June 2016 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results
by nek5000-users＠lists.mcs.anl.gov 15 Jun '16

15 Jun '16

Philipp, I am investigating a switch for two reasons: 1) to see how it affects my results. This is why I want to converge pressure right away before performing more timesteps. I will be running several more simulations that are similar to this one, and I am interested in how PNPN will perform for the same flow. I have already put in a significant amount of compute time into my current case and so I don't want to start it over to perform this simple investigation. 2) I have an additional interest in post processing and analyzing the pressure fluctuation field. Using PNPN over PNPN-2 makes sense in this case since the pressure field is better resolved and enforces C0 continuity across element boundaries. Thanks, Phil On Wed, Jun 15, 2016 at 11:00 AM, <nek5000-users-request(a)lists.mcs.anl.gov> wrote: > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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: Restarting with PNPN using PNPN-2 results > (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 15 Jun 2016 10:44:04 +0200 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > <mailman.23825.1465980259.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi, > I guess the question is whether there is a similar type of Uzawa > iteration also for Pnpn, this I don't know and I have not looked into > the theory. I can only say that for PnPn-2, with the nested iterations > you can get a perfect pressure (i.e. not proportional to Delta p) in one > time step. I guess one needs a PnPn user to answer that question. > > Just as a side question; why do you want to go from PnPn-2 to PnPn? Out > of curiosity... > > Best regards, > PHilipp > > On 2016-06-15 00:44, nek5000-users(a)lists.mcs.anl.gov wrote: > > Philipp and Aleks, > > > > Thanks for the replies. The Uzawa method sounds exactly like what I am > > looking for. I would like to pay a penalty upfront to converge to a > > good pressure solution without taking too many (or really any) timesteps > > and then move forward with a resolved pressure solution. I am hoping > > there is a way to do this since a pressure projection method is being > used. > > > > My solution is already well resolved temporally and I don't want to > > perturbe it with a long time series of unresolved pressure > > fields/slightly divergent velocity fields. Can anyone comment on the use > > of Uzawa with PNPN? Also, Philipp is there a specific routine you call > > to perform just one of these iterations? I haven't used this method > before. > > > > Kind regards, > > > > Phil > > > > On Tue, Jun 14, 2016 at 11:00 AM, > > <nek5000-users-request(a)lists.mcs.anl.gov > > <mailto:[email protected]>> wrote: > > > > Send Nek5000-users mailing list submissions to > > nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]> > > > > 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(a)lists.mcs.anl.gov > > <mailto:[email protected]> > > > > You can reach the person managing the list at > > nek5000-users-owner(a)lists.mcs.anl.gov > > <mailto:[email protected]> > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Nek5000-users digest..." > > > > > > Today's Topics: > > > > 1. Restarting with PNPN using PNPN-2 results > > (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > 2. Re: Restarting with PNPN using PNPN-2 results > > (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > 3. Re: Restarting with PNPN using PNPN-2 results > > (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > 4. Re: lambda2 in turbChannel (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > 5. g2gi() no geometry found (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > 6. Re: g2gi() no geometry found (nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]>) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 13 Jun 2016 13:09:05 -0600 > > From: nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]> > > To: nek5000-users(a)lists.mcs.anl.gov > > <mailto:[email protected]> > > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > > Message-ID: > > > > <mailman.23731.1465844987.24727.nek5000-users(a)lists.mcs.anl.gov > > <mailto: > mailman.23731.1465844987.24727.nek5000-users(a)lists.mcs.anl.gov>> > > Content-Type: text/plain; charset="utf-8" > > > > Hello neks, > > > > I have a DNS simulation that I was running as PNPN-2 and I would > like to > > run it as PNPN without starting back at the initial conditions. > > I am curious if anyone has experience running a PNPN case with > initial > > conditions from a PNPN-2 simulation? I have tried this and the > > simulation > > runs okay, except the pressure term never seems to converge when > running > > the PNPN simulation. This dramatically increases runtime and makes > the > > results questionable. It seems to me that restarting with PNPN-2 > > results > > should be doable, and that it should only take a few iterations for > the > > pressure term to start converging. However, my simulation is still > not > > converging after 100+ iterations, but it was converging fine when I > was > > running PNPN-2. > > > > Any suggestions for things I should look for that might cause the > > problem, > > or potential fixes? > > > > Thanks > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter > > Transport and Energy > > Tempe, Arizona > >

1 0

Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results
by nek5000-users＠lists.mcs.anl.gov 15 Jun '16

15 Jun '16

Philipp and Aleks, Thanks for the replies. The Uzawa method sounds exactly like what I am looking for. I would like to pay a penalty upfront to converge to a good pressure solution without taking too many (or really any) timesteps and then move forward with a resolved pressure solution. I am hoping there is a way to do this since a pressure projection method is being used. My solution is already well resolved temporally and I don't want to perturbe it with a long time series of unresolved pressure fields/slightly divergent velocity fields. Can anyone comment on the use of Uzawa with PNPN? Also, Philipp is there a specific routine you call to perform just one of these iterations? I haven't used this method before. Kind regards, Phil On Tue, Jun 14, 2016 at 11:00 AM, <nek5000-users-request(a)lists.mcs.anl.gov> wrote: > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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. Restarting with PNPN using PNPN-2 results > (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users(a)lists.mcs.anl.gov) > 4. Re: lambda2 in turbChannel (nek5000-users(a)lists.mcs.anl.gov) > 5. g2gi() no geometry found (nek5000-users(a)lists.mcs.anl.gov) > 6. Re: g2gi() no geometry found (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2016 13:09:05 -0600 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > <mailman.23731.1465844987.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would like to > run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with initial > conditions from a PNPN-2 simulation? I have tried this and the simulation > runs okay, except the pressure term never seems to converge when running > the PNPN simulation. This dramatically increases runtime and makes the > results questionable. It seems to me that restarting with PNPN-2 results > should be doable, and that it should only take a few iterations for the > pressure term to start converging. However, my simulation is still not > converging after 100+ iterations, but it was converging fine when I was > running PNPN-2. > > Any suggestions for things I should look for that might cause the problem, > or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of Matter > Transport and Energy > Tempe, Arizona >

1 1

lambda2 in turbChannel
by nek5000-users＠lists.mcs.anl.gov 14 Jun '16

14 Jun '16

Hello, In the userchk subroutine for the turbChannel example, lambda2 was computed. How can I visualize the isosurfaces (streamwise structures) in visit? if(mod(istep,iostep).eq.0 .and. istep.gt.0) then ! compute lambda2 vortex call lambda2(t(1,1,1,1,2)) ! compute vorticity --- 3 components returned in t(...) if(ldimt.ge.5) call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) endif Thank you, Virgilio A. Gomez

1 6

Restarting with PNPN using PNPN-2 results
by nek5000-users＠lists.mcs.anl.gov 13 Jun '16

13 Jun '16

Hello neks, I have a DNS simulation that I was running as PNPN-2 and I would like to run it as PNPN without starting back at the initial conditions. I am curious if anyone has experience running a PNPN case with initial conditions from a PNPN-2 simulation? I have tried this and the simulation runs okay, except the pressure term never seems to converge when running the PNPN simulation. This dramatically increases runtime and makes the results questionable. It seems to me that restarting with PNPN-2 results should be doable, and that it should only take a few iterations for the pressure term to start converging. However, my simulation is still not converging after 100+ iterations, but it was converging fine when I was running PNPN-2. Any suggestions for things I should look for that might cause the problem, or potential fixes? Thanks -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona

1 2

Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 8
by nek5000-users＠lists.mcs.anl.gov 13 Jun '16

13 Jun '16

Hello Jing, I tried your new python code for msh convert. I was able to read file successfully but not able to get .rea file. For my geometry I have following zones: (0 "Zone Sections") (39 (8 fluid CREATED_MATERIAL_6)()) (39 (9 interior int_CREATED_MATERIAL_6)()) (39 (10 wall W)()) (39 (11 velocity-inlet PA)()) (39 (12 velocity-inlet VEIN)()) (39 (13 pressure-outlet DA)()) I have attached error file with this mail(error file name = error(1).png and msh file is mesh_hexa_final.msh). what other changes should I make to convert .msh file to .rea. Thanks, Mansi Patel ________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: Wednesday, June 8, 2016 12:18 PM To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 8 Send Nek5000-users mailing list submissions to nek5000-users(a)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(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)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 88, Issue 5 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jun 2016 18:15:42 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 Message-ID: <mailman.23474.1465402725.24727.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="utf-8" Hello Jing, Recently I am also working on converting fluent mesh to nek5000. I have generated the *msh from gambit, then using the mshconvert.py tool to convert a simple mesh with a circular cylinder inside a square. simply, I can get the *rea file with circle of the "W", "v" and "O". but I have met two problems; 1. to impose the periodic boundary conditons: in the script, it strongly recommend to impose "P" through the script, then how to setup it in mshconvert.py? the way convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) can generate the rea field but failed in the step of genmap. so how to treat boundary 4 and 5 as periodic BCs? 2. about the curved wall. there is no problem to define a circle by "Circle" command, but if I want to using "m" to define a spline curve, how to seed middle points? I know in Gambit I can mesh the line using 3 node, I defined 3 node mode to mesh a circle, and using "m" instead of "circle", however, it failed to generate the rea file. the circle merged into a point, then what should I do to active the spline curve? Thanks! Wei 2016-06-08 15:46 GMT+02:00 <nek5000-users(a)lists.mcs.anl.gov>: > Hi Mansi, > > You can find the updated "mshconvert.py" in the attachment. You can run > the script for your case likes > > ### > $ ipython > > In [1]: from mshconvert import * > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > format > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > ... > ### > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > 'O' on zone 13. > > The snapshot for the Nek5000 mesh using visit is also attached in the > email. > > /Jing > > > ________________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov < > nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > nek5000-users-request(a)lists.mcs.anl.gov < > nek5000-users-request(a)lists.mcs.anl.gov> > Sent: Monday, June 6, 2016 22:09 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 5 > > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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 88, Issue 4, Problem creating > .rea file (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 19:58:31 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, > Problem creating .rea file > Message-ID: > <mailman.23344.1465243753.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > > Thanks jing, that was a lot helpful to me. > > I have generated the .msh file for the hexahedral mesh for my geometry. > File is attached to this mail. > > > I have given boundary condition in this file only let me know if there are > any changes to be made and file has only one zone( if by one zone you mean > only 1 type of mesh through out whole geometry). > > > Questions: > > 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea > file? > > 2) is there any way to smooth hexahedral mesh for unstructured geometry? > > > Thanks, > > Mansi Patel > > > ________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov < > nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > nek5000-users-request(a)lists.mcs.anl.gov < > nek5000-users-request(a)lists.mcs.anl.gov> > Sent: Friday, June 3, 2016 1:00 PM > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 4 > > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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 88, Issue 3 > (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 21:21:13 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 > Message-ID: > <mailman.23169.1464902611.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mansi, > > 1)what should I do to solve error? > > Right now mshconvert can only deal with single zone's case. So you should > have to manually merge the multi-zone to single-zone in the .msh file. > > Also we found that there are few bugs in the file. Could you please send > us your .msh file to test and then we will get back to you with the > corrected version? > > 2)what are mesh types that we can use? > Quadrant for 2D- and hexahedral for 3D-cases. > > 3) I there any other easy way to convert .msh file to .rea? > I leave this question to other users. > > Thanks. > > Regards, Jing > ________________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov < > nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > nek5000-users-request(a)lists.mcs.anl.gov < > nek5000-users-request(a)lists.mcs.anl.gov> > Sent: Thursday, June 2, 2016 19:17 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 3 > > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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. problems in generating .rea file (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 17:12:11 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: [Nek5000-users] problems in generating .rea file > Message-ID: > <mailman.23153.1464887866.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > I want to ask what type of mesh does Nek5000 accept? tetrahedral, > hexahedral,etc? > > Because I am using ICEM CFD for generating mesh which has extension .msh > and for that I used python code given for mshconvert to convert into .rea > file but I am getting error. the error image is attached. > > Please let me know following questions > > 1)what should I do to solve error? > > 2)what are mesh types that we can use? > > 3) I there any other easy way to convert .msh file to .rea? > > > Thanks, any help would be appreciated. > > > Thanks, > > Mansi Patel > > >

1 0

Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 8
by nek5000-users＠lists.mcs.anl.gov 12 Jun '16

12 Jun '16

Hi Wei, >1. to impose the periodic boundary conditons: in the script, it strongly >recommend to impose "P" through the script, then how to setup it in >mshconvert.py? the way >convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) > can generate the rea field but failed in the step of genmap. so how to > treat boundary 4 and 5 as periodic BCs? Probably you should have to do likes convert('mesh.msh', periodic_dx={(4,5) : [0, 0, 2]}, bcs={1:'W',2:'v',3:'O'}) Where the "periodic_dx" is to specify which pair-zone is periodic and what is the orientation of zones. in the example, zones 4,5 are the periodic boundaries and on the z-direction with distance of 2. >2. about the curved wall. there is no problem to define a circle by >"Circle" command, but if I want to using "m" to define a spline curve, how t>o seed middle points? I know in Gambit I can mesh the line using 3 node, I >defined 3 node mode to mesh a circle, and using "m" instead of "circle", >however, it failed to generate the rea file. the circle merged into a >point, then what should I do to active the spline curve? Yes, it seems to be bugs in the python script with "m" method. In the python script, the midpoints is (somehow) defined by ... x_m = (x_1+x_2)/2; y_m = (y_1+y_2)/2; ... However, in the nek5000 (tools/prenek/zipper2.f) it read the values of (x_q, y_q) instead of (x_m,y_m) !? .... ! subroutine xyzquad(xl,yl,zl,nxl,nyl,nzl,e) ... do k=1,nedge if (ccurve(k,e).eq.'m') then j = eindx(k) xq(j) = curve(1,k,e) yq(j) = curve(2,k,e) zq(j) = curve(3,k,e) endif enddo ... This should be confirmed by nek5000 developers. Thanks. /Jing ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: Wednesday, June 8, 2016 18:18 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 8 Send Nek5000-users mailing list submissions to nek5000-users(a)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(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)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 88, Issue 5 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jun 2016 18:15:42 +0200 From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 Message-ID: <mailman.23474.1465402725.24727.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="utf-8" Hello Jing, Recently I am also working on converting fluent mesh to nek5000. I have generated the *msh from gambit, then using the mshconvert.py tool to convert a simple mesh with a circular cylinder inside a square. simply, I can get the *rea file with circle of the "W", "v" and "O". but I have met two problems; 1. to impose the periodic boundary conditons: in the script, it strongly recommend to impose "P" through the script, then how to setup it in mshconvert.py? the way convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) can generate the rea field but failed in the step of genmap. so how to treat boundary 4 and 5 as periodic BCs? 2. about the curved wall. there is no problem to define a circle by "Circle" command, but if I want to using "m" to define a spline curve, how to seed middle points? I know in Gambit I can mesh the line using 3 node, I defined 3 node mode to mesh a circle, and using "m" instead of "circle", however, it failed to generate the rea file. the circle merged into a point, then what should I do to active the spline curve? Thanks! Wei 2016-06-08 15:46 GMT+02:00 <nek5000-users(a)lists.mcs.anl.gov>: > Hi Mansi, > > You can find the updated "mshconvert.py" in the attachment. You can run > the script for your case likes > > ### > $ ipython > > In [1]: from mshconvert import * > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > format > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > ... > ### > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > 'O' on zone 13. > > The snapshot for the Nek5000 mesh using visit is also attached in the > email. > > /Jing > >

1 1

Nek5000 Users Meeting, Aug. 10-12, 2016, Cambridge, MA
by nek5000-users＠lists.mcs.anl.gov 09 Jun '16

09 Jun '16

Dear Neks, Registration is now open for the 5th Nek5000 Users Meeting, to be held August 10-12, 2016, on the M.I.T. campus in Cambridge, Massachussets. As this year marks the 30th anniversary of Nek5000, which started as Nekton 2.0 in 1986, we have planned a special format for this meeting. The first day will feature several invited speakers who made significant contributions to the theory and development of high-order methods, as well as some of the principal user/developers who have pushed these methods to the limit in important application areas on the world's fastest computers. The second and third day will feature our standard User/Developer Meeting format, with 10 minute talks by each participant along with a handful of more extended presentations. We anticipate 40-60 participants. Invited speakers include Michel Deville (EPFL), Yvon Maday (Paris VI), Anthony Patera (MIT), Alfio Quarteroni(EPFL), Philipp Schlatter (KTH), and Ananias Tomboulides (AUT/ANL). There will be a conference dinner at Legal Seafood near the M.I.T. campus (walking distance from the meeting venue). We hope you will sign up for this opportunity to enjoy a collegial evening at a classic New England institution. We note that August is a busy tourist time in Boston and so encourage you to book your travel plans, hotel especially, early. Registration and instructions for submitting a presentation can be found at the following URL: https://www.regonline.com/builder/site/Default.aspx?EventID=1823410 We look forward to seeing you in August! Your local Nek development team.

1 0

rms in turbChannel
by nek5000-users＠lists.mcs.anl.gov 09 Jun '16

09 Jun '16

Hello, In the userchk subroutine in the .usr file for the turbChannel example, what line of code can I add so rms values can be written in a .dat file such as it is done for umean and reystresses values. ! write statistics to file iostep_avg = param(68) if (nid.eq.0 .and. istep.gt.0 .and. & mod(istep,iostep_avg).eq.0) then write(6,*) 'Dumping statistics ...' open(unit=56,file='reystresses.dat') write(56,'(A,1pe14.7)') '#time = ', time write(56,'(A)') & '# y y+ R_uu R_vv R_ww R_uv' open(unit=57,file='means.dat') write(57,'(A,1pe14.7)') '#time = ', time write(57,'(A)') & '# y y+ Umean' m = ny1*nely/2 do i=1,m write(56,3) yy(i)+1 & ,(yy(i)+1)*Re_tau & , (urms_pl(i)-(uavg_pl(i))**2)/u_tau**2 & , vrms_pl(i)/u_tau**2 & , wrms_pl(i)/u_tau**2 & , uvms_pl(i)/u_tau**2 write(57,3) yy(i) + 1. & , (yy(i)+1.)*Re_tau & , uavg_pl(i)/u_tau 3 format(1p15e17.9) enddo close(56) close(57) timel = time endif return end Thank you, Virgilio A. Gomez

1 0

getting velocity profile for laminar and turbulent re
by nek5000-users＠lists.mcs.anl.gov 09 Jun '16

09 Jun '16

dear NEKS I am trying a simple case of flow through a 2d antisymmetric pipe for laminar and turbulent Re. The pipe is vertical and the flow is upward with an initial velocity. I want to match the velocity curve with the analytical velocity curves. Any ideas how i should go about it?please help Apoorva

1 0

grid2grid interpolation
by nek5000-users＠lists.mcs.anl.gov 09 Jun '16

09 Jun '16

Hello Neks, I am trying to refine my current mesh using Prenek and interpolating my current data from the current grid to the refined one. I kept following the instructions for the function g2gi() and was able to run makenek successful. But using nek or nekmpi keeps giving me following error messages. For nek: /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1061 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 [satyajit-All-Series:17818] *** An error occurred in MPI_Bcast [satyajit-All-Series:17818] *** on communicator MPI COMMUNICATOR 3 DUP FROM 0 [satyajit-All-Series:17818] *** MPI_ERR_TYPE: invalid datatype [satyajit-All-Series:17818] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort real 0m0.029s user 0m0.005s sys 0m0.010s and for nekmpi: /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1061 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 2 REAL wdsize : 8 INTEGER wdsize : 4 ERROR (proc 0000, /home/michaelr/nek5_svn/trunk/nek/jl/fcrystal.c:94): comm_init_check: passed P=2, but not compiled with -DMPI call exitt: dying ... ERROR (proc 0000, /home/michaelr/nek5_svn/trunk/nek/jl/fcrystal.c:94): comm_init_check: passed P=2, but not compiled with -DMPI backtrace(): obtained 11 stack frames. ./nek5000() [0x4e6b0a] ./nek5000() [0x5a55e9] ./nek5000() [0x5dfe25] ./nek5000() [0x5dfeba] ./nek5000() [0x5e0053] ./nek5000() [0x5a7b96] ./nek5000() [0x5a8a28] ./nek5000() [0x402c5f] ./nek5000() [0x4022d4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f95d20b3ec5] ./nek5000() [0x402319] total elapsed time : 1.46547E+09 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec Any suggestions? Br, Michael

1 0