Lots of warnings! > From your answer on that thread it seems that you do not worry at all for the warning messages. Should we really not care about them? How to know which warnings are not of concern and which other are? Can you post your own .log file to see which warning messages are considered normal for you? Or how do you check everything went fine for the compilation? > Anyway, I will start running the examples in order to learn about the usage of the code. And I guess any abnormality would appear there. > Many thanks, > Alexis > Dr Alexis Espinosa > Supercomputing Specialist > Pawsey Supercomputing Centre > 26 Dick Perry Ave > Kensington? WA? 6151 > Australia > Tel ?+61 xxxx xxxx > Email? alexis.espinosa at pawsey.org.au Web? www.pawsey.org.au _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue May 8 10:39:47 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 01:39:47 +1000 Subject: [Nek5000-users] Opening/Editing of Output files (.f000*) Message-ID: Dear all, I am a new user to Nek5000 and I have been experimenting with DNS of turbulent channel flows using the turbchannel example. I believe I have gotten a basic case running. Now I would like to be able to open/edit the output files to be used as starting points for future simulations. The problem I am having is in understanding how to go about modifying the resultant files (.f000*), does this have to be done through the postprocessor? If so, can someone point me in the right direction as I am quite confused. Thanks in advance, William -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 8 12:22:07 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 8 May 2018 17:22:07 +0000 Subject: [Nek5000-users] Opening/Editing of Output files (.f000*) In-Reply-To: References: Message-ID: Dear William What type of editing are you proposing? Probably the easiest thing to do is to modify the velocity field from within the userchk() routine, either after loading the file for restart or just prior to saving. hth Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, May 8, 2018 10:39:47 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Opening/Editing of Output files (.f000*) Dear all, I am a new user to Nek5000 and I have been experimenting with DNS of turbulent channel flows using the turbchannel example. I believe I have gotten a basic case running. Now I would like to be able to open/edit the output files to be used as starting points for future simulations. The problem I am having is in understanding how to go about modifying the resultant files (.f000*), does this have to be done through the postprocessor? If so, can someone point me in the right direction as I am quite confused. Thanks in advance, William -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 8 13:00:00 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 8 May 2018 18:00:00 +0000 Subject: [Nek5000-users] Opening/Editing of Output files (.f000*) In-Reply-To: References: , Message-ID: Hi William, If your question is about how to visualize and analyze the field output files, you need to generate a .nek5000 metafile with visnek script (in Nek5000/bin) and then open it in VisIt or ParaView as mentioned below. Aleks https://nek5000.github.io/NekDoc/quickstart.html#visualization Quickstart ? Nek5000 17.0 documentation nek5000.github.io /tools. contains the sources for the pre- and post-processing tools which are stand-alone. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, May 8, 2018 12:22:07 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Opening/Editing of Output files (.f000*) Dear William What type of editing are you proposing? Probably the easiest thing to do is to modify the velocity field from within the userchk() routine, either after loading the file for restart or just prior to saving. hth Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, May 8, 2018 10:39:47 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Opening/Editing of Output files (.f000*) Dear all, I am a new user to Nek5000 and I have been experimenting with DNS of turbulent channel flows using the turbchannel example. I believe I have gotten a basic case running. Now I would like to be able to open/edit the output files to be used as starting points for future simulations. The problem I am having is in understanding how to go about modifying the resultant files (.f000*), does this have to be done through the postprocessor? If so, can someone point me in the right direction as I am quite confused. Thanks in advance, William -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 03:13:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 08:13:19 +0000 Subject: [Nek5000-users] Integral on the wall Message-ID: Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 05:55:29 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 10:55:29 +0000 Subject: [Nek5000-users] Integral on the wall In-Reply-To: References: Message-ID: Dear Valerio, You would need to modify torque calc to do this, assuming that your objective is to compute a line integral of the pressure on the GLL points. Assuming that your pipe mesh was made by sweeping the geometry in the z direction with n2to3, the modification should be quite easy. The routine I would start with would be drgtrq in navier5.f, which I see uses the two-index loop to traverse faces based on jskip1 and jskip2. For your case, I would use the facind() 3 index loop approach (e.g., as used in norcmp2 routine). Then you track the outer "k" loop and accumulate one value for each k value and for each z level of the elements. You will know the z level because it will be: klevel_e = 1 + (eg-1)/nelxy where nelxy is the number of elements in your pipe cross section. Hopefully this will get you pointed in the right direction... Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:13:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integral on the wall Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 08:05:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 13:05:39 +0000 Subject: [Nek5000-users] Integral on the wall In-Reply-To: References: , Message-ID: Dear Valerio, I've not tested or even compiled the attached code... But it should be fairly close to being functional. The idea would be to pass in the pressure on mesh 1, which means you need to interpolate from pr to pm1 ---- there are several routines floating around to do this. Please let me know if you have any questions and if you are able to make this routine work. Best, Paul PS - note that you should be able to send in "zm1" to this routine and get back the correct z distribution. This is what I would do if I wished to plot pr vs z. Also, you might want to dsavg() pm1 if you want a continuous pressure estimate. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 5:55:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Integral on the wall Dear Valerio, You would need to modify torque calc to do this, assuming that your objective is to compute a line integral of the pressure on the GLL points. Assuming that your pipe mesh was made by sweeping the geometry in the z direction with n2to3, the modification should be quite easy. The routine I would start with would be drgtrq in navier5.f, which I see uses the two-index loop to traverse faces based on jskip1 and jskip2. For your case, I would use the facind() 3 index loop approach (e.g., as used in norcmp2 routine). Then you track the outer "k" loop and accumulate one value for each k value and for each z level of the elements. You will know the z level because it will be: klevel_e = 1 + (eg-1)/nelxy where nelxy is the number of elements in your pipe cross section. Hopefully this will get you pointed in the right direction... Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:13:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integral on the wall Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: zfunc.f Type: application/octet-stream Size: 1842 bytes Desc: zfunc.f URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 08:11:34 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 13:11:34 +0000 Subject: [Nek5000-users] Integral on the wall In-Reply-To: References: , , Message-ID: Dear Paul, Thank you for the help, I will test the routine zfunc. Best, Valerio ________________________________ Da: Nek5000-users per conto di nek5000-users at lists.mcs.anl.gov Inviato: mercoled? 9 maggio 2018 15:05 A: nek5000-users at lists.mcs.anl.gov Oggetto: Re: [Nek5000-users] Integral on the wall Dear Valerio, I've not tested or even compiled the attached code... But it should be fairly close to being functional. The idea would be to pass in the pressure on mesh 1, which means you need to interpolate from pr to pm1 ---- there are several routines floating around to do this. Please let me know if you have any questions and if you are able to make this routine work. Best, Paul PS - note that you should be able to send in "zm1" to this routine and get back the correct z distribution. This is what I would do if I wished to plot pr vs z. Also, you might want to dsavg() pm1 if you want a continuous pressure estimate. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 5:55:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Integral on the wall Dear Valerio, You would need to modify torque calc to do this, assuming that your objective is to compute a line integral of the pressure on the GLL points. Assuming that your pipe mesh was made by sweeping the geometry in the z direction with n2to3, the modification should be quite easy. The routine I would start with would be drgtrq in navier5.f, which I see uses the two-index loop to traverse faces based on jskip1 and jskip2. For your case, I would use the facind() 3 index loop approach (e.g., as used in norcmp2 routine). Then you track the outer "k" loop and accumulate one value for each k value and for each z level of the elements. You will know the z level because it will be: klevel_e = 1 + (eg-1)/nelxy where nelxy is the number of elements in your pipe cross section. Hopefully this will get you pointed in the right direction... Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:13:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integral on the wall Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 15:15:11 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 17:15:11 -0300 Subject: [Nek5000-users] Separate temperature perturbation field Message-ID: Hello, I'm working with teh effects of a local temperature perturbation in a natural convection problem. To define the perturbations I intend to create a separate field that will be added to the regular temperature field when calculating the buoyancy force (ffz=Pr*(temp+temp_perturb)), but I'm having troubles initializating and setting the values. To build the field I added a common block in usric(), usrchk() and usrf() common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) To initialize I tried to use rzero() as is used in avg_all(): subroutine useric(ix,iy,iz,eg) integer ix,iy,iz,eg,eltot include 'SIZE' include 'TOTAL' include 'NEKUSE' common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) ux = 0.0 uy = 0.0 uz = 0.0 t = 0.0 eltot = lx1*ly1*lz1*nelt do i = 1,ldimt call rzero(temp_perturb(1,1,1,1,i),eltot) enddo return end To generate the files, in usrchk() subroutine userchk() include 'SIZE' include 'TOTAL' integer e,eg common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) call outpost(vx,vy,vz,pr,temp_perturb,'pt1') call outpost2(vx,vy,vz,pr,temp_perturb,ldimt,'pt2') return end But after running the simulation the temperature perturbation field is a mess of NaNs and numbers of order 1e+38. Also, there's no other operation with 'temp_perturb' in the .usr file. Thanks in advance, *Nicol?s Andr?s ?rdenes Leiva* Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 9 16:44:43 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 May 2018 21:44:43 +0000 Subject: [Nek5000-users] Separate temperature perturbation field In-Reply-To: References: Message-ID: Dear Nicolas, It looks like you need to declare eltot to be an integer - Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:15:11 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Separate temperature perturbation field Hello, I'm working with teh effects of a local temperature perturbation in a natural convection problem. To define the perturbations I intend to create a separate field that will be added to the regular temperature field when calculating the buoyancy force (ffz=Pr*(temp+temp_perturb)), but I'm having troubles initializating and setting the values. To build the field I added a common block in usric(), usrchk() and usrf() common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) To initialize I tried to use rzero() as is used in avg_all(): subroutine useric(ix,iy,iz,eg) integer ix,iy,iz,eg,eltot include 'SIZE' include 'TOTAL' include 'NEKUSE' common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) ux = 0.0 uy = 0.0 uz = 0.0 t = 0.0 eltot = lx1*ly1*lz1*nelt do i = 1,ldimt call rzero(temp_perturb(1,1,1,1,i),eltot) enddo return end To generate the files, in usrchk() subroutine userchk() include 'SIZE' include 'TOTAL' integer e,eg common /perturb/ temp_perturb(lx1,ly1,lz1,lelt,ldimt) call outpost(vx,vy,vz,pr,temp_perturb,'pt1') call outpost2(vx,vy,vz,pr,temp_perturb,ldimt,'pt2') return end But after running the simulation the temperature perturbation field is a mess of NaNs and numbers of order 1e+38. Also, there's no other operation with 'temp_perturb' in the .usr file. Thanks in advance, Nicol?s Andr?s ?rdenes Leiva Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat May 12 05:44:50 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 12 May 2018 10:44:50 +0000 Subject: [Nek5000-users] Integral on the wall In-Reply-To: References: , , , Message-ID: Dear Paul, using the subroutine in zfunc.f I got the value of the pressure averaged on the surface. However I would like to compute the force on the wall as the line integral of the pressure times the normal (maybe my first question was unclear). Do you think this can be achieved modifying a bit the subroutine in zfunc.f or should I do it from scratch? Thanks. Best, Valerio ________________________________ Da: Nek5000-users per conto di nek5000-users at lists.mcs.anl.gov Inviato: mercoled? 9 maggio 2018 15:11 A: nek5000-users at lists.mcs.anl.gov Oggetto: Re: [Nek5000-users] Integral on the wall Dear Paul, Thank you for the help, I will test the routine zfunc. Best, Valerio ________________________________ Da: Nek5000-users per conto di nek5000-users at lists.mcs.anl.gov Inviato: mercoled? 9 maggio 2018 15:05 A: nek5000-users at lists.mcs.anl.gov Oggetto: Re: [Nek5000-users] Integral on the wall Dear Valerio, I've not tested or even compiled the attached code... But it should be fairly close to being functional. The idea would be to pass in the pressure on mesh 1, which means you need to interpolate from pr to pm1 ---- there are several routines floating around to do this. Please let me know if you have any questions and if you are able to make this routine work. Best, Paul PS - note that you should be able to send in "zm1" to this routine and get back the correct z distribution. This is what I would do if I wished to plot pr vs z. Also, you might want to dsavg() pm1 if you want a continuous pressure estimate. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 5:55:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Integral on the wall Dear Valerio, You would need to modify torque calc to do this, assuming that your objective is to compute a line integral of the pressure on the GLL points. Assuming that your pipe mesh was made by sweeping the geometry in the z direction with n2to3, the modification should be quite easy. The routine I would start with would be drgtrq in navier5.f, which I see uses the two-index loop to traverse faces based on jskip1 and jskip2. For your case, I would use the facind() 3 index loop approach (e.g., as used in norcmp2 routine). Then you track the outer "k" loop and accumulate one value for each k value and for each z level of the elements. You will know the z level because it will be: klevel_e = 1 + (eg-1)/nelxy where nelxy is the number of elements in your pipe cross section. Hopefully this will get you pointed in the right direction... Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:13:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integral on the wall Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat May 12 05:56:45 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 12 May 2018 10:56:45 +0000 Subject: [Nek5000-users] Integral on the wall In-Reply-To: References: , , , , Message-ID: Dear Valerio, Just modify the routine I sent to compute the average, but now weight the average by unx to get the x-component. Do the same with uny for y, and unz for z. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Saturday, May 12, 2018 5:44:50 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Integral on the wall Dear Paul, using the subroutine in zfunc.f I got the value of the pressure averaged on the surface. However I would like to compute the force on the wall as the line integral of the pressure times the normal (maybe my first question was unclear). Do you think this can be achieved modifying a bit the subroutine in zfunc.f or should I do it from scratch? Thanks. Best, Valerio ________________________________ Da: Nek5000-users per conto di nek5000-users at lists.mcs.anl.gov Inviato: mercoled? 9 maggio 2018 15:11 A: nek5000-users at lists.mcs.anl.gov Oggetto: Re: [Nek5000-users] Integral on the wall Dear Paul, Thank you for the help, I will test the routine zfunc. Best, Valerio ________________________________ Da: Nek5000-users per conto di nek5000-users at lists.mcs.anl.gov Inviato: mercoled? 9 maggio 2018 15:05 A: nek5000-users at lists.mcs.anl.gov Oggetto: Re: [Nek5000-users] Integral on the wall Dear Valerio, I've not tested or even compiled the attached code... But it should be fairly close to being functional. The idea would be to pass in the pressure on mesh 1, which means you need to interpolate from pr to pm1 ---- there are several routines floating around to do this. Please let me know if you have any questions and if you are able to make this routine work. Best, Paul PS - note that you should be able to send in "zm1" to this routine and get back the correct z distribution. This is what I would do if I wished to plot pr vs z. Also, you might want to dsavg() pm1 if you want a continuous pressure estimate. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 5:55:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Integral on the wall Dear Valerio, You would need to modify torque calc to do this, assuming that your objective is to compute a line integral of the pressure on the GLL points. Assuming that your pipe mesh was made by sweeping the geometry in the z direction with n2to3, the modification should be quite easy. The routine I would start with would be drgtrq in navier5.f, which I see uses the two-index loop to traverse faces based on jskip1 and jskip2. For your case, I would use the facind() 3 index loop approach (e.g., as used in norcmp2 routine). Then you track the outer "k" loop and accumulate one value for each k value and for each z level of the elements. You will know the z level because it will be: klevel_e = 1 + (eg-1)/nelxy where nelxy is the number of elements in your pipe cross section. Hopefully this will get you pointed in the right direction... Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 9, 2018 3:13:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integral on the wall Dear all, I want to compute the integral of the pressure on pipe wall at different cross-sections. I tried using the routine set_obj, setting as many objects as the number of elements along the pipe length and then using the routine torque_calc. However I would like to compute it on each circumference where GLL nodes are defined, for example if I use lx1 = 8 I would like to compute it on 8 cross-sections per element. Is there an efficient way to do this using the set_obj routine? Thanks. Best regards. Valerio -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 14 17:26:23 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 May 2018 18:26:23 -0400 Subject: [Nek5000-users] Temperature Perturbation Zone Message-ID: Hi, I'm setting a 3D box to perform natural convection problems in a closed cavity. After trying several method i can't manage to define a zone with a variable temperature perturbation in the usrchk() routine. Let's say, that temp = temp + A*sin(w*time) in a square of boundaries [x_min, x_max] x [y_min, y_max] x [z_min, z_max] for x, y, z. Any advice for implementing this? Regards, *Nicol?s Andr?s ?rdenes Leiva* Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 14 18:15:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 May 2018 23:15:24 +0000 Subject: [Nek5000-users] Temperature Perturbation Zone In-Reply-To: References: Message-ID: Dear Nicolas, For time-dependent boundary conditions, you could use something like the expression you have in your email. You would need "t " ( "tee" space space) for the thermal boundary conditions in your .rea or .box file. Please let me know if this solves your problem. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, May 14, 2018 5:26:23 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Temperature Perturbation Zone Hi, I'm setting a 3D box to perform natural convection problems in a closed cavity. After trying several method i can't manage to define a zone with a variable temperature perturbation in the usrchk() routine. Let's say, that temp = temp + A*sin(w*time) in a square of boundaries [x_min, x_max] x [y_min, y_max] x [z_min, z_max] for x, y, z. Any advice for implementing this? Regards, Nicol?s Andr?s ?rdenes Leiva Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 14 20:21:28 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 May 2018 21:21:28 -0400 Subject: [Nek5000-users] Temperature Perturbation Zone In-Reply-To: References: Message-ID: Hi Paul, It's not the boundary temperature what I'm trying to modify but a arbitrary zone inside the fluid domain. Boundary condition are 6 walls, 4 isolated and 2 with constant temperature, but that is already settled up. After reading some entries on the mailing list I tried this ----------------------------------------------------------------- subroutine userchk() include 'SIZE' include 'TOTAL' real period,amplitude,perturb real px1,px2,py1,py2 integer n amplitude = 1.2 period = 0.75 perturb = amplitude * sin( (2.0*pi/period)*time ) px1 = 0.25/2.0-0.05 px2 = 0.25/2.0+0.05 pz1 = 0.5-0.1 pz2 = 0.5+0.1 n = lx1*ly1*lz1*nelt do i=1,n x=xm1(i,1,1,1) y=ym1(i,1,1,1) z=zm1(i,1,1,1) if(x.ge.px1.and.x.le.px2)then if(z.ge.pz1.and.z.le.pz2)then (1) temp = temp + perturb ! Nothing happens (2) t = t + perturb ! WARNING: DIV(V)-QTL too large! endif endif end do return end ----------------------------------------------------------------- After running the simulations, with (1) I get the same results that without it; with (2) the solver indicates "WARNING: DIV(V)-QTL too large!" in every timestep, makes some really small timesteps (1e-5 sec. vs 1e-2) and doesn't seem to converge. I guess that the addition of the perturbation is bad defined. Nicol?s *Nicol?s Andr?s ?rdenes Leiva* Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 2018-05-14 19:15 GMT-04:00 : > Dear Nicolas, > > > For time-dependent boundary conditions, you could > > use something like the expression you have in your email. > > > You would need "t " ( "tee" space space) for the thermal > > boundary conditions in your .rea or .box file. > > > Please let me know if this solves your problem. > > > Paul > > > ------------------------------ > *From:* Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > *Sent:* Monday, May 14, 2018 5:26:23 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Temperature Perturbation Zone > > Hi, > > I'm setting a 3D box to perform natural convection problems in a closed > cavity. After trying several method i can't manage to define a zone with a > variable temperature perturbation in the usrchk() routine. > > Let's say, that temp = temp + A*sin(w*time) in a square of boundaries > [x_min, x_max] x [y_min, y_max] x [z_min, z_max] for x, y, z. > > Any advice for implementing this? > > Regards, > > *Nicol?s Andr?s ?rdenes Leiva* > > Estudiante de Ingenier?a Civil Mec?nica > Universidad T?cnica Federico Santa Mar?a > Tel: +56 9 7619 2857 > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 14 21:07:43 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 May 2018 02:07:43 +0000 Subject: [Nek5000-users] Temperature Perturbation Zone In-Reply-To: References: , Message-ID: Hi Nicolas, OK. You probably don't want to do that every time step (I'm just guessing...), but in any case, you would do it as written below. Best, Paul do i=1,n x=xm1(i,1,1,1) y=ym1(i,1,1,1) z=zm1(i,1,1,1) if(x.ge.px1.and.x.le.px2)then if(z.ge.pz1.and.z.le.pz2)then t(i,1,1,1,1) = t(i,1,1,1,1) + perturb endif endif end do ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, May 14, 2018 8:21:28 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Temperature Perturbation Zone Hi Paul, It's not the boundary temperature what I'm trying to modify but a arbitrary zone inside the fluid domain. Boundary condition are 6 walls, 4 isolated and 2 with constant temperature, but that is already settled up. After reading some entries on the mailing list I tried this ----------------------------------------------------------------- subroutine userchk() include 'SIZE' include 'TOTAL' real period,amplitude,perturb real px1,px2,py1,py2 integer n amplitude = 1.2 period = 0.75 perturb = amplitude * sin( (2.0*pi/period)*time ) px1 = 0.25/2.0-0.05 px2 = 0.25/2.0+0.05 pz1 = 0.5-0.1 pz2 = 0.5+0.1 n = lx1*ly1*lz1*nelt do i=1,n x=xm1(i,1,1,1) y=ym1(i,1,1,1) z=zm1(i,1,1,1) if(x.ge.px1.and.x.le.px2)then if(z.ge.pz1.and.z.le.pz2)then (1) temp = temp + perturb ! Nothing happens (2) t = t + perturb ! WARNING: DIV(V)-QTL too large! endif endif end do return end ----------------------------------------------------------------- After running the simulations, with (1) I get the same results that without it; with (2) the solver indicates "WARNING: DIV(V)-QTL too large!" in every timestep, makes some really small timesteps (1e-5 sec. vs 1e-2) and doesn't seem to converge. I guess that the addition of the perturbation is bad defined. Nicol?s Nicol?s Andr?s ?rdenes Leiva Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 2018-05-14 19:15 GMT-04:00 >: Dear Nicolas, For time-dependent boundary conditions, you could use something like the expression you have in your email. You would need "t " ( "tee" space space) for the thermal boundary conditions in your .rea or .box file. Please let me know if this solves your problem. Paul ________________________________ From: Nek5000-users > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Monday, May 14, 2018 5:26:23 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Temperature Perturbation Zone Hi, I'm setting a 3D box to perform natural convection problems in a closed cavity. After trying several method i can't manage to define a zone with a variable temperature perturbation in the usrchk() routine. Let's say, that temp = temp + A*sin(w*time) in a square of boundaries [x_min, x_max] x [y_min, y_max] x [z_min, z_max] for x, y, z. Any advice for implementing this? Regards, Nicol?s Andr?s ?rdenes Leiva Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 15 00:48:43 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 May 2018 13:48:43 +0800 Subject: [Nek5000-users] hillp tutorial case, minimal updates are needed. Message-ID: Dear all, This is really not a major problem at all, although I believe is good to mention it in order to keep your documentation up-to-date as possible. I was able to run the tutorial case hillp by reading the instructions in the documentation. Nevertheless, it seems that the tutorial notes have not been updated to the latest version of Nek5000, and there are small difference from what is written in the ?code? blocks and within the general template-files copied from the installation. So, I suggest you to take a look into this small differences and update the tutorial accordingly. Also, the setting for: targetCFL is missing in the tutorial notes. I suggest to add the suggested setting for this variable within the ?code? block. Many thanks, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 57128 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue May 15 12:29:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 May 2018 17:29:42 +0000 Subject: [Nek5000-users] hillp tutorial case, minimal updates are needed. In-Reply-To: References: Message-ID: Alexis, Thanks, we appreciate your feedback. The tutorial has been updated accordingly. For future reference, we encourage any user to submit issues with documentation through github at https://github.com/Nek5000/NekDoc -Dillon From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, May 15, 2018 12:49 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] hillp tutorial case, minimal updates are needed. Dear all, This is really not a major problem at all, although I believe is good to mention it in order to keep your documentation up-to-date as possible. I was able to run the tutorial case hillp by reading the instructions in the documentation. Nevertheless, it seems that the tutorial notes have not been updated to the latest version of Nek5000, and there are small difference from what is written in the ?code? blocks and within the general template-files copied from the installation. So, I suggest you to take a look into this small differences and update the tutorial accordingly. Also, the setting for: targetCFL is missing in the tutorial notes. I suggest to add the suggested setting for this variable within the ?code? block. Many thanks, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au [cid:image001.png at 01D3EC3D.91780B00] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 57128 bytes Desc: image001.png URL: From nek5000-users at lists.mcs.anl.gov Wed May 16 03:34:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 May 2018 08:34:42 +0000 Subject: [Nek5000-users] gmers solver issue Message-ID: Hello, I trying to run the DNS of a pipe-like configuration with NEK-5000 but I'm facing some issues that I cannot fully understand. More specifically, I am using the PN-PN formulation and the simulation slows down drastically after certain time. I have observed that when this happens the number of GMRES iteration for the pressure solver increases (from 50 at the beginning of the simulation to 170) and the norm of the divergence of the velocity increases and I get a WARNING DIV(V)-QTL to large (~ 1.2E-1). The problem appeared initially using a 3rd order polynomial, but even using higher order (9 th) does not solve the issue. Do you have some hints about the nature of this issue? Kind regards, Dante -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 16 08:38:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 May 2018 15:38:39 +0200 Subject: [Nek5000-users] gmers solver issue In-Reply-To: References: Message-ID: Can you please provide a link to your logfile. This makes it easier for us to understand what's going wrong. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 16th May 2018 15:36 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] gmers solver issue > > Hello, > I trying to run the DNS of a pipe-like configuration with NEK-5000 ?but Im facing some issues that I cannot fully understand. > More specifically, I am using the PN-PN formulation and the simulation slows down drastically after certain time. I have observed that when > this? happens the number of GMRES iteration for the pressure solver increases (from 50 at the beginning of the simulation to 170) > and the norm of the divergence of the velocity increases and I get a WARNING DIV(V)-QTL to large (~ 1.2E-1). > The problem appeared initially using a 3rd order polynomial, but even using higher order (9 > th) does not solve the issue. > Do you have some hints about the nature of this issue? > Kind regards, > Dante > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed May 16 08:40:22 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 May 2018 13:40:22 +0000 Subject: [Nek5000-users] gmers solver issue In-Reply-To: References: Message-ID: Hi Dante, A few questions - Do you have the pressure projection turned on? (p93-95) What is your iteration tolerance (p22, divergence) ? Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 16, 2018 3:34:42 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] gmers solver issue Hello, I trying to run the DNS of a pipe-like configuration with NEK-5000 but I?m facing some issues that I cannot fully understand. More specifically, I am using the PN-PN formulation and the simulation slows down drastically after certain time. I have observed that when this happens the number of GMRES iteration for the pressure solver increases (from 50 at the beginning of the simulation to 170) and the norm of the divergence of the velocity increases and I get a WARNING DIV(V)-QTL to large (~ 1.2E-1). The problem appeared initially using a 3rd order polynomial, but even using higher order (9 th) does not solve the issue. Do you have some hints about the nature of this issue? Kind regards, Dante -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 16 15:17:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 May 2018 22:17:19 +0200 Subject: [Nek5000-users] gmers solver issue Message-ID: Hi, >> Do you have the pressure projection turned on? (p93-95) I am using P93=P94=P95=0, because when I was using the pressure projection I was getting NaN in the solver. Probably this is related to this issue: https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2017-October/004671.html >> What is your iteration tolerance (p22, divergence) ? At the moment I am using P21 = P22 = 1.0E-2 Kind regards Dante -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 17 10:43:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 May 2018 15:43:14 +0000 Subject: [Nek5000-users] Problem with Visit in-situ Message-ID: Dear all, I'm trying to do the Visit in-situ tutorial from this site: http://www.mcs.anl.gov/~oanam/old_page/index.php/Visit_in_situ I have Visit installed and I changed the makenek file appropriately. However, when I try to compile I get the following error error: /usr/local/visit/2.12.3/linux-x86_64/libsim/V2/lib/libsimV2f.a(visitfortransimV2interface.c.o): In function `VisItGetMixedVariable': /home/juandiego/Downloads/visit2.12.3/src/sim/V2/lib/visitfortransimV2interface.c:1759: undefined reference to `visitgetmixedvariable_' collect2: error: ld returned 1 exit status Does anyone know how to get around this so I can start using Libsim so I can post-process data in-situ? Additional information: I'm using GNU 5.4.0 compiler, the version of Nek5000 from the SVN repository. Thank you, Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 17 11:18:52 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 May 2018 12:18:52 -0400 Subject: [Nek5000-users] Temperature Perturbation Zone In-Reply-To: References: Message-ID: Hi Paul, That was exactly what I was looking for, although it didn't work the way I was expecting, so I defined the perturbation as a forced value instead. t(i,1,1,1,1) = perturb Thanks for your help. *Nicol?s Andr?s ?rdenes Leiva* Estudiante de Ingenier?a Civil Mec?nica Universidad T?cnica Federico Santa Mar?a Tel: +56 9 7619 2857 2018-05-14 22:07 GMT-04:00 : > > Hi Nicolas, > > > OK. You probably don't want to do that every time step (I'm just > guessing...), but in any case, you would do it as written below. > > > Best, Paul > > > do i=1,n > x=xm1(i,1,1,1) > y=ym1(i,1,1,1) > z=zm1(i,1,1,1) > > if(x.ge.px1.and.x.le.px2)then > if(z.ge.pz1.and.z.le.pz2)then > t(i,1,1,1,1) = t(i,1,1,1,1) + perturb > endif > endif > end do > ------------------------------ > *From:* Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > *Sent:* Monday, May 14, 2018 8:21:28 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] Temperature Perturbation Zone > > Hi Paul, > > It's not the boundary temperature what I'm trying to modify but a > arbitrary zone inside the fluid domain. Boundary condition are 6 walls, 4 > isolated and 2 with constant temperature, but that is already settled up. > > After reading some entries on the mailing list I tried this > > ----------------------------------------------------------------- > subroutine userchk() > > include 'SIZE' > include 'TOTAL' > > real period,amplitude,perturb > real px1,px2,py1,py2 > integer n > > amplitude = 1.2 > period = 0.75 > perturb = amplitude * sin( (2.0*pi/period)*time ) > > px1 = 0.25/2.0-0.05 > px2 = 0.25/2.0+0.05 > pz1 = 0.5-0.1 > pz2 = 0.5+0.1 > > n = lx1*ly1*lz1*nelt > > do i=1,n > x=xm1(i,1,1,1) > y=ym1(i,1,1,1) > z=zm1(i,1,1,1) > > if(x.ge.px1.and.x.le.px2)then > if(z.ge.pz1.and.z.le.pz2)then > (1) temp = temp + perturb ! Nothing happens > (2) t = t + perturb ! WARNING: DIV(V)-QTL > too large! > endif > endif > end do > > return > end > ----------------------------------------------------------------- > > After running the simulations, with (1) I get the same results that > without it; with (2) the solver indicates "WARNING: DIV(V)-QTL too large!" > in every timestep, makes some really small timesteps (1e-5 sec. vs 1e-2) > and doesn't seem to converge. > > I guess that the addition of the perturbation is bad defined. > > > > Nicol?s > > *Nicol?s Andr?s ?rdenes Leiva* > > Estudiante de Ingenier?a Civil Mec?nica > Universidad T?cnica Federico Santa Mar?a > Tel: +56 9 7619 2857 > > 2018-05-14 19:15 GMT-04:00 : > > Dear Nicolas, > > > For time-dependent boundary conditions, you could > > use something like the expression you have in your email. > > > You would need "t " ( "tee" space space) for the thermal > > boundary conditions in your .rea or .box file. > > > Please let me know if this solves your problem. > > > Paul > > > ------------------------------ > *From:* Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > *Sent:* Monday, May 14, 2018 5:26:23 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Temperature Perturbation Zone > > Hi, > > I'm setting a 3D box to perform natural convection problems in a closed > cavity. After trying several method i can't manage to define a zone with a > variable temperature perturbation in the usrchk() routine. > > Let's say, that temp = temp + A*sin(w*time) in a square of boundaries > [x_min, x_max] x [y_min, y_max] x [z_min, z_max] for x, y, z. > > Any advice for implementing this? > > Regards, > > *Nicol?s Andr?s ?rdenes Leiva* > > Estudiante de Ingenier?a Civil Mec?nica > Universidad T?cnica Federico Santa Mar?a > Tel: +56 9 7619 2857 > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri May 18 06:58:03 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 May 2018 13:58:03 +0200 Subject: [Nek5000-users] Curved boundary Message-ID: Hi all, I have a case with a curved boundary with SYM boundary condition, stress formulation and PN/PN. In the file core/bdry.f there is a function called CHKCBC, which checks the consistency of boundary conditions. In the latest release (mver=17.0.4), this routine requires stress formulation AND PN/PN-2 for a non-aligned boundary, whereas in mver=17.0.0 stress formulation with PN/PN was accepted. My question is whether this change was intentional? The test "IF ( .NOT.IFSTRS ) CALL CHKCBC" in function SETLOG in v17.0.0 was replaced by "if (ifstrs .and. .not.ifsplit) return" inside CHKCBC in v17.0.4. As a test, I commented out the check in CHKCBC, and the simulation seems to run just fine with stress formulation and PN/PN. Thanks, Carl Erik, FFI, Norway From nek5000-users at lists.mcs.anl.gov Fri May 18 07:24:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 May 2018 14:24:20 +0200 Subject: [Nek5000-users] Curved boundary Message-ID: Note, all triple digit versions like 17.0.4 and 17.0.0 are _internal_ development versions. The only official release up to now is v17.0 (available as tarball only). Anyway, yes even in v17.0 we disabled certain features for PnPn as some combinations are not yet supported or well tested. It's very likely that some of the might work out of the box but we offically we don't support them (at least for now). Stefan. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 18th May 2018 13:58 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Curved boundary > > Hi all, > > I have a case with a curved boundary with SYM boundary condition, stress > formulation and PN/PN. > > In the file core/bdry.f there is a function called CHKCBC, which checks > the consistency of boundary conditions. > > In the latest release (mver=17.0.4), this routine requires stress > formulation AND PN/PN-2 for a non-aligned boundary, whereas in > mver=17.0.0 stress formulation with PN/PN was accepted. > > My question is whether this change was intentional? > > The test > "IF ( .NOT.IFSTRS ) CALL CHKCBC" > in function SETLOG in v17.0.0 was replaced by > "if (ifstrs .and. .not.ifsplit) return" > inside CHKCBC in v17.0.4. > > As a test, I commented out the check in CHKCBC, and the simulation seems > to run just fine with stress formulation and PN/PN. > > Thanks, > Carl Erik, > FFI, Norway > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri May 18 07:51:27 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 May 2018 14:51:27 +0200 Subject: [Nek5000-users] Curved boundary In-Reply-To: References: Message-ID: Thank you, Stefan! The tarball v17.0 has version 17.0.4, so I suppose the 17.0.0 version I have was downloaded from github before the current v17.0 tarball (17.0.4) was available. As long as it seems to work for my application, I think I'll just keep the test disabled. If you want to consider enabling this feature again at a later time, I can give details about my case. (It is simply flow between two cylinders, where the inner is solid and the outer is SYM. We want the pressure field at the inner surface, thus the PN/PN.) Carl Erik On 05/18/2018 02:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > Note, all triple digit versions like 17.0.4 and 17.0.0 are _internal_ development versions. The only official release up to now is v17.0 (available as tarball only). Anyway, yes even in v17.0 we disabled certain features for PnPn as some combinations are not yet supported or well tested. It's very likely that some of the might work out of the box but we offically we don't support them (at least for now). > > Stefan. > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 18th May 2018 13:58 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Curved boundary >> >> Hi all, >> >> I have a case with a curved boundary with SYM boundary condition, stress >> formulation and PN/PN. >> >> In the file core/bdry.f there is a function called CHKCBC, which checks >> the consistency of boundary conditions. >> >> In the latest release (mver=17.0.4), this routine requires stress >> formulation AND PN/PN-2 for a non-aligned boundary, whereas in >> mver=17.0.0 stress formulation with PN/PN was accepted. >> >> My question is whether this change was intentional? >> >> The test >> "IF ( .NOT.IFSTRS ) CALL CHKCBC" >> in function SETLOG in v17.0.0 was replaced by >> "if (ifstrs .and. .not.ifsplit) return" >> inside CHKCBC in v17.0.4. >> >> As a test, I commented out the check in CHKCBC, and the simulation seems >> to run just fine with stress formulation and PN/PN. >> >> Thanks, >> Carl Erik, >> FFI, Norway >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri May 18 07:55:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 May 2018 14:55:30 +0200 Subject: [Nek5000-users] Curved boundary In-Reply-To: References: Message-ID: The official version number is printed to the logfile (v17.0). Note, mver is used for internal purposes only (e.g. compatability of makenek) It's on our list to support the full sress-formulation for PnPn. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 18th May 2018 14:51 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Curved boundary > > Thank you, Stefan! > > The tarball v17.0 has version 17.0.4, so I suppose the 17.0.0 version I > have was downloaded from github before the current v17.0 tarball > (17.0.4) was available. > > As long as it seems to work for my application, I think I'll just keep > the test disabled. If you want to consider enabling this feature again > at a later time, I can give details about my case. (It is simply flow > between two cylinders, where the inner is solid and the outer is SYM. We > want the pressure field at the inner surface, thus the PN/PN.) > > Carl Erik > > > > On 05/18/2018 02:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Note, all triple digit versions like 17.0.4 and 17.0.0 are _internal_ development versions. The only official release up to now is v17.0 (available as tarball only). Anyway, yes even in v17.0 we disabled certain features for PnPn as some combinations are not yet supported or well tested. It's very likely that some of the might work out of the box but we offically we don't support them (at least for now). > > > > Stefan. > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Friday 18th May 2018 13:58 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: [Nek5000-users] Curved boundary > >> > >> Hi all, > >> > >> I have a case with a curved boundary with SYM boundary condition, stress > >> formulation and PN/PN. > >> > >> In the file core/bdry.f there is a function called CHKCBC, which checks > >> the consistency of boundary conditions. > >> > >> In the latest release (mver=17.0.4), this routine requires stress > >> formulation AND PN/PN-2 for a non-aligned boundary, whereas in > >> mver=17.0.0 stress formulation with PN/PN was accepted. > >> > >> My question is whether this change was intentional? > >> > >> The test > >> "IF ( .NOT.IFSTRS ) CALL CHKCBC" > >> in function SETLOG in v17.0.0 was replaced by > >> "if (ifstrs .and. .not.ifsplit) return" > >> inside CHKCBC in v17.0.4. > >> > >> As a test, I commented out the check in CHKCBC, and the simulation seems > >> to run just fine with stress formulation and PN/PN. > >> > >> Thanks, > >> Carl Erik, > >> FFI, Norway > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri May 18 11:03:16 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 May 2018 16:03:16 +0000 Subject: [Nek5000-users] Problem with Visit in-situ Message-ID: Dear all, I downloaded the newest version of Nek5000 and the code compiles with Visit. I noticed the old version was missing the definition of the "visitgetmixedvariable" in the visit.f file. However, the code is still not working correctly. I'm using the eddy_uv as example. I am able to connect to the simulation using VisIt but when I try to add a pseudocolor plot of "x_velocity", VisIt throws the following error: Pseudocolor: () viewer: The pipeline object is being used improperly: The simulation returned a handle for an object other than a variable. The mesh is plotted correctly, but I cannot visualize anything else. Any ideas? Thanks, Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 21 04:12:21 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 May 2018 10:12:21 +0100 Subject: [Nek5000-users] mesh import options Message-ID: Hi all, Is exo2nek still the best way to import meshes with relatively complex geometries to nek5000? If yes, can someone please help me out regarding exo2nek import: 1. I made my mesh using Pointwise and exported to exodusII format, but exo2nek throws the following error: """ EXODUS: ERROR: Attempting to open the netcdf-4 file: 'pipe.exo' . Either the netcdf library does not support netcdf-4 or there is a filesystem or some other issue ERROR: cannot open file pipe.exo """ 2. I exported exodus from ICEM-CFD, here the error from exo2nek reads: """ element block id = 1 element type = HEX num_elem_in_block = 24500 num_nodes_per_elem = 8 ERROR: Only HEX27 elements are allowed in a 3D mesh! num_nodes_per_elem= 8 Note: The following floating-point exceptions are signalling: IEEE_DENORMAL """ 3. The popular option looks exporting exodus file from Gambit with hex27 elements, however I was not able to find Gambit meshing software. Is it open source now or comes in with Fluent? I've Fluent 18.0 license at my university. *Cheers,Vishal* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 21 04:26:56 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 May 2018 11:26:56 +0200 Subject: [Nek5000-users] mesh import options In-Reply-To: References: Message-ID: Can you try again using the latest MASTER on GitHub. We fixed recently an issue importing meshes from ICEM. Not sure if Pointwise works. This is something we need to test. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 21st May 2018 11:12 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] mesh import options > > Hi all, > > Is exo2nek still the best way to import meshes with relatively complex geometries to nek5000? > > If yes, can someone please help me out regarding exo2nek import: > > 1. I made my mesh using Pointwise and exported to exodusII format, but exo2nek throws the following error: > """ > EXODUS: ERROR: Attempting to open the netcdf-4 file: > ??? pipe.exo > ??? . Either the netcdf library does not support netcdf-4 or there is a filesystem or some other issue > ERROR: cannot open file pipe.exo > """ > > 2. I exported exodus from ICEM-CFD, here the error from exo2nek reads: > """ > element block id?? =??????? 1 > element type?????? = HEX???? > num_elem_in_block? =??? 24500 > num_nodes_per_elem =??????? 8 > ERROR: Only HEX27 elements are allowed in a 3D mesh! > num_nodes_per_elem=?? 8 > Note: The following floating-point exceptions are signalling: IEEE_DENORMAL > """ > 3. The popular option looks exporting exodus file from Gambit with hex27 elements, however I > was not able to find Gambit meshing software. Is it open source now or comes in with Fluent? > Ive Fluent 18.0 license at my university. > >
Cheers, > Vishal > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon May 21 07:01:50 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 May 2018 13:01:50 +0100 Subject: [Nek5000-users] ffx ffy ffz from current run Message-ID: Dear Paul, After last request email ( https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2018-March/005178.html), the ffz value of 0.01525 was obtained by 'grep volf logfile'. Then I used this value as ffz in usr file with changing para54 and 55 as 0 in the same time. The case was started from previous stop which is based on keeping flowrate. After long time running (delt t*=200), the streamwise velocity was decreased compared with previous running . May I know what I can do to get the turbulence and velocity back? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 21 07:53:17 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 May 2018 12:53:17 +0000 Subject: [Nek5000-users] ffx ffy ffz from current run In-Reply-To: References: Message-ID: Dear Zhai, I've also tested the procedure and did not have any difficulty. What, exactly, is your target Reynolds number? When you were running the fixed flow-rate case, what were the settings for ffx,ffy,ffz in your usr file? Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, May 21, 2018 7:01:50 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] ffx ffy ffz from current run Dear Paul, After last request email (https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2018-March/005178.html), the ffz value of 0.01525 was obtained by 'grep volf logfile'. Then I used this value as ffz in usr file with changing para54 and 55 as 0 in the same time. The case was started from previous stop which is based on keeping flowrate. After long time running (delt t*=200), the streamwise velocity was decreased compared with previous running . May I know what I can do to get the turbulence and velocity back? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon May 21 12:26:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 May 2018 18:26:30 +0100 Subject: [Nek5000-users] ffx ffy ffz from current run Message-ID: Hi Paul, The shear Reynolds number of my case is 361 which corresponding to 11700. Can you please have a look my attached usr file? https://drive.google.com/open?id=1hFLyRNQ55vXGcT9uyMNvVNt7kX6dBRXE Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 22 02:21:32 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 May 2018 15:21:32 +0800 Subject: [Nek5000-users] Mesh optimisation for the cylinder case ext_cyl Message-ID: Dear Nek5000 masters, I have been able to run the ext_cyl example. And, after postprocessing the case, it made me wonder if Nek5000 is able to run this case with a more optimized mesh? That is, refined just close to the cylinder and coarse away from it. Clearly, for this case, the refinement around the cylinder extends in sort of a ?+? shape away from the cylinder. This refinement away from the cylinder is not necessary, specially towards the sides and towards the upstream. But even in the downstream the mesh could be (ideally) a bit coarser. Some other CFD codes are able to handle this problem by accepting refinement of the mesh just close to the cylinder (obviously at the surface of the refinement an element from the coarser side becomes neighbour of two or more elements on the refined side). I?m wondering if Nek5000 is already capable of handling this kind of refinement (or possibly any other solution/trick {maybe lowering the order of the elements themselves}) in order to avoid this typical problem of excessive refinement where it?s not needed/desired? Wondering and hoping, indeed, because this problem may become serious for some other configurations, for example for an array of cylinders, which then my cause the mesh to be refined all over the domain and not just in the ?+? shape region. Thanks a lot, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au From: Alexis Espinosa Gayosso Date: Tuesday, 8 May 2018 at 4:46 pm To: Subject: Compiling Problems in "Running your very first simulation" Hello, The title of my thread is the same as for an already existing thread (26-Sept-2017) because: I receive very similar warning messages when compiling nek5000 (./maketools all). Lots of warnings! >From your answer on that thread it seems that you do not worry at all for the warning messages. Should we really not care about them? How to know which warnings are not of concern and which other are? Can you post your own .log file to see which warning messages are considered normal for you? Or how do you check everything went fine for the compilation? Anyway, I will start running the examples in order to learn about the usage of the code. And I guess any abnormality would appear there. Many thanks, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 57128 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 57129 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue May 22 08:50:41 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 May 2018 13:50:41 +0000 Subject: [Nek5000-users] Mesh optimisation for the cylinder case ext_cyl In-Reply-To: References: Message-ID: Dear Alexis, The ext_cyl demo was an early example of start-to-finish meshing for flow past a cylinder. It's certainly not the case that it is optimized---users have many options for building meshes that are optimized for their particular flow conditions as the elements may be connected in any unstructured way. We also have new mesh smoothing tools and a nonconforming overlapping domain capability that would allow for a fine mesh in the cylinder and cylinder wake with a relatively coarse mesh in the far field. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, May 22, 2018 2:21:32 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Mesh optimisation for the cylinder case ext_cyl Dear Nek5000 masters, I have been able to run the ext_cyl example. And, after postprocessing the case, it made me wonder if Nek5000 is able to run this case with a more optimized mesh? That is, refined just close to the cylinder and coarse away from it. Clearly, for this case, the refinement around the cylinder extends in sort of a ?+? shape away from the cylinder. This refinement away from the cylinder is not necessary, specially towards the sides and towards the upstream. But even in the downstream the mesh could be (ideally) a bit coarser. Some other CFD codes are able to handle this problem by accepting refinement of the mesh just close to the cylinder (obviously at the surface of the refinement an element from the coarser side becomes neighbour of two or more elements on the refined side). I?m wondering if Nek5000 is already capable of handling this kind of refinement (or possibly any other solution/trick {maybe lowering the order of the elements themselves}) in order to avoid this typical problem of excessive refinement where it?s not needed/desired? Wondering and hoping, indeed, because this problem may become serious for some other configurations, for example for an array of cylinders, which then my cause the mesh to be refined all over the domain and not just in the ?+? shape region. Thanks a lot, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au [cid:image001.png at 01D3F1E0.9083C740] From: Alexis Espinosa Gayosso Date: Tuesday, 8 May 2018 at 4:46 pm To: Subject: Compiling Problems in "Running your very first simulation" Hello, The title of my thread is the same as for an already existing thread (26-Sept-2017) because: I receive very similar warning messages when compiling nek5000 (./maketools all). Lots of warnings! >From your answer on that thread it seems that you do not worry at all for the warning messages. Should we really not care about them? How to know which warnings are not of concern and which other are? Can you post your own .log file to see which warning messages are considered normal for you? Or how do you check everything went fine for the compilation? Anyway, I will start running the examples in order to learn about the usage of the code. And I guess any abnormality would appear there. Many thanks, Alexis Dr Alexis Espinosa Supercomputing Specialist Pawsey Supercomputing Centre 26 Dick Perry Ave Kensington WA 6151 Australia Tel +61 xxxx xxxx Email alexis.espinosa at pawsey.org.au Web www.pawsey.org.au [cid:image002.png at 01D3F1E0.9083C740] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 57128 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 57129 bytes Desc: image002.png URL: From nek5000-users at lists.mcs.anl.gov Tue May 22 15:47:37 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 May 2018 16:47:37 -0400 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton Message-ID: Hey Neks, I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 23 04:50:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 May 2018 11:50:19 +0200 Subject: [Nek5000-users] dealias; mass matrix; interp_rstd Message-ID: Dear Neks, I solve \partial A/\partial t = \nabla^2 A + u x Curl A, where A = (s1,s2,s3) I solve three scalar equations with respective components of u x Curl A as forcing terms in qvol. I would like to compute the dealiased product of u x Curl A I build my code based on kov_stokes_test.usr and subroutines in induct.f I compute local curl, project curl and U onto fine mesh, perform product and project the product back to coarse mesh using interp_rstd However, I am not sure about the multiplication of mass matrices for the product in these subroutines. I attach my usr, rea and SIZE files. Your suggestions are welcome. Thanks, Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: conj_ht.rea Type: application/octet-stream Size: 304787 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: conj_ht.usr Type: application/octet-stream Size: 11669 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SIZE Type: application/octet-stream Size: 4155 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Wed May 23 07:37:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 May 2018 12:37:14 +0000 Subject: [Nek5000-users] dealias; mass matrix; interp_rstd In-Reply-To: References: Message-ID: Dear Sandeep, Look for routines intp_rst, grad_rstd, etc., and calls to them in convect.f and induct.f There are several routines that map onto the finer GL mesh from the base GLL mesh. The metrics, J*dr/dx, J*dr/dy, etc., are already on the fine mesh and collocated with the quadrature weight on that fine mesh when they are constructed (in set_dealias_rx in induct.f). The mathematics of these procedure is described in Sec. 3 of Stabilization of the spectral element method in convection dominated flows by recovery of skew-symmetry * Johan Malm, * Philipp Schlatter * Paul F. Fischer * Dan S. Henningson NOTE: After you create your nonlinear source term, you should divide the value each point x_{ijke} by bm1(i,j,k,e), because Nek multiplies the entry in qvol by bm1(i,j,k,e). In your case, however, you've already accounted for the mass matrix by incorporated the mass matrix on the fine-GL points. I would set up your u x nabla term via a call to userchk and store the result (already divided by bm1), then just dereference it inside qvol. via: subroutine qvol(i,j,k,eg) ... ... common /mynonlin/ s(lx1,ly1,lz1,lelt,ldim) integer e,eg e=gllel(eg) qvol=s(i,j,k,e,ifield-2) return end or something like that. The time step will all be correct and you will get 2nd or 3rd-order accuracy in time via Nek's standard BDFk/EXTk hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 23, 2018 4:50:19 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] dealias; mass matrix; interp_rstd Dear Neks, I solve \partial A/\partial t = \nabla^2 A + u x Curl A, where A = (s1,s2,s3) I solve three scalar equations with respective components of u x Curl A as forcing terms in qvol. I would like to compute the dealiased product of u x Curl A I build my code based on kov_stokes_test.usr and subroutines in induct.f I compute local curl, project curl and U onto fine mesh, perform product and project the product back to coarse mesh using interp_rstd However, I am not sure about the multiplication of mass matrices for the product in these subroutines. I attach my usr, rea and SIZE files. Your suggestions are welcome. Thanks, Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 24 23:55:40 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 25 May 2018 00:55:40 -0400 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: Hey all, Just following up on the query. Would appreciate any input. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee wrote: > Hey Neks, > > I have a forcing function which is in the form of a look up table in X-Y > cartesian grid. I would like to use this forcing function in the 2-D fluid > momentum equation that Nekton solves. Is there a way to do this in the .usr > file or elsewhere? > > Thanks, > Saikat > > > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat May 26 21:54:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 26 May 2018 20:54:20 -0600 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: Hi Saikat, You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. On Thu, May 24, 2018 at 10:55 PM, wrote: > Hey all, > > Just following up on the query. Would appreciate any input. > > Thanks, > Saikat > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee wrote: > >> Hey Neks, >> >> I have a forcing function which is in the form of a look up table in X-Y >> cartesian grid. I would like to use this forcing function in the 2-D fluid >> momentum equation that Nekton solves. Is there a way to do this in the .usr >> file or elsewhere? >> >> Thanks, >> Saikat >> >> >> >> Saikat Mukherjee, >> PhD Student, >> Paul Research Group - http://www.me.vt.edu/mpaul/ >> Engineering Science and Mechanics, >> Virginia Tech. >> > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 29 09:28:32 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 May 2018 16:28:32 +0200 (CEST) Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format Message-ID: Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 29 12:50:00 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 May 2018 19:50:00 +0200 Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format In-Reply-To: References: Message-ID: Sorry mshconvert is not a part of Nek5000 so we cannot offer any support. On 29 May 2018, at 16:33, "nek5000-users at lists.mcs.anl.gov " > wrote: Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 29 12:52:09 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 May 2018 17:52:09 +0000 Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format In-Reply-To: References: Message-ID: Can you export your mesh in an exodus format and use the exo2nek script to convert the mesh in a Nek5000 format? Marco On May 29, 2018, at 1:50 PM, nek5000-users at lists.mcs.anl.gov wrote: Sorry mshconvert is not a part of Nek5000 so we cannot offer any support. On 29 May 2018, at 16:33, "nek5000-users at lists.mcs.anl.gov" > wrote: Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue May 29 13:36:21 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 May 2018 18:36:21 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 26 In-Reply-To: References: Message-ID: Re: Converting problem from .msh to NEK5000 format 1. is your fluent mesh in binary format ? I think you should have it ascii format. 2. or, as an alternative, you should try exo2nek utility. if you have access to ICEM, you could import your mesh in ICEM, and export your mesh to exodus format. Then exo2nek will convert it to re2 format. Haomin (Kirk) Yuan ________________________________ From: Nek5000-users on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Tuesday, May 29, 2018 12:00:13 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 111, Issue 26 Send Nek5000-users mailing list submissions to nek5000-users at lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request at lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner at lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Converting problem from .msh to NEK5000 format (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 May 2018 16:28:32 +0200 (CEST) From: nek5000-users at lists.mcs.anl.gov To: nek5000-users Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format Message-ID: Content-Type: text/plain; charset="utf-8" Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ------------------------------ End of Nek5000-users Digest, Vol 111, Issue 26 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 03:02:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 10:02:42 +0200 (CEST) Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format In-Reply-To: References: Message-ID: Thanks. I will give a try. De: "nek5000-users" ?: "nek5000-users" Envoy?: Mardi 29 Mai 2018 19:52:09 Objet: Re: [Nek5000-users] Converting problem from .msh to NEK5000 format Can you export your mesh in an exodus format and use the exo2nek script to convert the mesh in a Nek5000 format? Marco On May 29, 2018, at 1:50 PM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: Sorry mshconvert is not a part of Nek5000 so we cannot offer any support. On 29 May 2018, at 16:33, " [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] " < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > wrote: BQ_BEGIN Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 03:07:36 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 10:07:36 +0200 (CEST) Subject: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 26 In-Reply-To: References: Message-ID: De: "nek5000-users" ?: "nek5000-users" Envoy?: Mardi 29 Mai 2018 20:36:21 Objet: Re: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 26 Re: Converting problem from .msh to NEK5000 format 1. is your fluent mesh in binary format ? I think you should have it ascii format. 2. or, as an alternative, you should try exo2nek utility. if you have access to ICEM, you could import your mesh in ICEM, and export your mesh to exodus format. Then exo2nek will convert it to re2 format. Answers to your question : 1. It is in ascii format 2. I will give a try for that. Thank you Sijo GEORGE From: Nek5000-users on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Tuesday, May 29, 2018 12:00:13 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 111, Issue 26 Send Nek5000-users mailing list submissions to nek5000-users at lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] or, via email, send a message with subject or body 'help' to nek5000-users-request at lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner at lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Converting problem from .msh to NEK5000 format (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 May 2018 16:28:32 +0200 (CEST) From: nek5000-users at lists.mcs.anl.gov To: nek5000-users Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format Message-ID: Content-Type: text/plain; charset="utf-8" Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE -------------- next part -------------- An HTML attachment was scrubbed... URL: < [ http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20180529/67eedc6b/attachment-0001.html | http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20180529/67eedc6b/attachment-0001.html ] > ------------------------------ Subject: Digest Footer _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] ------------------------------ End of Nek5000-users Digest, Vol 111, Issue 26 ********************************************** _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 04:56:55 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 11:56:55 +0200 (CEST) Subject: [Nek5000-users] Mesh conversion from exo to nek using exo2nek Message-ID: Hi Neks, I was trying to convert my mesh with exo format to NEK frmat using exo2nek tool from NEK5000. When I run exo2nek I am facing a trouble shown below: Could you please tell me what are the options that I have to solve this: exodus.exo is an EXODUSII file; version 0.00 I/O word size 8 database parameters: title = Created by ICEMCFD - EXODUS II Interface num_dim = 2 num_nodes = 296877 num_elem = 295536 num_elem_blk = 1 num_side_sets = 0 element block id = 1 element type = QUAD num_elem_in_block = 295536 num_nodes_per_elem = 4 ERROR: Only QUAD9 elements are allowed in a 2D mesh! num_nodes_per_elem= 4 Note: The following floating-point exceptions are signalling: IEEE_DENORMAL Thanks Sijo GEORGE -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 12:19:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 13:19:14 -0400 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: Hi, Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Sat, May 26, 2018 at 10:54 PM, wrote: > Hi Saikat, > > You can always do the reading from the look up table from .usr file, at > once then feed the data to your ffx ffy and ffz through a common block. > > On Thu, May 24, 2018 at 10:55 PM, wrote: > >> Hey all, >> >> Just following up on the query. Would appreciate any input. >> >> Thanks, >> Saikat >> >> Saikat Mukherjee, >> PhD Student, >> Paul Research Group - http://www.me.vt.edu/mpaul/ >> Engineering Science and Mechanics, >> Virginia Tech. >> >> On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee >> wrote: >> >>> Hey Neks, >>> >>> I have a forcing function which is in the form of a look up table in X-Y >>> cartesian grid. I would like to use this forcing function in the 2-D fluid >>> momentum equation that Nekton solves. Is there a way to do this in the .usr >>> file or elsewhere? >>> >>> Thanks, >>> Saikat >>> >>> >>> >>> Saikat Mukherjee, >>> PhD Student, >>> Paul Research Group - http://www.me.vt.edu/mpaul/ >>> Engineering Science and Mechanics, >>> Virginia Tech. >>> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 12:36:51 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 19:36:51 +0200 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton Message-ID: Let's consider ffx = f(x,y,z) here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. hth -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 30th May 2018 19:19 > To: nek5000-users > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > Hi, > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Sat, May 26, 2018 at 10:54 PM, > wrote: > Hi Saikat, > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > On Thu, May 24, 2018 at 10:55 PM, > wrote: > Hey all, > > Just following up on the query. Would appreciate any input. > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee > wrote: > Hey Neks, > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > Thanks, > Saikat > > >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed May 30 13:17:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 14:17:15 -0400 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: Hi, Thanks for the reply. My problem is f is given as a discrete data set described in finite difference grid. I want to interpolate this to 'ffx' like you said in my .usr file. Would like to know how to proceed. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Wed, May 30, 2018 at 1:36 PM, wrote: > Let's consider > > ffx = f(x,y,z) > > here f is an user function (something you have to provide) which get > evaluated at x,y,z (your grid points). Interpolation is required if f is > given by a discrete data set. > > hth > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 30th May 2018 19:19 > > To: nek5000-users > > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > > > Hi, > > > > Thanks for the reply. The look up table is in a finite difference grid. > Are you saying I can still feed it to the .usr file and it should be fine? > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ < > http://www.me.vt.edu/mpaul/> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Sat, May 26, 2018 at 10:54 PM, > wrote: > > Hi Saikat, > > > > You can always do the reading from the look up table from .usr file, at > once then feed the data to your ffx ffy and ffz through a common block. > > > > On Thu, May 24, 2018 at 10:55 PM, > wrote: > > Hey all, > > > > Just following up on the query. Would appreciate any input. > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ < > http://www.me.vt.edu/mpaul/> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee > wrote: > > Hey Neks, > > > > I have a forcing function which is in the form of a look up table in X-Y > cartesian grid. I would like to use this forcing function in the 2-D fluid > momentum equation that Nekton solves. Is there a way to do this in the .usr > file or elsewhere? > > > > Thanks, > > Saikat > > > > > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ < > http://www.me.vt.edu/mpaul/> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 13:48:16 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 20:48:16 +0200 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: What?s your question? How to do the interpolation in your function f? On 30 May 2018, at 20:17, "nek5000-users at lists.mcs.anl.gov " > wrote: Hi, Thanks for the reply. My problem is f is given as a discrete data set described in finite difference grid. I want to interpolate this to 'ffx' like you said in my .usr file. Would like to know how to proceed. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group -?http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Wed, May 30, 2018 at 1:36 PM, > wrote: Let's consider ffx = f(x,y,z) here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. hth -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 30th May 2018 19:19 > To: nek5000-users > > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > Hi, > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > Engineering Science and Mechanics, > Virginia Tech. > > On Sat, May 26, 2018 at 10:54 PM,? >> wrote: > Hi Saikat, > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > On Thu, May 24, 2018 at 10:55 PM,? >> wrote: > Hey all, > > Just following up on the query. Would appreciate any input. > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > Engineering Science and Mechanics, > Virginia Tech. > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee >> wrote: > Hey Neks, > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > Thanks, > Saikat > > >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > Engineering Science and Mechanics, > Virginia Tech. > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 14:25:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 15:25:24 -0400 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: The question is how to read in a discrete data set defined in a finite difference grid in 'ffx' or forcing in the .usr file. It seems like there will be some sort of interpolation to the spectral element grid. So yes, that is my question. Thank you, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Wed, May 30, 2018 at 2:48 PM, wrote: > What?s your question? How to do the interpolation in your function f? > > On 30 May 2018, at 20:17, "nek5000-users at lists.mcs.anl.gov" < > nek5000-users at lists.mcs.anl.gov> wrote: > > Hi, > > Thanks for the reply. My problem is f is given as a discrete data set > described in finite difference grid. I want to interpolate this to 'ffx' > like you said in my .usr file. Would like to know how to proceed. > > Thanks, > Saikat > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 1:36 PM, wrote: > >> Let's consider >> >> ffx = f(x,y,z) >> >> here f is an user function (something you have to provide) which get >> evaluated at x,y,z (your grid points). Interpolation is required if f is >> given by a discrete data set. >> >> hth >> >> >> -----Original message----- >> > From:nek5000-users at lists.mcs.anl.gov >> > Sent: Wednesday 30th May 2018 19:19 >> > To: nek5000-users >> > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton >> > >> > Hi, >> > >> > Thanks for the reply. The look up table is in a finite difference grid. >> Are you saying I can still feed it to the .usr file and it should be fine? >> > >> > Thanks, >> > Saikat >> >
Saikat Mukherjee, >> > PhD Student, >> > Paul Research Group - http://www.me.vt.edu/mpaul/ < >> http://www.me.vt.edu/mpaul/> >> > Engineering Science and Mechanics, >> > Virginia Tech. >> > >> > On Sat, May 26, 2018 at 10:54 PM, > > wrote: >> > Hi Saikat, >> > >> > You can always do the reading from the look up table from .usr file, at >> once then feed the data to your ffx ffy and ffz through a common block. >> > >> > On Thu, May 24, 2018 at 10:55 PM, > > wrote: >> > Hey all, >> > >> > Just following up on the query. Would appreciate any input. >> > >> > Thanks, >> > Saikat >> >
Saikat Mukherjee, >> > PhD Student, >> > Paul Research Group - http://www.me.vt.edu/mpaul/ < >> http://www.me.vt.edu/mpaul/> >> > Engineering Science and Mechanics, >> > Virginia Tech. >> > >> > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee > > wrote: >> > Hey Neks, >> > >> > I have a forcing function which is in the form of a look up table in >> X-Y cartesian grid. I would like to use this forcing function in the 2-D >> fluid momentum equation that Nekton solves. Is there a way to do this in >> the .usr file or elsewhere? >> > >> > Thanks, >> > Saikat >> > >> > >> >
Saikat Mukherjee, >> > PhD Student, >> > Paul Research Group - http://www.me.vt.edu/mpaul/ < >> http://www.me.vt.edu/mpaul/> >> > Engineering Science and Mechanics, >> > Virginia Tech. >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> >> > >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed May 30 14:42:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 May 2018 21:42:14 +0200 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton Message-ID: There is nothing spectral element specific here. You could do e.g. a trilinear interpolation but that's something you have to code yourself. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 30th May 2018 21:26 > To: nek5000-users > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > The question is how to read in a discrete data set defined in a finite difference grid in ffx or forcing in the .usr file. It seems like there will be some sort of interpolation to the spectral element grid. So yes, that is my question. > > Thank you, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 2:48 PM, > wrote: > What?s your question? How to do the interpolation in your function f? > > On 30 May 2018, at 20:17, "nek5000-users at lists.mcs.anl.gov " > wrote: > > Hi, > > Thanks for the reply. My problem is f is given as a discrete data set described in finite difference grid. I want to interpolate this to ffx like you said in my .usr file. Would like to know how to proceed. > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group -?http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 1:36 PM, > wrote: > Lets consider > > ffx = f(x,y,z) > > here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. > > hth > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > > Sent: Wednesday 30th May 2018 19:19 > > To: nek5000-users > > > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > > > Hi, > > > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Sat, May 26, 2018 at 10:54 PM,? >> wrote: > > Hi Saikat, > > > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > > > On Thu, May 24, 2018 at 10:55 PM,? >> wrote: > > Hey all, > > > > Just following up on the query. Would appreciate any input. > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee >> wrote: > > Hey Neks, > > > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > > > Thanks, > > Saikat > > > > > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group -?http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu May 31 06:58:13 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 11:58:13 +0000 Subject: [Nek5000-users] Using Cartesian grid lookup table in Nekton In-Reply-To: References: Message-ID: Hi Saikat, How large is your finite-difference look up table? (1 million points? 1 billion? 1000?) If it's not too large you can just copy it onto each mpi rank and then call your own serial interpolation routine for each SEM point, x,y,z, and store the results into an array in a common block that you can then reference in users Presumably you'd have to do this interpolation only one time and then de-reference the values from the common block on each time step with fairly low overhead. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, May 30, 2018 2:42:14 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton There is nothing spectral element specific here. You could do e.g. a trilinear interpolation but that's something you have to code yourself. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 30th May 2018 21:26 > To: nek5000-users > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > The question is how to read in a discrete data set defined in a finite difference grid in ffx or forcing in the .usr file. It seems like there will be some sort of interpolation to the spectral element grid. So yes, that is my question. > > Thank you, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 2:48 PM, > wrote: > What?s your question? How to do the interpolation in your function f? > > On 30 May 2018, at 20:17, "nek5000-users at lists.mcs.anl.gov " > wrote: > > Hi, > > Thanks for the reply. My problem is f is given as a discrete data set described in finite difference grid. I want to interpolate this to ffx like you said in my .usr file. Would like to know how to proceed. > > Thanks, > Saikat >
Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 1:36 PM, > wrote: > Lets consider > > ffx = f(x,y,z) > > here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. > > hth > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > > Sent: Wednesday 30th May 2018 19:19 > > To: nek5000-users > > > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > > > Hi, > > > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Sat, May 26, 2018 at 10:54 PM, >> wrote: > > Hi Saikat, > > > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > > > On Thu, May 24, 2018 at 10:55 PM, >> wrote: > > Hey all, > > > > Just following up on the query. Would appreciate any input. > > > > Thanks, > > Saikat > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee >> wrote: > > Hey Neks, > > > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > > > Thanks, > > Saikat > > > > > >
Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ > > > Engineering Science and Mechanics, > > Virginia Tech. > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 07:50:13 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:50:13 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 07:52:40 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 12:52:40 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 07:56:36 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:56:36 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: Thank you . So here the 1,2,3,4 refers to the Side set numbers that we give as B.C in ICEM? Thank you very much Sijo De: "nek5000-users" ?: "nek5000-users" Envoy?: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 07:58:17 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 12:58:17 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: Yes, you are correct. 1, 2, .. are the boundary indices in your exodus file. The ?1? in bc(5,j,i,1) refers to the velocity field. Marco On May 31, 2018, at 8:56 AM, nek5000-users at lists.mcs.anl.gov wrote: Thank you . So here the 1,2,3,4 refers to the Side set numbers that we give as B.C in ICEM? Thank you very much Sijo ________________________________ De: "nek5000-users" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:00:46 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 15:00:46 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: Perfect. i will give a try Thanks Marco. De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 14:58:17 Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file Yes, you are correct. 1, 2, .. are the boundary indices in your exodus file. The ?1? in bc(5,j,i,1) refers to the velocity field. Marco On May 31, 2018, at 8:56 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: Thank you . So here the 1,2,3,4 refers to the Side set numbers that we give as B.C in ICEM? Thank you very much Sijo De: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:11:22 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 15:11:22 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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" ?: "nek5000-users" Envoy?: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:12:55 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 13:12:55 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:17:06 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 15:17:06 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: Thanks . I tried W on both sides but stil i get the same error. I also tried to convert re2 to rea but the converter did not work well. Could you please tell me what is this error? Thank you Sijo De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 15:12:55 Objet: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:22:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 13:22:49 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: , Message-ID: Did you generate a new map file after changing the BCs? This matters when switching periodic bcs on or off... Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:37:54 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 15:37:54 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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" ?: "nek5000-users" Envoy?: 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 on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:43:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 13:43:20 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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 > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:51:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 15:51:30 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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" ?: "nek5000-users" Envoy?: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 < [ mailto:nek5000-users-bounces at lists.mcs.anl.gov | nek5000-users-bounces at lists.mcs.anl.gov ] > on behalf of [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Sent: Thursday, May 31, 2018 8:12:55 AM To: [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 BQ_BEGIN On May 31, 2018, at 9:11 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 08:54:04 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 13:54:04 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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 > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:07:41 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 16:07:41 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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" ?: "nek5000-users" Envoy?: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 9:37 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 < [ mailto:nek5000-users-bounces at lists.mcs.anl.gov | nek5000-users-bounces at lists.mcs.anl.gov ] > on behalf of [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Sent: Thursday, May 31, 2018 8:12:55 AM To: [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 BQ_BEGIN On May 31, 2018, at 9:11 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:12:12 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:12:12 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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 > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:25:48 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 16:25:48 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: 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" ?: "nek5000-users" Envoy?: 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, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 9:51 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 9:37 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 < [ mailto:nek5000-users-bounces at lists.mcs.anl.gov | nek5000-users-bounces at lists.mcs.anl.gov ] > on behalf of [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Sent: Thursday, May 31, 2018 8:12:55 AM To: [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 BQ_BEGIN On May 31, 2018, at 9:11 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:28:59 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:28:59 +0000 Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: you have to add the print statement before you enter the if statements. Marco On May 31, 2018, at 10:25 AM, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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 > on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Thursday, May 31, 2018 8:12:55 AM To: nek5000-users at lists.mcs.anl.gov 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, nek5000-users at lists.mcs.anl.gov 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" > ?: "nek5000-users" > Envoy?: 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, nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:33:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:33:35 +0000 Subject: [Nek5000-users] studying materials to understand genmap code Message-ID: Hi Neks, I want to have a thorough understand of the genmap code, especially subroutine "periodic_vtx" and "rec_bisect". Do you know if there are some existing documents that can help me quickly understand those code? Thanks, Keke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:36:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 14:36:15 +0000 Subject: [Nek5000-users] Issue with visit In-situ Message-ID: Dear Neks, I was having issues visualizing pseudocolor plots when using VisIt in-situ processing with Nek5000. I talked to the developer of the Libsim library, Brad Whitlock, and he pointed out that the VISIT_ERROR handles in the "visit.f" should be changed to VISIT_INVALID_HANDLE. After doing this, I was able to visualize the pseudocolor plots. I tested it with Visit 2.10.2 and 2.12.3. I believe this should be changed in the code for correct functioning of in-situ processing. Thank you, Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:38:08 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 16:38:08 +0200 (CEST) Subject: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file In-Reply-To: References: Message-ID: Yes. The same results. Could you please tell me why there is a 5 on the bc(5,j,i,1)? And the value of bc(5,j,i,1) was zero for all the iteration. Thank you De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 16:28:59 Objet: Re: [Nek5000-users] How to give NEK5000 boundary conditions to exodus mesh file you have to add the print statement before you enter the if statements. Marco On May 31, 2018, at 10:25 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 10:07 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 9:51 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 9:37 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 < [ mailto:nek5000-users-bounces at lists.mcs.anl.gov | nek5000-users-bounces at lists.mcs.anl.gov ] > on behalf of [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Sent: Thursday, May 31, 2018 8:12:55 AM To: [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 BQ_BEGIN On May 31, 2018, at 9:11 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: 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 BQ_BEGIN On May 31, 2018, at 8:50 AM, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] 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 [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 09:37:37 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 16:37:37 +0200 Subject: [Nek5000-users] Issue with visit In-situ In-Reply-To: References: Message-ID: It would be great to receive a pull request with the proposed changes. -Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 31st May 2018 16:36 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Issue with visit In-situ > > Dear Neks, > > I was having issues visualizing pseudocolor plots when using VisIt in-situ processing with Nek5000. I talked to the developer of the Libsim library, Brad Whitlock, and he pointed out that the VISIT_ERROR handles in the > "visit.f" should be changed to VISIT_INVALID_HANDLE. After doing this, I was able to visualize the pseudocolor plots. I tested it with Visit 2.10.2 and 2.12.3.? > > I believe this should be changed in the code for correct functioning of in-situ processing. > > Thank you, > > Juan Diego > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu May 31 10:21:58 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:21:58 +0200 (CEST) Subject: [Nek5000-users] Conversion problem using exo2nek Message-ID: Hi, I read the informations regarding the BC from exo2nek folder of NEK5000. There it says the 5th argument of fluid bc array. But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) Could you please tell me if there is any problem with my conversion of exo2nek? Thank you Sijo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 10:25:47 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:25:47 +0200 Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: Can you post the exo2nek output? > On 31 May 2018, at 17:21, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, > > I read the informations regarding the BC from exo2nek folder of NEK5000. > > There it says the 5th argument of fluid bc array. > > But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) > > Could you please tell me if there is any problem with my conversion of exo2nek? > > Thank you > Sijo > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 10:39:47 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:39:47 +0200 (CEST) Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: I checked the exo2nek.f file and I try to see the outputs to see wether is there any side sets. Then i encountered that there is no side sets. But i believe that I gave the side set numbers correctly on ICEM. Anyway I am gonna try again. So please dont care about the previous .re2 file. and sorry for lots of emails. Thank you De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 17:25:47 Objet: Re: [Nek5000-users] Conversion problem using exo2nek Can you post the exo2nek output? On 31 May 2018, at 17:21, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: Hi, I read the informations regarding the BC from exo2nek folder of NEK5000. There it says the 5th argument of fluid bc array. But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) Could you please tell me if there is any problem with my conversion of exo2nek? Thank you Sijo _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 10:43:07 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:43:07 +0200 Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: Details about the side sets included in the exodus file are printed during exo2nek execution. If none are reported, then the problem is most likely in the ICEM export step. > On 31 May 2018, at 17:39, nek5000-users at lists.mcs.anl.gov wrote: > > I checked the exo2nek.f file and I try to see the outputs to see wether is there any side sets. Then i encountered that there is no side sets. But i believe that I gave the side set numbers correctly on ICEM. > > Anyway I am gonna try again. So please dont care about the previous .re2 file. and sorry for lots of emails. > > Thank you > > > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 31 Mai 2018 17:25:47 > Objet: Re: [Nek5000-users] Conversion problem using exo2nek > > Can you post the exo2nek output? > > On 31 May 2018, at 17:21, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, > > I read the informations regarding the BC from exo2nek folder of NEK5000. > > There it says the 5th argument of fluid bc array. > > But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) > > Could you please tell me if there is any problem with my conversion of exo2nek? > > Thank you > Sijo > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 10:47:28 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:47:28 +0200 (CEST) Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: yes you are right..it shows like this now : title = Created by ICEMCFD - EXODUS II Interface num_dim = 3 num_nodes = 9261 num_elem = 1000 num_elem_blk = 1 num_side_sets = 6 element block id = 1 element type = num_elem_in_block = 1000 num_nodes_per_elem = 27 side set 0 num_sides = 0 side set 0 num_sides = 0 side set 0 num_sides = 0 side set 0 num_sides = 0 side set 0 num_sides = 0 side set 0 num_sides = 0 QA records = Converting elements ... done :: Converting elements Converting SideSets ... Sideset 0 ... done :: Sideset 0 Sideset 0 ... done :: Sideset 0 Sideset 0 ... done :: Sideset 0 Sideset 0 ... done :: Sideset 0 Sideset 0 ... done :: Sideset 0 Sideset 0 ... done :: Sideset 0 done :: Converting SideSets De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 17:43:07 Objet: Re: [Nek5000-users] Conversion problem using exo2nek Details about the side sets included in the exodus file are printed during exo2nek execution. If none are reported, then the problem is most likely in the ICEM export step. On 31 May 2018, at 17:39, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: I checked the exo2nek.f file and I try to see the outputs to see wether is there any side sets. Then i encountered that there is no side sets. But i believe that I gave the side set numbers correctly on ICEM. Anyway I am gonna try again. So please dont care about the previous .re2 file. and sorry for lots of emails. Thank you De: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > ?: "nek5000-users" < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > Envoy?: Jeudi 31 Mai 2018 17:25:47 Objet: Re: [Nek5000-users] Conversion problem using exo2nek Can you post the exo2nek output? BQ_BEGIN On 31 May 2018, at 17:21, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: Hi, I read the informations regarding the BC from exo2nek folder of NEK5000. There it says the 5th argument of fluid bc array. But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) Could you please tell me if there is any problem with my conversion of exo2nek? Thank you Sijo _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users BQ_END _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 10:52:08 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 17:52:08 +0200 Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: Can you try again with the latest version available on GitHub. I know we fixed some importing issues from ICEM. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 31st May 2018 17:48 > To: nek5000-users > Subject: Re: [Nek5000-users] Conversion problem using exo2nek > > yes you are right..it shows like this now : > title???????? =? Created by ICEMCFD - EXODUS II Interface??????????????????????????????????????? > > num_dim?????? =??????? 3 > num_nodes???? =???? 9261 > num_elem????? =???? 1000 > num_elem_blk? =??????? 1 > num_side_sets =??????? 6 > > element block id?? =??????? 1 > element type?????? =???????? > num_elem_in_block? =???? 1000 > num_nodes_per_elem =?????? 27 > > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > > QA records = > ? > Converting elements ... > done :: Converting elements > > Converting SideSets ... > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > done :: Converting SideSets > > > ----------- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 31 Mai 2018 17:43:07 > Objet: Re: [Nek5000-users] Conversion problem using exo2nek > > Details about the side sets included in the exodus file are printed during exo2nek execution. > If none are reported, then the problem is most likely in the ICEM export step. >


On 31 May 2018, at 17:39, nek5000-users at lists.mcs.anl.gov wrote: >
I checked the exo2nek.f file and I try to see the outputs to see wether is there any side sets. Then i encountered that there is no side sets. But i believe that I gave the side set numbers correctly on ICEM.

Anyway I am gonna try again. So please dont care about the previous .re2 file. and sorry for lots of emails.

Thank you


----------- > De: "nek5000-users" >
?: "nek5000-users" >
Envoy?: Jeudi 31 Mai 2018 17:25:47
Objet: Re: [Nek5000-users] Conversion problem using exo2nek

Can you post the exo2nek output? >
On 31 May 2018, at 17:21, nek5000-users at lists.mcs.anl.gov wrote: >
Hi,

I read the informations regarding the BC from exo2nek folder of NEK5000.

There it says the 5th argument of fluid bc array.

But when I acces it throught the user file everything is zero it seems.? (like this bc(5,j,i,1) )

Could you please tell me if there is any problem with my conversion of exo2nek?

Thank you
Sijo
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https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users


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> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu May 31 11:20:16 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 16:20:16 +0000 Subject: [Nek5000-users] studying materials to understand genmap code In-Reply-To: References: Message-ID: Hi Keke, Please email me off list and I can explain more of the details to you. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, May 31, 2018 9:33:35 AM To: shivang agarwal Subject: [Nek5000-users] studying materials to understand genmap code Hi Neks, I want to have a thorough understand of the genmap code, especially subroutine "periodic_vtx" and "rec_bisect". Do you know if there are some existing documents that can help me quickly understand those code? Thanks, Keke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu May 31 12:02:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 31 May 2018 19:02:39 +0200 (CEST) Subject: [Nek5000-users] Conversion problem using exo2nek In-Reply-To: References: Message-ID: I tried and I think there is a problem. I am not able to figure it out where. Probably from ICEM to exodus or in exo2nek. Because I dont find the side set numbers while converting. Could yu please verify with any test cases if you have? Thank you ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 31 Mai 2018 17:52:08 Objet: Re: [Nek5000-users] Conversion problem using exo2nek Can you try again with the latest version available on GitHub. I know we fixed some importing issues from ICEM. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 31st May 2018 17:48 > To: nek5000-users > Subject: Re: [Nek5000-users] Conversion problem using exo2nek > > yes you are right..it shows like this now : > title???????? =? Created by ICEMCFD - EXODUS II Interface??????????????????????????????????????? > > num_dim?????? =??????? 3 > num_nodes???? =???? 9261 > num_elem????? =???? 1000 > num_elem_blk? =??????? 1 > num_side_sets =??????? 6 > > element block id?? =??????? 1 > element type?????? =???????? > num_elem_in_block? =???? 1000 > num_nodes_per_elem =?????? 27 > > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > side set? 0 num_sides =??????? 0 > > QA records = > ? > Converting elements ... > done :: Converting elements > > Converting SideSets ... > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > Sideset? 0 ... > done :: Sideset? 0 > > done :: Converting SideSets > > > ----------- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 31 Mai 2018 17:43:07 > Objet: Re: [Nek5000-users] Conversion problem using exo2nek > > Details about the side sets included in the exodus file are printed during exo2nek execution. > If none are reported, then the problem is most likely in the ICEM export step. >


On 31 May 2018, at 17:39, nek5000-users at lists.mcs.anl.gov wrote: >
I checked the exo2nek.f file and I try to see the outputs to see wether is there any side sets. Then i encountered that there is no side sets. But i believe that I gave the side set numbers correctly on ICEM.

Anyway I am gonna try again. So please dont care about the previous .re2 file. and sorry for lots of emails.

Thank you


----------- > De: "nek5000-users" >
?: "nek5000-users" >
Envoy?: Jeudi 31 Mai 2018 17:25:47
Objet: Re: [Nek5000-users] Conversion problem using exo2nek

Can you post the exo2nek output? >
On 31 May 2018, at 17:21, nek5000-users at lists.mcs.anl.gov wrote: >
Hi,

I read the informations regarding the BC from exo2nek folder of NEK5000.

There it says the 5th argument of fluid bc array.

But when I acces it throught the user file everything is zero it seems.? (like this bc(5,j,i,1) )

Could you please tell me if there is any problem with my conversion of exo2nek?

Thank you
Sijo
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> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu May 31 20:53:51 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 1 Jun 2018 09:53:51 +0800 Subject: [Nek5000-users] why I can`t change .rea with 2.1M elements to .re2 Message-ID: ? pipe.tar.gz ?hi,manager.I have a problam that I want to make a example with 2.1M elements but I can`t change .rea to .re2, and reatore2 will give me wrong answer as below: ------------------------------------------------------------------------------------------------------- Start converting ... read: **MESH DATA** 6 lines are X,Y,Z;X,Y,Z. Columns corners 1-4;5-8 Abort: number of elements too large 2100000 change MAXNEL and recompile ------------------------------------------------------------------------------------------------------- How to solve this problem? if I can`t change reatore2,when I run the example also have a wrong problem: ------------------------------------------------------------------------------------------------------- EXIT:Problem size requires .re2 ------------------------------------------------------------------------------------------------------- I have sent you my file..~!! -------------- next part -------------- An HTML attachment was scrubbed... URL: