From nek5000-users at lists.mcs.anl.gov Mon Oct 3 03:15:29 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 3 Oct 2016 08:15:29 +0000 Subject: [Nek5000-users] Dirichlet BC for scalars Message-ID: I am a new user of Nek, and am learning to possibilities of the program. I have successfully implemented a lid-driven cavity. I now want to, in addidtion, solve the problem for a scalar with certain boundary conditions (I did choose the temperature for this). I use the .box file: reafile.rea 2 2 # Box 1 -20 -20 0.0 1.0 1.0 0.0 1.0 1.0 W ,W ,W ,v , t ,t ,O ,I , Thus: the domains is a 2D 1x1 square where: * The y = 1 boundary is the "lid" whose velocity can be set in the .usr file (Dirichlet BC) * The vertical walls also have Dirichlet BC * The bottom wall is an "open boundary" for the temperature * The top wall is a n "insulator" for the temperature Given the .rea file generated with this .box file, I set the initial conditions in useric: subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=0.0 uy=0.0 uz=0.0 temp=0 return end I set the Dirichlet BC in userbc: subroutine userbc (ix,iy,iz,iside,ieg) c NOTE ::: This subroutine MAY NOT be called by every process include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=1 uy=0.0 uz=0.0 temp=x return end I expected this to initialize the velocity and temperature to zero in the entire domain, except for: * Top boundary has velocity 1 in the x-direction * The right boundary has temperature 1 But when I visualize the results of the simulation, I find that the temperature is set to "x" in the entire domain, not only at the boundarys that "should be set". However, the velocity boundary condition works as I expected, and is set only for the "v" boundaries. What am I doing wrong here? How may I set up dirichlet BC for the temperature? -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 5 08:03:33 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 5 Oct 2016 15:03:33 +0200 Subject: [Nek5000-users] Issue in 3D NEKNEK simulations Message-ID: Hi, I am coupling the Navier-Stokes and Darcy equations using the NekNek framework. Everything is working fine in 2D. However, any 3D example in neknek is stuck endlessly in the following line callmpi_send (jsend,len,mpi_byte,id ,100+nid, intercomm,ierr) within the "intpts_locate" subroutine in multimesh.f. When I modify the eddy_neknek test case given in the example folder, the behavior is the same, so the issue is not specific to my examples. I already checked that the problem is not the memory or the length of the data processed in MPI_send. Did anyone experience the same before? Thank you very much, Best regards, Sudhakar The Royal institute of Technology (KTH) -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 5 12:03:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 5 Oct 2016 10:03:36 -0700 Subject: [Nek5000-users] Issue in 3D NEKNEK simulations In-Reply-To: References: Message-ID: Hi Sudhakar, Thank you for sharing your experiences with using NekNek. We have run many 3D examples with it, and it has been working fine. Maybe, you can send your modification to an eddy_neknek case where you experience this problem offline, and we can look at it? Best regards, Yulia Peet -------------------------------------------------------------------------------------------- Yulia T. Peet Assistant Professor of Aerospace and Mechanical Engineering Arizona State University School for Engineering of Matter, Transport and Energy (SEMTE) Office: ERC 379 Tel: 480-965-0735 E-mail: ypeet at asu.edu Web: isim.asu.edu --------------------------------------------------------------------------------------------- On Wed, Oct 5, 2016 at 6:03 AM, wrote: > Hi, > > I am coupling the Navier-Stokes and Darcy equations using the NekNek > framework. Everything is working fine in 2D. However, any 3D example in > neknek is stuck endlessly in the following line > > call mpi_send (jsend,len,mpi_byte,id ,100+nid, intercomm,ierr) > > > within the "intpts_locate" subroutine in multimesh.f. When I modify the > eddy_neknek test case given in the example folder, the behavior is the > same, so the issue is not specific to my examples. I already checked that > the problem is not the memory or the length of the data processed in > MPI_send. Did anyone experience the same before? > > Thank you very much, > > Best regards, > > Sudhakar > > The Royal institute of Technology (KTH) > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- -------------------------------------------------------------------------------------------- Yulia T. Peet Assistant Professor of Aerospace and Mechanical Engineering Arizona State University School for Engineering of Matter, Transport and Energy (SEMTE) Office: ERC 379 Tel: 480-965-0735 E-mail: ypeet at asu.edu Web: isim.asu.edu --------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 04:59:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 09:59:24 +0000 Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation Message-ID: Dear Neks, I am trying to understand what is actually meant by an "open boundary" in Nek. Un the user documentation, eqn (4.5) sais that, for the temperature, it is grad(T) dot n = 0, where n is the normal to the boundary. Since the heat flux is q = - grad(T), I would rather interpret this as a zero flux boundary condition. And indeed, the insulated boundary described by equation (4.6) is identical to the open boundary condition. Is equation (4.5) a type-O or is the open boundary for the temperature actually the same as an insulated boundary? Also: Should not the open boundary condition for the "no-stress forumlation" also be given by the same expression as for the "stress-formulation" eqn (4.2)? Best Regards, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 04:41:35 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 06 Oct 2016 11:41:35 +0200 Subject: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2 In-Reply-To: References: Message-ID: Hi all, Sorry for the confusion in the first post. Any 3D Neknek simulation is stuck endlessly in the following line call mpi_send(jsend,len,mpi_byte,id,100+nid, intercomm,ierr) within "intpts_locate" subroutine in multimesh.f. Could anyone please share if you have experienced similar issues, and how can this be resolved? Thank you very much, Best regards, Sudhakar Quoting nek5000-users-request at lists.mcs.anl.gov: > 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. Issue in 3D NEKNEK simulations (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Oct 2016 15:03:33 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Issue in 3D NEKNEK simulations > Message-ID: > > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi, > > I am coupling the Navier-Stokes and Darcy equations using the NekNek > framework. Everything is working fine in 2D. However, any 3D example in > neknek is stuck endlessly in the following line > > callmpi_send > (jsend,len,mpi_byte,id > ,100+nid, > intercomm,ierr) > > within the "intpts_locate" subroutine in multimesh.f. When I modify the > eddy_neknek test case given in the example folder, the behavior is the > same, so the issue is not specific to my examples. I already checked > that the problem is not the memory or the length of the data processed > in MPI_send. Did anyone experience the same before? > > Thank you very much, > > Best regards, > > Sudhakar > > The Royal institute of Technology (KTH) > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > 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 92, Issue 2 > ******************************************** From nek5000-users at lists.mcs.anl.gov Thu Oct 6 05:40:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 10:40:42 +0000 Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation In-Reply-To: References: Message-ID: Dear Johan, The outflow boundary condition, 'O ', is indeed the same as 'I ' for the thermal problem since they both enforce grad T . nhat = 0. However, both also admit thermal flux by advection for cases where U . nhat is > 0, and that is the intent of outflow --- to allow thermal flux to be carried out. For velocity, the situation is a bit more delicate. To leading order, however, 'O ' imposes d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the viscous fluxes and Dirichlet for pressure. hth, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 4:59 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Neks, I am trying to understand what is actually meant by an "open boundary" in Nek. Un the user documentation, eqn (4.5) sais that, for the temperature, it is grad(T) dot n = 0, where n is the normal to the boundary. Since the heat flux is q = - grad(T), I would rather interpret this as a zero flux boundary condition. And indeed, the insulated boundary described by equation (4.6) is identical to the open boundary condition. Is equation (4.5) a type-O or is the open boundary for the temperature actually the same as an insulated boundary? Also: Should not the open boundary condition for the "no-stress forumlation" also be given by the same expression as for the "stress-formulation" eqn (4.2)? Best Regards, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 06:38:04 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 11:38:04 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2 In-Reply-To: References: , Message-ID: Dear Sudhakar, Thank you for bringing this to our attention. We're looking into it. The issue is that mpi_irecv is not posted prior to the mpi_send. This situation yields platform-dependent behavior. (We normally would write mpi_irecv(X) followed by mpi_send(Y) to X. We're currently working with the neknek group on a rewrite that will fix the problem. In the meantime, if you are targeting an HPC system, you might find that there is no issue on that system and in fact be able to proceed with your development. (We've had many people using neknek in the past on fairly large systems without running into the problem---but it is technically not correct as written and we're going to resolve it.) Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 4:41 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2 Hi all, Sorry for the confusion in the first post. Any 3D Neknek simulation is stuck endlessly in the following line call mpi_send(jsend,len,mpi_byte,id,100+nid, intercomm,ierr) within "intpts_locate" subroutine in multimesh.f. Could anyone please share if you have experienced similar issues, and how can this be resolved? Thank you very much, Best regards, Sudhakar Quoting nek5000-users-request at lists.mcs.anl.gov: > 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. Issue in 3D NEKNEK simulations (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Oct 2016 15:03:33 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Issue in 3D NEKNEK simulations > Message-ID: > > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi, > > I am coupling the Navier-Stokes and Darcy equations using the NekNek > framework. Everything is working fine in 2D. However, any 3D example in > neknek is stuck endlessly in the following line > > callmpi_send > (jsend,len,mpi_byte,id > ,100+nid, > intercomm,ierr) > > within the "intpts_locate" subroutine in multimesh.f. When I modify the > eddy_neknek test case given in the example folder, the behavior is the > same, so the issue is not specific to my examples. I already checked > that the problem is not the memory or the length of the data processed > in MPI_send. Did anyone experience the same before? > > Thank you very much, > > Best regards, > > Sudhakar > > The Royal institute of Technology (KTH) > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > 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 92, Issue 2 > ******************************************** _______________________________________________ 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 Oct 6 06:58:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 11:58:39 +0000 Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation In-Reply-To: References: , Message-ID: Thank you for a good answer! Just to clarify, is it in LaTeX written as this: (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? If the wall normal is in the z-direction, then the open boundary condition for the velocity is: d/dz u_z = 0? Best regards, Johan ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 6, 2016 12:40 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Johan, The outflow boundary condition, 'O ', is indeed the same as 'I ' for the thermal problem since they both enforce grad T . nhat = 0. However, both also admit thermal flux by advection for cases where U . nhat is > 0, and that is the intent of outflow --- to allow thermal flux to be carried out. For velocity, the situation is a bit more delicate. To leading order, however, 'O ' imposes d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the viscous fluxes and Dirichlet for pressure. hth, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 4:59 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Neks, I am trying to understand what is actually meant by an "open boundary" in Nek. Un the user documentation, eqn (4.5) sais that, for the temperature, it is grad(T) dot n = 0, where n is the normal to the boundary. Since the heat flux is q = - grad(T), I would rather interpret this as a zero flux boundary condition. And indeed, the insulated boundary described by equation (4.6) is identical to the open boundary condition. Is equation (4.5) a type-O or is the open boundary for the temperature actually the same as an insulated boundary? Also: Should not the open boundary condition for the "no-stress forumlation" also be given by the same expression as for the "stress-formulation" eqn (4.2)? Best Regards, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 07:22:03 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 12:22:03 +0000 Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation In-Reply-To: References: , , Message-ID: Dear Johan, Actually - I was mistaken. What we use is: d/dn (u_i) = 0 for i=1,...,3 We could however (and sometimes do) require Neumann only on the normal velocity component -- grad (phi) . nhat = 0 where phi = U . nhat The tangential components can be prescribed. That is the capability provided by the "on " BC. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 6:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Thank you for a good answer! Just to clarify, is it in LaTeX written as this: (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? If the wall normal is in the z-direction, then the open boundary condition for the velocity is: d/dz u_z = 0? Best regards, Johan ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 6, 2016 12:40 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Johan, The outflow boundary condition, 'O ', is indeed the same as 'I ' for the thermal problem since they both enforce grad T . nhat = 0. However, both also admit thermal flux by advection for cases where U . nhat is > 0, and that is the intent of outflow --- to allow thermal flux to be carried out. For velocity, the situation is a bit more delicate. To leading order, however, 'O ' imposes d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the viscous fluxes and Dirichlet for pressure. hth, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 4:59 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Neks, I am trying to understand what is actually meant by an "open boundary" in Nek. Un the user documentation, eqn (4.5) sais that, for the temperature, it is grad(T) dot n = 0, where n is the normal to the boundary. Since the heat flux is q = - grad(T), I would rather interpret this as a zero flux boundary condition. And indeed, the insulated boundary described by equation (4.6) is identical to the open boundary condition. Is equation (4.5) a type-O or is the open boundary for the temperature actually the same as an insulated boundary? Also: Should not the open boundary condition for the "no-stress forumlation" also be given by the same expression as for the "stress-formulation" eqn (4.2)? Best Regards, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 08:12:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 13:12:15 +0000 Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation In-Reply-To: References: , , , Message-ID: Thank you, this makes sense to me. /Johan ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 6, 2016 2:22 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Johan, Actually - I was mistaken. What we use is: d/dn (u_i) = 0 for i=1,...,3 We could however (and sometimes do) require Neumann only on the normal velocity component -- grad (phi) . nhat = 0 where phi = U . nhat The tangential components can be prescribed. That is the capability provided by the "on " BC. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 6:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Thank you for a good answer! Just to clarify, is it in LaTeX written as this: (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? If the wall normal is in the z-direction, then the open boundary condition for the velocity is: d/dz u_z = 0? Best regards, Johan ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 6, 2016 12:40 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Johan, The outflow boundary condition, 'O ', is indeed the same as 'I ' for the thermal problem since they both enforce grad T . nhat = 0. However, both also admit thermal flux by advection for cases where U . nhat is > 0, and that is the intent of outflow --- to allow thermal flux to be carried out. For velocity, the situation is a bit more delicate. To leading order, however, 'O ' imposes d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the viscous fluxes and Dirichlet for pressure. hth, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 4:59 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation Dear Neks, I am trying to understand what is actually meant by an "open boundary" in Nek. Un the user documentation, eqn (4.5) sais that, for the temperature, it is grad(T) dot n = 0, where n is the normal to the boundary. Since the heat flux is q = - grad(T), I would rather interpret this as a zero flux boundary condition. And indeed, the insulated boundary described by equation (4.6) is identical to the open boundary condition. Is equation (4.5) a type-O or is the open boundary for the temperature actually the same as an insulated boundary? Also: Should not the open boundary condition for the "no-stress forumlation" also be given by the same expression as for the "stress-formulation" eqn (4.2)? Best Regards, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 10:37:21 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 17:37:21 +0200 Subject: [Nek5000-users] userbc to set BC from velocity field computed in userchk Message-ID: Good afternoon Neks, I am trying to set boundary conditions from a velocity field computed in the userchk subroutine. The nature of the velocity field is defined as follows : real boundx(lx1,ly1,lz1,lelt) real boundy(lx1,ly1,lz1,lelt) real boundz(lx1,ly1,lz1,lelt) I was wondering what was the proper syntax to set the user defined Dirichlet velocity; is the following syntax in the userbc correct ? ux=boundx(ix,iy,iz,iside,ie) uy=boundy(ix,iy,iz,iside,ie) uz=boundz(ix,iy,iz,iside,ie) Thank you for your time, Best wishes, Arnold From nek5000-users at lists.mcs.anl.gov Thu Oct 6 10:41:19 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 11:41:19 -0400 Subject: [Nek5000-users] conjugate heat transfer with variable material properties Message-ID: Hey NEKS I am trying to run the conj HT example with variable properties where the density(param(1)), viscosity(param(2)), Cp(param(7)) and thermal conductivity(param(8)) are all functions of temperature. I have made functions for all of these in the .usr file. However, the program blows up. I am putting parts from the .usr file. please help subroutine uservp (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' if (ifield.eq.1) then param(1) = 298+(0.833/temp) param(2) = (-15.837*temp*temp)+(167.47*temp)+159.626 utrans = param(1) udiff = param(2) else param(7) = param(1)*((1.61*temp*temp)+(0.973*temp)+29.176) param(8) = (-0.00177*temp*temp)+(0.0279*temp)+0.02479 utrans = param(7) ! thermal properties udiff = param(8) if (ieg .gt. nelgv) then ! properties in the solid udiff = 0.1*param(8) ! conductivity utrans = 1.0 endif endif return end c----------------------------------------------------------------------- subroutine userf (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ffx = 0.0 ffy = 0.0 ffz = 0.0 return end c----------------------------------------------------------------------- subroutine userq (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' qvol = 0.0 if (ieg.gt.nelgv) qvol = 1.0 return end c----------------------------------------------------------------------- subroutine userbc (ix,iy,iz,iside,ieg) c NOTE ::: This subroutine MAY NOT be called by every process C Set boundary conditions include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 4.0 uy = 0.0 uz = 0.0 TINF = 298.0 temp = 1.0 return end c----------------------------------------------------------------------- subroutine useric (ix,iy,iz,ieg) C Set initial conditions include 'SIZE' include 'TOTAL' include 'NEKUSE' ux = 0.0 uy = 0.0 uz = 0.0 temp = 0.0 return end Apoorva Vinayak Rudra Graduate Research Assistant Department of Chemical Engineering City College of New York (CCNY) -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 6 11:43:47 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Oct 2016 16:43:47 +0000 Subject: [Nek5000-users] userbc to set BC from velocity field computed in userchk In-Reply-To: References: Message-ID: Hi Arnold, Correct syntax would be: subroutine userbc(i,j,k,f,eg) include 'SIZE' include 'TOTAL' YOUR COMMON BLOCK HERE (to pass boundx...) integer e,eg,f e = gllel(eg) ! To get the local element number ux = boundx(i,j,k,e) uy = boundy(i,j,k,e) uz = boundz(i,j,k,e) return end Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 06, 2016 10:37 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] userbc to set BC from velocity field computed in userchk Good afternoon Neks, I am trying to set boundary conditions from a velocity field computed in the userchk subroutine. The nature of the velocity field is defined as follows : real boundx(lx1,ly1,lz1,lelt) real boundy(lx1,ly1,lz1,lelt) real boundz(lx1,ly1,lz1,lelt) I was wondering what was the proper syntax to set the user defined Dirichlet velocity; is the following syntax in the userbc correct ? ux=boundx(ix,iy,iz,iside,ie) uy=boundy(ix,iy,iz,iside,ie) uz=boundz(ix,iy,iz,iside,ie) Thank you for your time, Best wishes, Arnold _______________________________________________ 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 Oct 6 16:03:40 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 06 Oct 2016 23:03:40 +0200 Subject: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 4 In-Reply-To: References: Message-ID: Dear Yulia and Paul, Thanks for your response regarding the Neknek issue. As Paul pointed out, the simulations are working fine in HPC environments. Best regards, Sudhakar. Quoting nek5000-users-request at lists.mcs.anl.gov: > 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: Nek5000-users Digest, Vol 92, Issue 2 > (nek5000-users at lists.mcs.anl.gov) > 2. Re: Open Boundary condition in NEK user Documentation > (nek5000-users at lists.mcs.anl.gov) > 3. Re: Open Boundary condition in NEK user Documentation > (nek5000-users at lists.mcs.anl.gov) > 4. Re: Open Boundary condition in NEK user Documentation > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 6 Oct 2016 11:38:04 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2 > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Dear Sudhakar, > > Thank you for bringing this to our attention. We're looking into it. > > The issue is that mpi_irecv is not posted prior to the mpi_send. > This situation yields platform-dependent behavior. (We normally would write > mpi_irecv(X) followed by mpi_send(Y) to X. > > We're currently working with the neknek group on a rewrite that > will fix the problem. In the meantime, if you are targeting an HPC system, > you might find that there is no issue on that system and in fact be able to > proceed with your development. (We've had many people using neknek in > the past on fairly large systems without running into the problem---but > it is technically not correct as written and we're going to resolve it.) > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 4:41 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2 > > Hi all, > > Sorry for the confusion in the first post. Any 3D Neknek simulation is > stuck endlessly in the following line > > call mpi_send(jsend,len,mpi_byte,id,100+nid, intercomm,ierr) > > within "intpts_locate" subroutine in multimesh.f. > > Could anyone please share if you have experienced similar issues, and > how can this be resolved? > Thank you very much, > > Best regards, > Sudhakar > > > Quoting nek5000-users-request at lists.mcs.anl.gov: > >> 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. Issue in 3D NEKNEK simulations (nek5000-users at lists.mcs.anl.gov) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 5 Oct 2016 15:03:33 +0200 >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Issue in 3D NEKNEK simulations >> Message-ID: >> >> Content-Type: text/plain; charset="utf-8"; Format="flowed" >> >> Hi, >> >> I am coupling the Navier-Stokes and Darcy equations using the NekNek >> framework. Everything is working fine in 2D. However, any 3D example in >> neknek is stuck endlessly in the following line >> >> callmpi_send >> (jsend,len,mpi_byte,id >> ,100+nid, >> intercomm,ierr) >> >> within the "intpts_locate" subroutine in multimesh.f. When I modify the >> eddy_neknek test case given in the example folder, the behavior is the >> same, so the issue is not specific to my examples. I already checked >> that the problem is not the memory or the length of the data processed >> in MPI_send. Did anyone experience the same before? >> >> Thank you very much, >> >> Best regards, >> >> Sudhakar >> >> The Royal institute of Technology (KTH) >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> _______________________________________________ >> 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 92, Issue 2 >> ******************************************** > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 2 > Date: Thu, 6 Oct 2016 11:58:39 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for a good answer! > > > Just to clarify, is it in LaTeX written as this: > > > (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? > > > If the wall normal is in the z-direction, then the open boundary > condition for the velocity is: > > > d/dz u_z = 0? > > > Best regards, > > > Johan > > > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Thursday, October 6, 2016 12:40 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Dear Johan, > > The outflow boundary condition, 'O ', is indeed the same as 'I ' > for the thermal problem > since they both enforce grad T . nhat = 0. > > However, both also admit thermal flux by advection for cases where U > . nhat is > 0, and that is > the intent of outflow --- to allow thermal flux to be carried out. > > For velocity, the situation is a bit more delicate. To leading > order, however, 'O ' imposes > d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the > viscous fluxes and Dirichlet > for pressure. > > hth, > > Paul > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 4:59 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation > > > Dear Neks, > > > I am trying to understand what is actually meant by an "open > boundary" in Nek. > > Un the user documentation, eqn (4.5) sais that, for the temperature, it is > > > grad(T) dot n = 0, where n is the normal to the boundary. > > > Since the heat flux is q = - grad(T), I would rather interpret this > as a zero flux boundary condition. > > > And indeed, the insulated boundary described by equation (4.6) is > identical to the open boundary condition. > > > Is equation (4.5) a type-O or is the open boundary for the > temperature actually the same as an insulated boundary? > > > Also: Should not the open boundary condition for the "no-stress > forumlation" also be given by the same expression as for the > "stress-formulation" eqn (4.2)? > > > Best Regards, > > > Johan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 3 > Date: Thu, 6 Oct 2016 12:22:03 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > Dear Johan, > > Actually - I was mistaken. > > What we use is: > > d/dn (u_i) = 0 > > for i=1,...,3 > > We could however (and sometimes do) require Neumann only on the > normal velocity component -- > > grad (phi) . nhat = 0 > > where phi = U . nhat > > The tangential components can be prescribed. That is the > capability provided by the "on " > BC. > > Paul > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 6:58 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Thank you for a good answer! > > > Just to clarify, is it in LaTeX written as this: > > > (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? > > > If the wall normal is in the z-direction, then the open boundary > condition for the velocity is: > > > d/dz u_z = 0? > > > Best regards, > > > Johan > > > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Thursday, October 6, 2016 12:40 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Dear Johan, > > The outflow boundary condition, 'O ', is indeed the same as 'I ' > for the thermal problem > since they both enforce grad T . nhat = 0. > > However, both also admit thermal flux by advection for cases where U > . nhat is > 0, and that is > the intent of outflow --- to allow thermal flux to be carried out. > > For velocity, the situation is a bit more delicate. To leading > order, however, 'O ' imposes > d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the > viscous fluxes and Dirichlet > for pressure. > > hth, > > Paul > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 4:59 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation > > > Dear Neks, > > > I am trying to understand what is actually meant by an "open > boundary" in Nek. > > Un the user documentation, eqn (4.5) sais that, for the temperature, it is > > > grad(T) dot n = 0, where n is the normal to the boundary. > > > Since the heat flux is q = - grad(T), I would rather interpret this > as a zero flux boundary condition. > > > And indeed, the insulated boundary described by equation (4.6) is > identical to the open boundary condition. > > > Is equation (4.5) a type-O or is the open boundary for the > temperature actually the same as an insulated boundary? > > > Also: Should not the open boundary condition for the "no-stress > forumlation" also be given by the same expression as for the > "stress-formulation" eqn (4.2)? > > > Best Regards, > > > Johan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 4 > Date: Thu, 6 Oct 2016 13:12:15 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you, > > > this makes sense to me. > > > /Johan > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Thursday, October 6, 2016 2:22 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Dear Johan, > > Actually - I was mistaken. > > What we use is: > > d/dn (u_i) = 0 > > for i=1,...,3 > > We could however (and sometimes do) require Neumann only on the > normal velocity component -- > > grad (phi) . nhat = 0 > > where phi = U . nhat > > The tangential components can be prescribed. That is the > capability provided by the "on " > BC. > > Paul > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 6:58 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Thank you for a good answer! > > > Just to clarify, is it in LaTeX written as this: > > > (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ? > > > If the wall normal is in the z-direction, then the open boundary > condition for the velocity is: > > > d/dz u_z = 0? > > > Best regards, > > > Johan > > > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Thursday, October 6, 2016 12:40 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Open Boundary condition in NEK user > Documentation > > > Dear Johan, > > The outflow boundary condition, 'O ', is indeed the same as 'I ' > for the thermal problem > since they both enforce grad T . nhat = 0. > > However, both also admit thermal flux by advection for cases where U > . nhat is > 0, and that is > the intent of outflow --- to allow thermal flux to be carried out. > > For velocity, the situation is a bit more delicate. To leading > order, however, 'O ' imposes > d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the > viscous fluxes and Dirichlet > for pressure. > > hth, > > Paul > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 4:59 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation > > > Dear Neks, > > > I am trying to understand what is actually meant by an "open > boundary" in Nek. > > Un the user documentation, eqn (4.5) sais that, for the temperature, it is > > > grad(T) dot n = 0, where n is the normal to the boundary. > > > Since the heat flux is q = - grad(T), I would rather interpret this > as a zero flux boundary condition. > > > And indeed, the insulated boundary described by equation (4.6) is > identical to the open boundary condition. > > > Is equation (4.5) a type-O or is the open boundary for the > temperature actually the same as an insulated boundary? > > > Also: Should not the open boundary condition for the "no-stress > forumlation" also be given by the same expression as for the > "stress-formulation" eqn (4.2)? > > > Best Regards, > > > Johan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > 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 92, Issue 4 > ******************************************** From nek5000-users at lists.mcs.anl.gov Fri Oct 7 04:31:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 7 Oct 2016 11:31:51 +0200 Subject: [Nek5000-users] userbc to set BC from velocity field computed in userchk In-Reply-To: References: Message-ID: Thank you for your quick answer! Best wishes, Arnold Le 06/10/2016 18:43, nek5000-users at lists.mcs.anl.gov a ?crit : > Hi Arnold, > > Correct syntax would be: > > subroutine userbc(i,j,k,f,eg) > include 'SIZE' > include 'TOTAL' > YOUR COMMON BLOCK HERE (to pass boundx...) > > integer e,eg,f > > e = gllel(eg) ! To get the local element number > > ux = boundx(i,j,k,e) > uy = boundy(i,j,k,e) > uz = boundz(i,j,k,e) > > return > end > > > Paul > > > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 06, 2016 10:37 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] userbc to set BC from velocity field computed in userchk > > Good afternoon Neks, > > I am trying to set boundary conditions from a velocity field computed in > the userchk subroutine. The nature of the velocity field is defined as > follows : > > real boundx(lx1,ly1,lz1,lelt) > real boundy(lx1,ly1,lz1,lelt) > real boundz(lx1,ly1,lz1,lelt) > > I was wondering what was the proper syntax to set the user defined > Dirichlet velocity; is the following syntax in the userbc correct ? > > ux=boundx(ix,iy,iz,iside,ie) > uy=boundy(ix,iy,iz,iside,ie) > uz=boundz(ix,iy,iz,iside,ie) > > Thank you for your time, > > Best wishes, > > Arnold > _______________________________________________ > 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 Mon Oct 10 03:20:09 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 10 Oct 2016 10:20:09 +0200 Subject: [Nek5000-users] Integrate velocity field along a line Message-ID: Good morning Neks! I was wondering if it possible to integrate a function over the boundary in the userchk. Let me develop : The domain is a box, I want to integrate the boundary velocity field (prescribed in userbc) at the wall (bottom boundary) : In latex it would be int_{bottom boundary } u_{bound}^2 + v_{bound}^2 + w_{bound}^2v dx_{bound} Is there a function like glsc3() that would allow me to do so? Thank you for your time, Best wishes, Arnold From nek5000-users at lists.mcs.anl.gov Mon Oct 10 08:41:58 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 10 Oct 2016 13:41:58 +0000 Subject: [Nek5000-users] Integrate velocity field along a line In-Reply-To: References: Message-ID: Hi Arnold, You have to decide which faces of elements belong to the boundary --- but here is a code that would integrate over all surfaces with "v " boundary conditions that you could us as an example. Paul common /mystuff/ v2(lx1*ly1*lz1*lelt) integer e,f n = nx1*ny1*nz1*nelt do i=1,n v2(i)=vx(i,1,1,1)**2+vy(i,1,1,1)**2+vz(i,1,1,1)**2 enddo v2surf = 0 do e=1,nelv ! Integrate over all surfaces with cbc='v ' do f=1,2*ndim if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) enddo enddo v2surf = glsum(v2surf,1) ! Sum across all processors Note that "area" is passed in the TOTAL common block, which I assume you are including in the routine. ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, October 10, 2016 3:20 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Integrate velocity field along a line Good morning Neks! I was wondering if it possible to integrate a function over the boundary in the userchk. Let me develop : The domain is a box, I want to integrate the boundary velocity field (prescribed in userbc) at the wall (bottom boundary) : In latex it would be int_{bottom boundary } u_{bound}^2 + v_{bound}^2 + w_{bound}^2v dx_{bound} Is there a function like glsc3() that would allow me to do so? Thank you for your time, Best wishes, Arnold _______________________________________________ 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 Oct 11 10:53:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 11 Oct 2016 12:53:42 -0300 Subject: [Nek5000-users] Vorticity In-Reply-To: References: Message-ID: Hi, I need to monitor the vorticity in a single point of my domain, i've already add comp_vort3() and hpts() to userchk but only get velocity, pressure and temperature in hpts.out file. How i could modify hpts subroutine to get vorticity as output?. Best regards, Nicol?s Thier From nek5000-users at lists.mcs.anl.gov Tue Oct 11 11:16:02 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 11 Oct 2016 16:16:02 +0000 Subject: [Nek5000-users] Vorticity In-Reply-To: References: , Message-ID: Hi Nicolas, You could look at the hemi.usr in the nekexamples directory. There you will see a routine: subroutine interp_v(uvw,xyz,n) that could be modified to get the vorticity at the point in question. If the point of interest is a grid point you could alternatively just print the value at that point --- but it's a bit of a pain to identify such points, particularly in parallel. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, October 11, 2016 10:53 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Vorticity Hi, I need to monitor the vorticity in a single point of my domain, i've already add comp_vort3() and hpts() to userchk but only get velocity, pressure and temperature in hpts.out file. How i could modify hpts subroutine to get vorticity as output?. Best regards, Nicol?s Thier _______________________________________________ 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 Oct 11 17:06:10 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 11 Oct 2016 18:06:10 -0400 Subject: [Nek5000-users] Problem reading in binary files in Postnek Message-ID: Hi everyone, I am having some problems importing my binary files into postnek. When I do I have some elements missing and I get this message in the terminal - postx window width and/or height > MAX_WINDOWW/H! -*-Helvetica-Medium-R-Normal--*-*-*-*-*-*-*-* NEKTON Version 2.6 Enter Session Name --Default= g40cond_as Beginning Session g40cond_as renaming SESSION.NAME SESSION.NAME~ Session name: g40cond_as renaming g40cond_as.plt01 g40cond_as.plt01~ LTRUNC: string: 28 Tue Oct 11 15:13:33 PDT 2016 Reading geometry from g40cond_as .rea XYZ Min,Max: -40.0000 40.0000 -40.0000 40.0000 0.00000 1.00000 3072 3017 1 TRYING TO READ BC 3072 3072 2 TRYING TO READ BC 3072 3072 3 TRYING TO READ BC 3072 3072 4 TRYING TO READ BC 3072 3072 5 TRYING TO READ BC LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E this is iffmat: F 6.0000000 E E I E E I E E I E E E E I E E E E E E E E E E E E E E E I E E I E E I E E E E I E E E E E E E E E E E E E opening file: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E this is param(66): 6.0000000 LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E WARNING: Could not open file. E E I E E I E E I E E E E I E E E E E E E E E E E E E ** ERROR ** Can't open file g40cond_as.his Resetting NX to 4. setwrk: F X PRESSURE ifnew_work: T F -33 1 T quant: PRESSURE derivative: E ( 64) wkmax,delt:PRESSURE 0.0000000 0.0000000 0.0000000 WORK - MAX,MIN: 0.0000 0.0000 wkmin: 0.0000E+00 1.5722E+01 1.5722E+01 7.5000E-01 1 wkmax: 0.0000E+00 1.5722E+01 1.5722E+01 7.5000E-01 1 Volume of domain: 0.00000 Integral of function: 0.00000 calling setquad locglob: 1 1 24576 locglob: 2 395 24576 locglob: 3 801 24576 locglob: 1 4005 24576 locglob: 2 4005 24576 locglob: 3 4005 24576 locglob: 1 4005 24576 locglob: 2 4005 24576 locglob: 3 4005 24576 done locglob_lexico: 4005 4005 24576 11044 36864 NEDGE!! THIS is nglob 91117 THIS IS MULT MAX 0.32749921 2.4454923 1.0000000 196608 calling setsrfp done setsrfp 11044 36864 NEDGE!! THIS is nglob 91117 THIS IS MULT MAX 0.32749921 2.4454923 1.0000000 196608 setwrk: T X PRESSURE ifnew_work: T T PRESSURE 1 1 T quant: PRESSURE derivative: E ( 64) wkmax,delt:PRESSURE 0.0000000 0.0000000 0.0000000 WORK - MAX,MIN: 0.0000 0.0000 wkmin: 0.0000E+00 1.5722E+01 1.5722E+01 7.5000E-01 1 wkmax: 0.0000E+00 1.5722E+01 1.5722E+01 7.5000E-01 1 Volume of domain: 5026.56 Integral of function: 0.00000 1 EXIT 2 CLEAR 3 PLOT 4 SET QUANTITY 5 SET LOCATION 6 SET PLOT FORMAT 7 SET TIME 8 SET ATTRIBUTE 9 SET SCREEN 10 SAVE STATE 11 MAKE MOVIE 12 OUTPUT FILE I believe I am using the latest version. And the parameter 66 is 4. I have also tried with 6, and it doesn't work. I am grateful for any suggestion. 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 Oct 12 01:56:33 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 12 Oct 2016 06:56:33 +0000 Subject: [Nek5000-users] Naiver-Stokes eigenfunctions on a sheared grid Message-ID: Hi All, Attached is a pdf that shows how element shearing affects the accuracy of the spectral element method (an extension of the Eddy example in Nek5000 repo). Thanks, Ketan Mittal -------------- next part -------------- A non-text attachment was scrubbed... Name: shear.pdf Type: application/pdf Size: 924929 bytes Desc: shear.pdf URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 14 11:07:52 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 14 Oct 2016 18:07:52 +0200 Subject: [Nek5000-users] HPTS issue Message-ID: Hi Neks, I have an issue with hpts-routine. As indicated, I have created a file with the list of points, indicating the number at the first line; in SIZE file I put lpart = number of point and in in .usr file i have called hpts(). In the output file I have only the values of time but there are no pressure and speed values. They are zeros. Can someone help me to understand what is going wrong here? Regards, Andrey -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 14 11:15:58 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 14 Oct 2016 16:15:58 +0000 Subject: [Nek5000-users] HPTS issue In-Reply-To: References: Message-ID: Hi Andrey, Have you looked at the hemi example ? It shows an example of calling interpolation routine (for purposes of Lagrangian particle tracking). Best, Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, October 14, 2016 11:07 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] HPTS issue Hi Neks, I have an issue with hpts-routine. As indicated, I have created a file with the list of points, indicating the number at the first line; in SIZE file I put lpart = number of point and in in .usr file i have called hpts(). In the output file I have only the values of time but there are no pressure and speed values. They are zeros. Can someone help me to understand what is going wrong here? Regards, Andrey -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 18 08:15:30 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 15:15:30 +0200 Subject: [Nek5000-users] fix_geom Message-ID: Hi Neks, Does anyone have any experience using the fix_geom routine? As I understand it, it is supposed to adjust the interior GLL points based on the perturbation to the element verticies/edges/faces using gordon hall. I am trying to use it for one of my cases but it doesn't seem to have any effect. What I do is adjust the locations of some boundary elements in usrdat2 and then call fix geom. Something like the following: subroutine usrdat2 call fix_naca call fix_geom end subroutine Where fix naca adjusts the GLL points on the wall surface to the closest point given by a naca profile. The internal points do not seem to change after I call fix_geom. I looked at the routine in navier5.f and it appears to me that the perturbation applied is always being set to zero (unless I understand it wrong). First xm1 is copied to xb, and then xm1 is subtracted from xb to find local displacements. And the same for y and z coordinates. Which should always result in zero local displacements...? So I guess the question is if things are working correctly and I am doing something wrong or if there is a bug in the routine? Regards, Prabal From nek5000-users at lists.mcs.anl.gov Tue Oct 18 08:24:34 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 13:24:34 +0000 Subject: [Nek5000-users] Grid to Grid interpolation Message-ID: Dear Neks, I'm having a bit problem with grid to grid interpolation. The g2gi worked well with my earlier case when I interpolated my flow field (300000 elements with 7th order polynomial) to a new geometry (800000 elements with 7th order polynomial). Now I'm interpolating another flow field (300000 elements with 9th order polynomial) to a new geometry (400000 elements with 9th order polynomial), however the interpolation hangs at the stage 'call findpts' and never moves on. I'm wondering what could cause the interpolation to hang at 'findpts'. I do have more grid points to handle in the new case but I also increased number of processors when running the case. Does anyone have idea on this issue? Or is there any parameter I forgot to tune for my new case? Looking forward to any comments. Thank you very much in advance. Best regards, Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 18 08:58:47 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 15:58:47 +0200 Subject: [Nek5000-users] Failure when changing geometry in usrdat2 In-Reply-To: References: Message-ID: Hi all, I am currently using Nek to look at the effect of convection in slightly varying geometries, e.g. I start with a basic grid and then deform it in usrdat2: call rescale_x(zm1,-ellip*r_out,ellip*r_out) param(59) = 1 r_out is the maximum value of the original grid in z-direction (glmax(zm1,n)) and ellip is some scale factor (usually <1). If I just use the original grid with no deformation, the whole case runs fine (as far as i have checked), but as soon as i introduce some deformation (ellip=0.9999 is enough), the code seems to not converge anymore, e.g. I get Starting time loop ... Step 1, t= 1.0000000E-04, DT= 1.0000000E-04, C= 0.000 0.0000E+00 0.0000E+00 Solving for heat Solving for fluid F T T Temperature/Passive scalar solution 1.0000000000000000E-008 p22 1 2 1 1 Helmholtz TEMP F: 9.1518E-01 4.0000E+00 1.0000E+00 1.0000E+04 1 Hmholtz TEMP: 0 9.1518E-01 9.1518E-01 4.0000E+00 1 1.0000E-04 1.0291E-01 Heat done 1.0000000000000000E-008 p22 1 1 1 1 Helmholtz VELX F: NaN 1.0000E-08 1.0000E-03 1.0000E+04 1 2 Helmholtz VELX F: NaN 1.0000E-08 1.0000E-03 1.0000E+04 1 3 Helmholtz VELX F: NaN 1.0000E-08 1.0000E-03 1.0000E+04 1 4 Helmholtz VELX F: NaN 1.0000E-08 1.0000E-03 1.0000E+04 (...) 1 100 **ERROR**: Failed in HMHOLTZ: VELZ NaN NaN 1.0000E-08 1 1.00000E-06 NaN NaN NaN 1 Divergence 2 1.00000E-06 NaN NaN NaN 1 Divergence 3 1.00000E-06 NaN NaN NaN 1 Divergence 4 1.00000E-06 NaN NaN NaN 1 Divergence (...) DT/DTCFL/DTFS/DTINIT 0.100E-01 0.500E-01 0.000E+00 0.100E-01 Step 2, t= 2.2000000E-04, DT= 1.2000000E-04, C=******* 7.9370E+00 7.9370E+00 Solving for heat Solving for fluid F T T 1.0000000000000000E-008 p22 2 2 2 2.2000E-04 4.9921E-02 Heat done 1.0000000000000000E-008 p22 2 1 1.0000000000000000E-008 p22 2 1 1.0000000000000000E-008 p22 2 1 2 U-PRES gmres: 120 NaN 1.0000E-06 NaN 1.6777E+00 4.4202E+00 2 DNORM, DIVEX NaN NaN 2 2.2000E-04 4.5553E+00 Fluid done numrec= 10 WARNING: DT<0 or DTFS<0 Reset DT and so on for the following time steps. The max/min velocity seems to be +- 0.990000E+22. I have run similar cases without a temperature field before (mechanical forcings) without any problems. Is there anything special I have to change when adding a temp. field? Cheers, Jan From nek5000-users at lists.mcs.anl.gov Tue Oct 18 11:37:06 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 16:37:06 +0000 Subject: [Nek5000-users] Compute spatial average pressure in a cross section Message-ID: Hello, I am running Nek to simulate the flow in a 7-pin bundle and I am trying to compute the pressure drop between the inlet and outlet of my geometry. Is there any example I can use as a start point? Thanks, Marco From nek5000-users at lists.mcs.anl.gov Tue Oct 18 11:59:45 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 16:59:45 +0000 Subject: [Nek5000-users] fix_geom In-Reply-To: References: Message-ID: Hi Prabal, fix_geom was designed to repair geometry that has small rips or tears --- I've just verified that it seems to do that for a 2x2 example in 2D (attached). To project boundary displacements into the domain, I would normally solve Laplace's equation, with high conductivity in the BL. The main reason is that if you have very thin Boundary Layer resolving elements then accommodating all of the deformation in the BL elements via Gordon-Hall will not suffice --- you have to push the displacement out to the second or third layer (or more) depending on how thin the elements are w.r.t. the displacement. I can post some code on how to do that if you wish. Best, Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, October 18, 2016 8:15 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] fix_geom Hi Neks, Does anyone have any experience using the fix_geom routine? As I understand it, it is supposed to adjust the interior GLL points based on the perturbation to the element verticies/edges/faces using gordon hall. I am trying to use it for one of my cases but it doesn't seem to have any effect. What I do is adjust the locations of some boundary elements in usrdat2 and then call fix geom. Something like the following: subroutine usrdat2 call fix_naca call fix_geom end subroutine Where fix naca adjusts the GLL points on the wall surface to the closest point given by a naca profile. The internal points do not seem to change after I call fix_geom. I looked at the routine in navier5.f and it appears to me that the perturbation applied is always being set to zero (unless I understand it wrong). First xm1 is copied to xb, and then xm1 is subtracted from xb to find local displacements. And the same for y and z coordinates. Which should always result in zero local displacements...? So I guess the question is if things are working correctly and I am doing something wrong or if there is a bug in the routine? Regards, Prabal _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- A non-text attachment was scrubbed... Name: t.tgz Type: application/x-gzip Size: 4082 bytes Desc: t.tgz URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 18 14:44:20 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Oct 2016 21:44:20 +0200 Subject: [Nek5000-users] fix_geom In-Reply-To: References: Message-ID: Hi Paul, Thanks for the clarification. I guess I misunderstood the purpose of the routine. The code would not be necessary. I think I have something that fits the bill. Thank you Regards, Prabal On 10/18/2016 06:59 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Prabal, > > fix_geom was designed to repair geometry that has small rips or tears --- > > I've just verified that it seems to do that for a 2x2 example in 2D (attached). > > To project boundary displacements into the domain, I would > normally solve Laplace's equation, with high conductivity in the BL. > > The main reason is that if you have very thin Boundary Layer > resolving elements then accommodating all of the deformation in the BL elements > via Gordon-Hall will not suffice --- you have to push the displacement out to the second > or third layer (or more) depending on how thin the elements are w.r.t. the displacement. > > I can post some code on how to do that if you wish. > > Best, > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Tuesday, October 18, 2016 8:15 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] fix_geom > > Hi Neks, > > Does anyone have any experience using the fix_geom routine? > > As I understand it, it is supposed to adjust the interior GLL points > based on the perturbation to the element verticies/edges/faces using > gordon hall. > > I am trying to use it for one of my cases but it doesn't seem to have > any effect. > > What I do is adjust the locations of some boundary elements in usrdat2 > and then call fix geom. Something like the following: > > subroutine usrdat2 > > call fix_naca > > call fix_geom > > end subroutine > > Where fix naca adjusts the GLL points on the wall surface to the closest > point given by a naca profile. The internal points do not seem to change > after I call fix_geom. > > I looked at the routine in navier5.f and it appears to me that the > perturbation applied is always being set to zero (unless I understand it > wrong). First xm1 is copied to xb, and then xm1 is subtracted from xb to > find local displacements. And the same for y and z coordinates. Which > should always result in zero local displacements...? > > So I guess the question is if things are working correctly and I am > doing something wrong or if there is a bug in the routine? > > Regards, > > Prabal > > > > > _______________________________________________ > 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 Oct 18 22:01:10 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 19 Oct 2016 11:01:10 +0800 (GMT+08:00) Subject: [Nek5000-users] 3D cylinder mesh converting error Message-ID: Hi! nek, I met a trouble in using the .msh to .rea convert program mshconvert. When I tried to convert a 3D cylindrical mesh, I input the command as follow: convert('cylRB.msh',curves={4:{'type':'C','radius':0.25 ,'depth': 4,'circle_center':(0,0,0)}},bcs={3:'W',4:'W'},temperature={3:'t',4:'I'}) and then an error appeared on the screen : /home/xbl/case/mshconvert.pyc in read_curved_sides(curves) 769 cell = max(face[2]) 770 nds = face[1] --> 771 cell_face_m.append((cell, face_map[cell][(nds[0], nds[1])], face_number)) 772 if curve['type'] == 'C': 773 for jj in range(curve['depth']): KeyError: (6741, 97) '4' in the command means that the curved surface in the mesh is zone 4,says the lateral surface of the cylinder. I succeeded in converting a 2D-circle mesh before, so I want to know how to input correct command for 3D case. Does anyone meet that kind of error ever? Any help is appreciated. regards, Xu -- Xu Bolun, University of Science and Technology of China, Hefei,Anhui,China -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 20 09:59:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 20 Oct 2016 10:59:51 -0400 Subject: [Nek5000-users] Genbox for expansion channel Message-ID: Hi, I would like to generate a mesh as Figure 2 in http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf My .box file should be XXX.rea 2 (spatial dimension) 1 (number of fields) Box 1 (channel) Then I am not sure how to choose the number of elements x0,x1,...y0,y1, and so on. Could you please help me? Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com From nek5000-users at lists.mcs.anl.gov Fri Oct 21 07:10:35 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 21 Oct 2016 14:10:35 +0200 Subject: [Nek5000-users] Failure when changing geometry in usrdat2 In-Reply-To: References: Message-ID: Just a short update. I have tried the following: -using PN-PN instead of PN-PN-2 -characteristic time stepping -fiddling with the projection parameters P094,P095 -turning off the convective forcing (Rayleigh number 0) without any change. I also tried deforming the grid in the rayleigh example, which is a somewhat strongly simplified 2D version of my problem, and this worked perfectly. Jan From nek5000-users at lists.mcs.anl.gov Fri Oct 21 07:32:53 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 21 Oct 2016 12:32:53 +0000 Subject: [Nek5000-users] Failure when changing geometry in usrdat2 In-Reply-To: References: , Message-ID: Hi Jan, If you want to send me your .rea/.usr/SIZE file off-list I can take a look. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, October 21, 2016 7:10 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Failure when changing geometry in usrdat2 Just a short update. I have tried the following: -using PN-PN instead of PN-PN-2 -characteristic time stepping -fiddling with the projection parameters P094,P095 -turning off the convective forcing (Rayleigh number 0) without any change. I also tried deforming the grid in the rayleigh example, which is a somewhat strongly simplified 2D version of my problem, and this worked perfectly. Jan _______________________________________________ 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 Sat Oct 22 04:59:55 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 22 Oct 2016 11:59:55 +0200 Subject: [Nek5000-users] Data processing issue Message-ID: Hi Neks, I'm trying to work with Post-processing and before it worked well but now I have a strange error on the server: "Error obtaining unique transport key from ORTE (orte_precondition_transports not present in the environment). Local host: zeus -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): PML add procs failed --> Returned "Error" (-1) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [zeus:98839] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!" I don't understand what about it is. Thanks to everyone. Regards, Andrey -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Oct 24 02:47:44 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 24 Oct 2016 09:47:44 +0200 Subject: [Nek5000-users] Failure when changing geometry in usrdat2 In-Reply-To: References: Message-ID: Hello Paul, thanks for offering to help. I actually found the error while cleaning up the .usr file before sending it: a subroutine i called in userf produced NaNs for certain coordinates which did not appear in the undeformed case. Additionally, i learned that 0*NaN is still NaN, quite important if one wants to deactivate forcings by multiplying them with zero. Cheers, Jan > Am 21.10.2016 um 14:32 schrieb nek5000-users at lists.mcs.anl.gov: > > > Hi Jan, > > If you want to send me your .rea/.usr/SIZE file off-list I can take a > look. > > Paul > > > _______________________________________________ > 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 Oct 24 11:09:32 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 24 Oct 2016 12:09:32 -0400 Subject: [Nek5000-users] Maximum number of elements for Postnek Message-ID: Hi Neks, What is the setting that lets you change the limit of maximum number of elements in Postnek. Is it in the 'basicsp.inc'? 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 Mon Oct 24 11:10:37 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 24 Oct 2016 16:10:37 +0000 Subject: [Nek5000-users] Maximum number of elements for Postnek In-Reply-To: References: Message-ID: Hi Saikat, nelm in basics.inc upper bound on total points is set in basicsp.inc Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, October 24, 2016 11:09 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Maximum number of elements for Postnek Hi Neks, What is the setting that lets you change the limit of maximum number of elements in Postnek. Is it in the 'basicsp.inc'? 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 Tue Oct 25 03:07:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Oct 2016 08:07:51 +0000 Subject: [Nek5000-users] Dirichlet BC for scalars In-Reply-To: References: Message-ID: I found the problem finally. I used P007 (RHOCP) = 0. Changing to 1 made it work. /Johan ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 3, 2016 10:15 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Dirichlet BC for scalars I am a new user of Nek, and am learning to possibilities of the program. I have successfully implemented a lid-driven cavity. I now want to, in addidtion, solve the problem for a scalar with certain boundary conditions (I did choose the temperature for this). I use the .box file: reafile.rea 2 2 # Box 1 -20 -20 0.0 1.0 1.0 0.0 1.0 1.0 W ,W ,W ,v , t ,t ,O ,I , Thus: the domains is a 2D 1x1 square where: * The y = 1 boundary is the "lid" whose velocity can be set in the .usr file (Dirichlet BC) * The vertical walls also have Dirichlet BC * The bottom wall is an "open boundary" for the temperature * The top wall is a n "insulator" for the temperature Given the .rea file generated with this .box file, I set the initial conditions in useric: subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=0.0 uy=0.0 uz=0.0 temp=0 return end I set the Dirichlet BC in userbc: subroutine userbc (ix,iy,iz,iside,ieg) c NOTE ::: This subroutine MAY NOT be called by every process include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=1 uy=0.0 uz=0.0 temp=x return end I expected this to initialize the velocity and temperature to zero in the entire domain, except for: * Top boundary has velocity 1 in the x-direction * The right boundary has temperature 1 But when I visualize the results of the simulation, I find that the temperature is set to "x" in the entire domain, not only at the boundarys that "should be set". However, the velocity boundary condition works as I expected, and is set only for the "v" boundaries. What am I doing wrong here? How may I set up dirichlet BC for the temperature? -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 25 03:18:55 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Oct 2016 08:18:55 +0000 Subject: [Nek5000-users] Mesh consistency check failed for merged 2D meshes Message-ID: Hi, I have problems with merging two 2D meshes. I want to merge two meshes generated with genbox: 1. walls.box This mesh is an "Y"-type mesh. It goes from beeing a square of side 10 into a square of side 0.5 via two circles (of radii 1.1 and 1.0). 2. center.box This is an "Box"-type mesh. It is a square of size %%%%%%%%%%%%%%%%%%%%%%%% This is walls.box: reafile.rea 2 1 # Y 4 -8 0. 0. bbccb 0.5 0.6 1. 1.1 10. 0 1 1 W ,W ,E ,E , %%%%%%%%%%%%%%%%% And this is center.box: reafile.rea 2 1 # Box -2 -2 -0.5 0.5 1. -0.5 0.5 1. W ,W ,W ,W , %%%%%%% I can plot the two meshes on top of each other, and the elements seem to align perfectly. I use nekmerge2 (from the example case "expansion") to generate a merged .rea file: nekmerge2 center walls bottom I now obtain a bottom.rea file. I generate bottom.map using genmap (tolerance 0.2). I compile (using a bottom.usr file and a SIZE file) using makenek. I run serially using "nek". Now I get several warnings of the type: WARNING2 Element mesh mismatch at: I,J,K,IE: 1 2 1 1 Near Y = -0.50000000 -0.41269471 0.0000000 , d: 0.0000000 -0.36629354E-01 2.0000000 And then "Mesh consistency check failed. EXITING in VRDSMSH." No output is generated. What is the problem here? Have I missed some critical aspect of merging meshes? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 25 05:19:04 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Oct 2016 10:19:04 +0000 Subject: [Nek5000-users] Mesh consistency check failed for merged 2D meshes In-Reply-To: References: Message-ID: Hi Johan, I found that I could merge these with pretex (the text-based version of prenek), which is what I normally use. Here is a little script that also seems to work, given the outputs of genbox on your two files. I call the script "merge2d" and invoke it as: merge2d casea caseb casec to merge casea.rea with caseb.rea and yield casec.rea ln $1.rea tmp_mg1.rea; ln $2.rea tmp_mg2.rea; pretex << EOF tmp_mg3 1 READ PREVIOUS PARAMETERS tmp_mg1 1 BUILD FROM FILE tmp_mg1 10 IMPORT MESH tmp_mg2 n 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF mv tmp_mg3.rea $3.rea rm -f *.dra tmp* Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, October 25, 2016 3:18 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Mesh consistency check failed for merged 2D meshes Hi, I have problems with merging two 2D meshes. I want to merge two meshes generated with genbox: 1. walls.box This mesh is an "Y"-type mesh. It goes from beeing a square of side 10 into a square of side 0.5 via two circles (of radii 1.1 and 1.0). 2. center.box This is an "Box"-type mesh. It is a square of size %%%%%%%%%%%%%%%%%%%%%%%% This is walls.box: reafile.rea 2 1 # Y 4 -8 0. 0. bbccb 0.5 0.6 1. 1.1 10. 0 1 1 W ,W ,E ,E , %%%%%%%%%%%%%%%%% And this is center.box: reafile.rea 2 1 # Box -2 -2 -0.5 0.5 1. -0.5 0.5 1. W ,W ,W ,W , %%%%%%% I can plot the two meshes on top of each other, and the elements seem to align perfectly. I use nekmerge2 (from the example case "expansion") to generate a merged .rea file: nekmerge2 center walls bottom I now obtain a bottom.rea file. I generate bottom.map using genmap (tolerance 0.2). I compile (using a bottom.usr file and a SIZE file) using makenek. I run serially using "nek". Now I get several warnings of the type: WARNING2 Element mesh mismatch at: I,J,K,IE: 1 2 1 1 Near Y = -0.50000000 -0.41269471 0.0000000 , d: 0.0000000 -0.36629354E-01 2.0000000 And then "Mesh consistency check failed. EXITING in VRDSMSH." No output is generated. What is the problem here? Have I missed some critical aspect of merging meshes? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 25 08:34:28 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Oct 2016 15:34:28 +0200 Subject: [Nek5000-users] Arbitrary mesh deformation Message-ID: Hello, I would like to deform a mesh, given an arbitrary normal wall deformation. Ideally I would like to solve a laplace problem to find the "volumetric" deformation function, like in the ALE approach. Note that I need to deform the mesh only in the preprocessing, while for the simulation the mesh is kept fixed. Any hints? Thanks, Andrea -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 26 10:17:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Oct 2016 17:17:36 +0200 Subject: [Nek5000-users] Order of appearance : USERBC and USERCHECK Message-ID: Hi all, I was wondering what was being called first between USERBC and USERCHECK when we solve for fluid with nek. Does anyone know about this? I still could not tell even after checking the sources. Thank you for your help, Best wishes, Arnold From nek5000-users at lists.mcs.anl.gov Wed Oct 26 10:18:14 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Oct 2016 17:18:14 +0200 Subject: [Nek5000-users] Integrate velocity field along a line In-Reply-To: References: Message-ID: Thank you for your answer it works wonders! Best wishes, Arnold Le 10/10/2016 15:41, nek5000-users at lists.mcs.anl.gov a ?crit : > Hi Arnold, > > You have to decide which faces of elements belong to the boundary --- but here > is a code that would integrate over all surfaces with "v " boundary conditions > that you could us as an example. > > Paul > > > > common /mystuff/ v2(lx1*ly1*lz1*lelt) > integer e,f > > n = nx1*ny1*nz1*nelt > > do i=1,n > v2(i)=vx(i,1,1,1)**2+vy(i,1,1,1)**2+vz(i,1,1,1)**2 > enddo > > v2surf = 0 > do e=1,nelv ! Integrate over all surfaces with cbc='v ' > do f=1,2*ndim > if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) > enddo > enddo > > v2surf = glsum(v2surf,1) ! Sum across all processors > > Note that "area" is passed in the TOTAL common block, which I assume > you are including in the routine. > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Monday, October 10, 2016 3:20 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Integrate velocity field along a line > > Good morning Neks! > > I was wondering if it possible to integrate a function over the boundary > in the userchk. Let me develop : > The domain is a box, I want to integrate the boundary velocity field > (prescribed in userbc) at the wall (bottom boundary) : > > In latex it would be int_{bottom boundary } u_{bound}^2 + v_{bound}^2 + > w_{bound}^2v dx_{bound} > > Is there a function like glsc3() that would allow me to do so? > > Thank you for your time, > > Best wishes, > > Arnold > _______________________________________________ > 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 Oct 27 13:02:46 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Oct 2016 14:02:46 -0400 Subject: [Nek5000-users] Pauls v2 Integration routine... In-Reply-To: References: Message-ID: Paul, Hi... I'd like to use this also; however, was your intent for the argument of the facint_v() sub to be v2, and not v? Also, would you want to pass v2surf back in /mystuff/? if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) Thanks, Murph ----------------------------------------------------------------------------------------------------------- common /mystuff/ v2(lx1*ly1*lz1*lelt) integer e,f n = nx1*ny1*nz1*nelt do i=1,n v2(i)=vx(i,1,1,1)**2+vy(i,1,1,1)**2+vz(i,1,1,1)**2 enddo v2surf = 0 do e=1,nelv ! Integrate over all surfaces with cbc='v ' do f=1,2*ndim if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) enddo enddo v2surf = glsum(v2surf,1) ! Sum across all processors Note that "area" is passed in the TOTAL common block, which I assume you are including in the routine. On 10/26/2016 1:00 PM, nek5000-users-request at lists.mcs.anl.gov 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. Order of appearance : USERBC and USERCHECK > (nek5000-users at lists.mcs.anl.gov) > 2. Re: Integrate velocity field along a line > (nek5000-users at lists.mcs.anl.gov) > > > _______________________________________________ > 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 Oct 27 15:46:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Oct 2016 16:46:05 -0400 Subject: [Nek5000-users] Genbox error Message-ID: Hi all, I have troubles with genbox. I have tried all the possible combination ./genbox turbChannel.box ./genbox turbChannel and I get this error. Do you have any idea? input file name: turbChannel forrtl: No such file or directory forrtl: severe (29): file not found, unit 7, file /galileo/home/userexternal/aalla000/exam_2710/turbChannel Image PC Routine Line Source libifcore.so.5 00007F69D5EE1947 Unknown Unknown Unknown libifcore.so.5 00007F69D5F00730 Unknown Unknown Unknown genbox 00000000004014F5 Unknown Unknown Unknown genbox 000000000040134E Unknown Unknown Unknown libc.so.6 00007F69D3FFEB15 Unknown Unknown Unknown genbox 0000000000401259 Unknown Unknown Unknown Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com From nek5000-users at lists.mcs.anl.gov Thu Oct 27 17:49:30 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Oct 2016 22:49:30 +0000 Subject: [Nek5000-users] Genbox error In-Reply-To: References: Message-ID: Hi Alessandro, you need to specify the full name of .box including the extention file since nek5_svn/tools/genbox/genbox.f:126 write(6,*) 'input file name:' read (5,132) string 132 format(a132) open (unit=7,file=string,status='old') Aleks ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 27, 2016 3:46 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Genbox error Hi all, I have troubles with genbox. I have tried all the possible combination ./genbox turbChannel.box ./genbox turbChannel and I get this error. Do you have any idea? input file name: turbChannel forrtl: No such file or directory forrtl: severe (29): file not found, unit 7, file /galileo/home/userexternal/aalla000/exam_2710/turbChannel Image PC Routine Line Source libifcore.so.5 00007F69D5EE1947 Unknown Unknown Unknown libifcore.so.5 00007F69D5F00730 Unknown Unknown Unknown genbox 00000000004014F5 Unknown Unknown Unknown genbox 000000000040134E Unknown Unknown Unknown libc.so.6 00007F69D3FFEB15 Unknown Unknown Unknown genbox 0000000000401259 Unknown Unknown Unknown Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com _______________________________________________ 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 Oct 27 17:49:52 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Oct 2016 22:49:52 +0000 Subject: [Nek5000-users] Pauls v2 Integration routine... In-Reply-To: References: , Message-ID: Yes, Murph. Aleks ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, October 27, 2016 1:02 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Pauls v2 Integration routine... Paul, Hi... I'd like to use this also; however, was your intent for the argument of the facint_v() sub to be v2, and not v? Also, would you want to pass v2surf back in /mystuff/? if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) Thanks, Murph ----------------------------------------------------------------------------------------------------------- common /mystuff/ v2(lx1*ly1*lz1*lelt) integer e,f n = nx1*ny1*nz1*nelt do i=1,n v2(i)=vx(i,1,1,1)**2+vy(i,1,1,1)**2+vz(i,1,1,1)**2 enddo v2surf = 0 do e=1,nelv ! Integrate over all surfaces with cbc='v ' do f=1,2*ndim if (cbc(f,e,1).eq.'v ') v2surf=v2surf+facint_v(v,area,f,e) enddo enddo v2surf = glsum(v2surf,1) ! Sum across all processors Note that "area" is passed in the TOTAL common block, which I assume you are including in the routine. On 10/26/2016 1:00 PM, nek5000-users-request at lists.mcs.anl.gov 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. Order of appearance : USERBC and USERCHECK (nek5000-users at lists.mcs.anl.gov) 2. Re: Integrate velocity field along a line (nek5000-users at lists.mcs.anl.gov) _______________________________________________ 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 Oct 27 17:56:40 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Oct 2016 18:56:40 -0400 Subject: [Nek5000-users] Genbox error In-Reply-To: References: Message-ID: Thank you for your reply. Shall I do ./genbox whatever.box? I have tried that but it does not work. Sorry, Alessandro Il 27/10/16 18:49, nek5000-users at lists.mcs.anl.gov ha scritto: > Hi Alessandro, > > you need to specify the full name of .box including the extention file since nek5_svn/tools/genbox/genbox.f:126 > > write(6,*) 'input file name:' > read (5,132) string > 132 format(a132) > open (unit=7,file=string,status='old') > > Aleks > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Thursday, October 27, 2016 3:46 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Genbox error > > Hi all, > > I have troubles with genbox. I have tried all the possible combination > > ./genbox turbChannel.box ./genbox turbChannel > > and I get this error. Do you have any idea? > > input file name: > turbChannel > forrtl: No such file or directory > forrtl: severe (29): file not found, unit 7, file > /galileo/home/userexternal/aalla000/exam_2710/turbChannel > Image PC Routine Line Source > libifcore.so.5 00007F69D5EE1947 Unknown Unknown Unknown > libifcore.so.5 00007F69D5F00730 Unknown Unknown Unknown > genbox 00000000004014F5 Unknown Unknown Unknown > genbox 000000000040134E Unknown Unknown Unknown > libc.so.6 00007F69D3FFEB15 Unknown Unknown Unknown > genbox 0000000000401259 Unknown Unknown Unknown > > Thanks, > Alessandro > > -- > Dr Alessandro Alla > > Florida State University > Department of Scienfitic Computing > 400 Dirac Science Library > Tallahassee FL 32306-4120 > > Room: 462 > Phone: +1 8506441010 > > E-Mail: aalla at fsu.edu > Skype: alessandro.alla > www.alessandroalla.com > > _______________________________________________ > 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 -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com From nek5000-users at lists.mcs.anl.gov Sun Oct 30 15:26:55 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 30 Oct 2016 16:26:55 -0400 Subject: [Nek5000-users] How to assembly different geometry Message-ID: Hi All, I would like to generate a mesh as Figure 2 in http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf If I build three different boxes, how can I then assemble them? Could anyone please help me? Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Oct 30 15:09:30 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 30 Oct 2016 22:09:30 +0200 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: Message-ID: I can think of two options: - Create the three different boxes with genbox and merge them with nekmerge - Create the whole mesh with your favorite meshing tool, export it as EXODUSII and use exo2nek Von: on behalf of Antworten an: Datum: Sunday, October 30, 2016 at 10:26 PM An: Betreff: [Nek5000-users] How to assembly different geometry Hi All, I would like to generate a mesh as Figure 2 in http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Prepr int_No16-54.pdf If I build three different boxes, how can I then assemble them? Could anyone please help me? Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com _______________________________________________ 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 Sun Oct 30 16:31:34 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 30 Oct 2016 17:31:34 -0400 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: Message-ID: Thank you for your reply. Where can I find more information about nekmerge? Alessandro Il 30/10/16 16:09, nek5000-users at lists.mcs.anl.gov ha scritto: > > I can think of two options: > > - Create the three different boxes with genbox and merge them with > nekmerge > > - Create the whole mesh with your favorite meshing tool, export it as > EXODUSII and use exo2nek > > > Von: > on behalf of > > > Antworten an: > > Datum: Sunday, October 30, 2016 at 10:26 PM > An: > > Betreff: [Nek5000-users] How to assembly different geometry > > Hi All, > > I would like to generate a mesh as Figure 2 in > http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf > > If I build three different boxes, how can I then assemble them? Could anyone please help me? > > Thanks, > Alessandro > > -- > Dr Alessandro Alla > > Florida State University > Department of Scienfitic Computing > 400 Dirac Science Library > Tallahassee FL 32306-4120 > > Room: 462 > Phone: +1 8506441010 > > E-Mail:aalla at fsu.edu > Skype: alessandro.alla > www.alessandroalla.com > _______________________________________________ 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 -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Oct 30 21:25:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 02:25:42 +0000 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: , Message-ID: Hi Alessandro, Here is a multi-box file example that will generate something similar to what you're after. You can edit to suit your needs. Paul one2d.rea 2 spatial dimension 1 number of fields #======================================================== # Here is a multibox example #======================================================== # Box left lower -3 -2 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio -2 -.1 1.0 y0 y1 ratio v ,W ,SYM, , (bc's) Box left center -3 -3 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio v , , , , (bc's) Box left upper -3 -2 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio .1 2 1.0 y0 y1 ratio v ,W , ,SYM, (bc's) Box center center -4 -3 nelx,nely,nelz for Box) -1 0 1.0 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio , ,W ,W , (bc's) Box right lower -3 -2 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio -2 -.1 1.0 y0 y1 ratio ,O ,SYM, , (bc's) Box right center -3 -3 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio ,O , , , (bc's) Box right upper -3 -2 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio .1 2 1.0 y0 y1 ratio ,O , ,SYM, (bc's) .... PS ---- Be sure that you have 3 characters (counting spaces) for each BC. The "right upper" "right center" etc. are just comments. "Box" is a keyword, however... (so to distinguish from cylinder, etc.) ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, October 30, 2016 3:09 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] How to assembly different geometry I can think of two options: - Create the three different boxes with genbox and merge them with nekmerge - Create the whole mesh with your favorite meshing tool, export it as EXODUSII and use exo2nek Von: > on behalf of > Antworten an: > Datum: Sunday, October 30, 2016 at 10:26 PM An: > Betreff: [Nek5000-users] How to assembly different geometry Hi All, I would like to generate a mesh as Figure 2 in http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf If I build three different boxes, how can I then assemble them? Could anyone please help me? Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com _______________________________________________ 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 Sun Oct 30 22:32:18 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 30 Oct 2016 23:32:18 -0400 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: Message-ID: Hi Paul, Thank you so much. Are the BC's correct? I have slightly modified your script and I get the following error. What is wrong in your opinion? forrtl: severe (24): end-of-file during read, unit 99, file /galileo/home/userexternal/aalla000/channel/box.tmp Image PC Routine Line Source libifcore.so.5 00007FD15E583947 Unknown Unknown Unknown libifcore.so.5 00007FD15E5C209F Unknown Unknown Unknown libifcore.so.5 00007FD15E5C0538 Unknown Unknown Unknown genbox 0000000000416D0D Unknown Unknown Unknown genbox 000000000040270C Unknown Unknown Unknown genbox 000000000040134E Unknown Unknown Unknown libc.so.6 00007FD15C6A0B15 Unknown Unknown Unknown genbox 0000000000401259 Unknown Unknown Unknown Thanks a lot, Alessandro Il 30/10/16 22:25, nek5000-users at lists.mcs.anl.gov ha scritto: > > > Hi Alessandro, > > Here is a multi-box file example that will generate something similar > to what you're > after. You can edit to suit your needs. > > Paul > > one2d.rea > > 2 spatial dimension > > 1 number of fields > > #======================================================== > > # Here is a multibox example > > #======================================================== > > # > > Box left lower > > -3 -2 nelx,nely,nelz for Box) > > -2 -1 0.8 x0 x1 ratio > > -2 -.1 1.0 y0 y1 ratio > > v ,W ,SYM, , (bc's) > > Box left center > > -3 -3 nelx,nely,nelz for Box) > > -2 -1 0.8 x0 x1 ratio > > -.1 .1 1.0 y0 y1 ratio > > v , , , , (bc's) > > Box left upper > > -3 -2 nelx,nely,nelz for Box) > > -2 -1 0.8 x0 x1 ratio > > .1 2 1.0 y0 y1 ratio > > v ,W , ,SYM, (bc's) > > Box center center > > -4 -3 nelx,nely,nelz for Box) > > -1 0 1.0 x0 x1 ratio > > -.1 .1 1.0 y0 y1 ratio > > , ,W ,W , (bc's) > > Box right lower > > -3 -2 nelx,nely,nelz for Box) > > 0 2. 1.2 x0 x1 ratio > > -2 -.1 1.0 y0 y1 ratio > > ,O ,SYM, , (bc's) > > Box right center > > -3 -3 nelx,nely,nelz for Box) > > 0 2. 1.2 x0 x1 ratio > > -.1 .1 1.0 y0 y1 ratio > > ,O , , , (bc's) > > Box right upper > > -3 -2 nelx,nely,nelz for Box) > > 0 2. 1.2 x0 x1 ratio > > .1 2 1.0 y0 y1 ratio > > ,O , ,SYM, (bc's) > > > .... PS ---- Be sure that you have 3 characters (counting spaces) > > for each BC. > > > The "right upper" "right center" etc. are just comments. > > "Box" is a keyword, however... (so to distinguish from cylinder, etc.) > > > > > > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Sunday, October 30, 2016 3:09 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] How to assembly different geometry > > I can think of two options: > > - Create the three different boxes with genbox and merge them with > nekmerge > > - Create the whole mesh with your favorite meshing tool, export it as > EXODUSII and use exo2nek > > > Von: > on behalf of > > > Antworten an: > > Datum: Sunday, October 30, 2016 at 10:26 PM > An: > > Betreff: [Nek5000-users] How to assembly different geometry > > Hi All, > > I would like to generate a mesh as Figure 2 in > http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf > > If I build three different boxes, how can I then assemble them? Could anyone please help me? > > Thanks, > Alessandro > > -- > Dr Alessandro Alla > > Florida State University > Department of Scienfitic Computing > 400 Dirac Science Library > Tallahassee FL 32306-4120 > > Room: 462 > Phone: +1 8506441010 > > E-Mail:aalla at fsu.edu > Skype: alessandro.alla > www.alessandroalla.com > _______________________________________________ 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 -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Oct 30 23:01:49 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 04:01:49 +0000 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: , Message-ID: Hi Alessondro, Just to be clear, I attach the mbox.box file that I used. It works with the current repo version of genbox (and earlier ones). Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, October 30, 2016 10:32 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] How to assembly different geometry Hi Paul, Thank you so much. Are the BC's correct? I have slightly modified your script and I get the following error. What is wrong in your opinion? forrtl: severe (24): end-of-file during read, unit 99, file /galileo/home/userexternal/aalla000/channel/box.tmp Image PC Routine Line Source libifcore.so.5 00007FD15E583947 Unknown Unknown Unknown libifcore.so.5 00007FD15E5C209F Unknown Unknown Unknown libifcore.so.5 00007FD15E5C0538 Unknown Unknown Unknown genbox 0000000000416D0D Unknown Unknown Unknown genbox 000000000040270C Unknown Unknown Unknown genbox 000000000040134E Unknown Unknown Unknown libc.so.6 00007FD15C6A0B15 Unknown Unknown Unknown genbox 0000000000401259 Unknown Unknown Unknown Thanks a lot, Alessandro Il 30/10/16 22:25, nek5000-users at lists.mcs.anl.gov ha scritto: Hi Alessandro, Here is a multi-box file example that will generate something similar to what you're after. You can edit to suit your needs. Paul one2d.rea 2 spatial dimension 1 number of fields #======================================================== # Here is a multibox example #======================================================== # Box left lower -3 -2 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio -2 -.1 1.0 y0 y1 ratio v ,W ,SYM, , (bc's) Box left center -3 -3 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio v , , , , (bc's) Box left upper -3 -2 nelx,nely,nelz for Box) -2 -1 0.8 x0 x1 ratio .1 2 1.0 y0 y1 ratio v ,W , ,SYM, (bc's) Box center center -4 -3 nelx,nely,nelz for Box) -1 0 1.0 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio , ,W ,W , (bc's) Box right lower -3 -2 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio -2 -.1 1.0 y0 y1 ratio ,O ,SYM, , (bc's) Box right center -3 -3 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio -.1 .1 1.0 y0 y1 ratio ,O , , , (bc's) Box right upper -3 -2 nelx,nely,nelz for Box) 0 2. 1.2 x0 x1 ratio .1 2 1.0 y0 y1 ratio ,O , ,SYM, (bc's) .... PS ---- Be sure that you have 3 characters (counting spaces) for each BC. The "right upper" "right center" etc. are just comments. "Box" is a keyword, however... (so to distinguish from cylinder, etc.) ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, October 30, 2016 3:09 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] How to assembly different geometry I can think of two options: - Create the three different boxes with genbox and merge them with nekmerge - Create the whole mesh with your favorite meshing tool, export it as EXODUSII and use exo2nek Von: > on behalf of > Antworten an: > Datum: Sunday, October 30, 2016 at 10:26 PM An: > Betreff: [Nek5000-users] How to assembly different geometry Hi All, I would like to generate a mesh as Figure 2 in http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf If I build three different boxes, how can I then assemble them? Could anyone please help me? Thanks, Alessandro -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com _______________________________________________ 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 -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mbox.box Type: application/octet-stream Size: 1511 bytes Desc: mbox.box URL: From nek5000-users at lists.mcs.anl.gov Sun Oct 30 23:22:50 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 00:22:50 -0400 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: Message-ID: Hi Paul, Thanks a lot. Your .box file is also running. Mine is not... I have only modified the dimensions of the mesh according to what I need. Do you see anything wrong? rbsissa2d.rea 2 spatial dimension 1 number of fields #======================================================== # Here is a multibox example #======================================================== # Box left lower -3 -2 nelx,nely,nelz for Box) 0 1 1.0 x0 x1 ratio 0 0.47 1.0 y0 y1 ratio v ,W ,SYM, , (bc's) Box left center -3 -3 nelx,nely,nelz for Box) 0 1 1.0 x0 x1 ratio .47 .53 1.0 y0 y1 ratio v , , , , (bc's) Box left upper -3 -2 nelx,nely,nelz for Box) 0 1 1.0 x0 x1 ratio .53 1 1.0 y0 y1 ratio v ,W , ,SYM, (bc's) Box center center -3 -3 nelx,nely,nelz for Box) 1 1.47 1.0 x0 x1 ratio .47 .53 1.0 y0 y1 ratio , ,W ,W , (bc's) Box right lower -3 -4 nelx,nely,nelz for Box) 1.47 9.47 1.0 x0 x1 ratio 0 0.47 1.0 y0 y1 ratio ,O ,SYM, , (bc's) Box right center -3 -4 nelx,nely,nelz for Box) 1.47 9.47 1.0 x0 x1 ratio .47 .53 1.0 y0 y1 ratio ,O , , , (bc's) Box right upper -3 -4 nelx,nely,nelz for Box) 1.47 9.47 1.0 x0 x1 ratio .53 1 1.0 y0 y1 ratio ,O , ,SYM, (bc's) Il 31/10/16 00:01, nek5000-users at lists.mcs.anl.gov ha scritto: > > Hi Alessondro, > > Just to be clear, I attach the mbox.box file that I used. It works > with the current repo > version of genbox (and earlier ones). > > Paul > > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Sunday, October 30, 2016 10:32 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] How to assembly different geometry > > Hi Paul, > > Thank you so much. Are the BC's correct? > > I have slightly modified your script and I get the following error. > What is wrong in your opinion? > > > forrtl: severe (24): end-of-file during read, unit 99, file > /galileo/home/userexternal/aalla000/channel/box.tmp > Image PC Routine Line Source > libifcore.so.5 00007FD15E583947 Unknown Unknown Unknown > libifcore.so.5 00007FD15E5C209F Unknown Unknown Unknown > libifcore.so.5 00007FD15E5C0538 Unknown Unknown Unknown > genbox 0000000000416D0D Unknown Unknown Unknown > genbox 000000000040270C Unknown Unknown Unknown > genbox 000000000040134E Unknown Unknown Unknown > libc.so.6 00007FD15C6A0B15 Unknown Unknown Unknown > genbox 0000000000401259 Unknown Unknown Unknown > > Thanks a lot, > Alessandro > > Il 30/10/16 22:25, nek5000-users at lists.mcs.anl.gov ha scritto: >> >> >> Hi Alessandro, >> >> Here is a multi-box file example that will generate something >> similar to what you're >> after. You can edit to suit your needs. >> >> Paul >> >> one2d.rea >> >> 2 spatial dimension >> >> 1 number of fields >> >> #======================================================== >> >> # Here is a multibox example >> >> #======================================================== >> >> # >> >> Box left lower >> >> -3 -2 nelx,nely,nelz for Box) >> >> -2 -1 0.8 x0 x1 ratio >> >> -2 -.1 1.0 y0 y1 ratio >> >> v ,W ,SYM, , (bc's) >> >> Box left center >> >> -3 -3 nelx,nely,nelz for Box) >> >> -2 -1 0.8 x0 x1 ratio >> >> -.1 .1 1.0 y0 y1 ratio >> >> v , , , , (bc's) >> >> Box left upper >> >> -3 -2 nelx,nely,nelz for Box) >> >> -2 -1 0.8 x0 x1 ratio >> >> .1 2 1.0 y0 y1 ratio >> >> v ,W , ,SYM, (bc's) >> >> Box center center >> >> -4 -3 nelx,nely,nelz for Box) >> >> -1 0 1.0 x0 x1 ratio >> >> -.1 .1 1.0 y0 y1 ratio >> >> , ,W ,W , (bc's) >> >> Box right lower >> >> -3 -2 nelx,nely,nelz for Box) >> >> 0 2. 1.2 x0 x1 ratio >> >> -2 -.1 1.0 y0 y1 ratio >> >> ,O ,SYM, , (bc's) >> >> Box right center >> >> -3 -3 nelx,nely,nelz for Box) >> >> 0 2. 1.2 x0 x1 ratio >> >> -.1 .1 1.0 y0 y1 ratio >> >> ,O , , , (bc's) >> >> Box right upper >> >> -3 -2 nelx,nely,nelz for Box) >> >> 0 2. 1.2 x0 x1 ratio >> >> .1 2 1.0 y0 y1 ratio >> >> ,O , ,SYM, (bc's) >> >> >> .... PS ---- Be sure that you have 3 characters (counting spaces) >> >> for each BC. >> >> >> The "right upper" "right center" etc. are just comments. >> >> "Box" is a keyword, however... (so to distinguish from cylinder, etc.) >> >> >> >> >> >> ------------------------------------------------------------------------ >> *From:* nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> *Sent:* Sunday, October 30, 2016 3:09 PM >> *To:* nek5000-users at lists.mcs.anl.gov >> *Subject:* Re: [Nek5000-users] How to assembly different geometry >> >> I can think of two options: >> >> - Create the three different boxes with genbox and merge them with >> nekmerge >> >> - Create the whole mesh with your favorite meshing tool, export it as >> EXODUSII and use exo2nek >> >> >> Von: > > on behalf of >> > > >> Antworten an: > > >> Datum: Sunday, October 30, 2016 at 10:26 PM >> An: > > >> Betreff: [Nek5000-users] How to assembly different geometry >> >> Hi All, >> >> I would like to generate a mesh as Figure 2 in >> http://www.mathematics.uh.edu/docs/math/NASC-preprint-series/2015_2016/Preprint_No16-54.pdf >> >> If I build three different boxes, how can I then assemble them? Could anyone please help me? >> >> Thanks, >> Alessandro >> >> -- >> Dr Alessandro Alla >> >> Florida State University >> Department of Scienfitic Computing >> 400 Dirac Science Library >> Tallahassee FL 32306-4120 >> >> Room: 462 >> Phone: +1 8506441010 >> >> E-Mail:aalla at fsu.edu >> Skype: alessandro.alla >> www.alessandroalla.com >> _______________________________________________ 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 > > -- > Dr Alessandro Alla > > Florida State University > Department of Scienfitic Computing > 400 Dirac Science Library > Tallahassee FL 32306-4120 > > Room: 462 > Phone: +1 8506441010 > > E-Mail:aalla at fsu.edu > Skype: alessandro.alla > www.alessandroalla.com > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Oct 31 00:47:20 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 05:47:20 +0000 Subject: [Nek5000-users] How to assembly different geometry Message-ID: Hi Alessandro, I believe the problem with the box file that you pasted is that the boundary conditions are not of required length. Each boundary condition must be exactly 3 characters long, and the first boundary conditions that you specified for Box 4,5,6 and 7 is 4 characters long. Deleting one character from those empty boundary conditions makes them of the right length, and genbox runs fine after that. Ketan From nek5000-users at lists.mcs.anl.gov Mon Oct 31 07:00:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 08:00:42 -0400 Subject: [Nek5000-users] How to assembly different geometry In-Reply-To: References: Message-ID: Thank you very much. My .box file is now working. Next question: How can I include the box information into my rea file? **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. 308 2 308 NEL,NDIM,NELV That's what I have I so far, but It doesn't have any information about the elements. Thank you, Alessandro Il 31/10/16 01:47, nek5000-users at lists.mcs.anl.gov ha scritto: > Hi Alessandro, > > I believe the problem with the box file that you pasted is that the boundary conditions are not of required length. Each boundary condition must be exactly 3 characters long, and the first boundary conditions that you specified for Box 4,5,6 and 7 is 4 characters long. > > Deleting one character from those empty boundary conditions makes them of the right length, and genbox runs fine after that. > > Ketan > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Dr Alessandro Alla Florida State University Department of Scienfitic Computing 400 Dirac Science Library Tallahassee FL 32306-4120 Room: 462 Phone: +1 8506441010 E-Mail: aalla at fsu.edu Skype: alessandro.alla www.alessandroalla.com From nek5000-users at lists.mcs.anl.gov Mon Oct 31 10:15:52 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 31 Oct 2016 15:15:52 +0000 Subject: [Nek5000-users] How to assembly different geometry Message-ID: Hi Alessandro, Running genbox creates a box.rea file. You can copy box.rea to blah.rea where blah is your case name. Ketan