From nek5000-users at lists.mcs.anl.gov Tue Nov 1 03:07:43 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Nov 2016 16:07:43 +0800 (GMT+08:00) Subject: [Nek5000-users] Setting self-defined variable properties in USERVP Message-ID: Hello,neks In my simulation, fluid density 'Rho', dynamic viscosity 'Visco', thermal diffusivity 'Conduct' are all the function of the temperature, so I define them in USERVP as below: subroutine uservp (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' common /nob_coef/Kn(1:3),Bn(1:3),Cn(1:3),Dn(1:3), $ En(1:3),Fn(1:3) common /constant/Rhom,Cpm,Tm,Alpham,Kappam,Km, $ Viscom,delta_T,rho0 real*8 Kn,Bn,Cn,Dn,En,Fn, $ Rhom,Cpm,Tm,Alpham,Kappam,Km, $ Viscom,delta_T,rho0 integer i,j,k,e,n,iel Rhom = 0.9922*1e3 Cpm = 4.1690*1e3 Alpham = 3.8810*1e-4 Km = 0.6297 Kappam = 0.1528*1e-6 Viscom = 0.669*1e-6 Tm = 40 Kn=[ -175.9*1e-4,295.8*1e-6,-460*1e-8] Bn=[23.52*1e-4,-14.9*1e-6,0.] Cn= [-3.736*1e3,-3.98*1e3,0.] Dn= [0.084*1e3,4.6*1e3,0.] En = [195*1e-4,-159.8*1e-4,207*1e-4] Fn=[21.99,-17.8,0.] iel=gllel(ieg) if (IFIELD.eq. 1)then udiff = Rhom utrans = 0. rho0 = 0. do i=1,3 utrans = utrans + Kn(i)*((temp-0.5)*delta_T)**i rho0 = rho0 + Cn(i)*((temp-0.5)*delta_T)**i enddo utrans=utrans*Viscom+Viscom rho0=rho0*Rhom+Rhom utrans=utrans*rho0 endif if (IFIELD.eq. 2)then udiff = Rhom*Cpm utrans = 0. do i=1,3 utrans = utrans + Fn(i)*((temp-0.5)*delta_T)**i enddo utrans=utrans*Km+Km endif return end then I set p30=1 in .rea file. But the program cannot run, it seems that some errors occured when reading .rea file. I know from the user guide that variable properties are supported but I am little confused about if the properties which are the functions of other flow field variables(like u, v, w or temperature) also can be set correctly in USERVP. Did anyone meet problems like this before? 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 Wed Nov 2 07:44:09 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Nov 2016 08:44:09 -0400 Subject: [Nek5000-users] Read Nek output in Matlab Message-ID: Hi Neks, I would like to make some postprocessing with the Nek output. Can I read that files in Matlab (or C)? Just to make it clear: If my .rea file is called whatever.rea and the output is whatever0.f00**** I would like to read whatever0.f00**** and make some postprocessing. It will be also very helpful to learn how to extrapolate the mesh so that I can plot combinations of the solutions for instance. Thank you so much, 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 Wed Nov 2 09:20:57 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Nov 2016 14:20:57 +0000 Subject: [Nek5000-users] Read Nek output in Matlab In-Reply-To: References: Message-ID: Alessandro, Set, in usrdat2 in your .usr file the following lines: param(66)=0 param(67)=0 this will give you an ascii file output. blah.fld01 blah.fld02 etc You can edit these files or write a short script to take off the header or whatever and then load the data into matlab. Usual data lay out (for 2D) is: x y u v p T for fld01 and u v p T for all other fields. 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: Wednesday, November 02, 2016 7:44 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Read Nek output in Matlab Hi Neks, I would like to make some postprocessing with the Nek output. Can I read that files in Matlab (or C)? Just to make it clear: If my .rea file is called whatever.rea and the output is whatever0.f00**** I would like to read whatever0.f00**** and make some postprocessing. It will be also very helpful to learn how to extrapolate the mesh so that I can plot combinations of the solutions for instance. Thank you so much, 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 Nov 3 15:24:30 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Nov 2016 20:24:30 +0000 Subject: [Nek5000-users] How to put cyclic BCs in a .rea file... Message-ID: For those of you who have used the cyclic BC, how do you normally specify the periodic connectivity in the .rea file ? Do you first feed it a regular mesh and then morph the geometry to have the desired curvature? Otherwise I don't see how genmap would figure out the proper periodicity. Thanks! Paul (genmap author....) -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 3 14:37:35 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 03 Nov 2016 21:37:35 +0200 Subject: [Nek5000-users] How to put cyclic BCs in a .rea file... Message-ID: Dear genmap author, if I recall correctly genmap figured that out somehow. It was always magic to me but it worked ;) Cheers, Stefan Von: on behalf of Antworten an: Datum: Thursday, November 3, 2016 at 10:24 PM An: "nek5000-users at lists.mcs.anl.gov" Betreff: [Nek5000-users] How to put cyclic BCs in a .rea file... For those of you who have used the cyclic BC, how do you normally specify the periodic connectivity in the .rea file ? Do you first feed it a regular mesh and then morph the geometry to have the desired curvature? Otherwise I don't see how genmap would figure out the proper periodicity. Thanks! Paul (genmap author....) _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 4 13:21:28 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 Nov 2016 18:21:28 +0000 (UTC) Subject: [Nek5000-users] Saving ddot References: <29577131.373243.1478283688147.ref@mail.yahoo.com> Message-ID: Hello Nek users,? Is there a way to save not only the current state (velocities and pressure fields) but also their time derivatives? I am particular interested in this information for perturbations... Thanks in Advance Eduardo MartiniPhd Candidate, ITA, Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 7 15:37:32 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 7 Nov 2016 16:37:32 -0500 Subject: [Nek5000-users] A problem in Prenek Message-ID: Hello Neks, I am encountering a typographic problem in the .rea file when I am increasing the number of elements beyond 1000, in the GLOBAL REFINE. The problem is in the spacings in the Boundary Condition's. For instance it says - E 30724 2731.00 2.00000 0.00000 0.00000 0.00000 While it should say, E 3072 4 2731.00 2.00000 0.00000 0.00000 0.00000 Since the number of elements exceeds 1000, a space is missing between 3072 and 4. I am sure this is a simple fix. Any help is appreciated. Attached is the .rea file. 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: #g40cond2.rea# Type: application/octet-stream Size: 4289289 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 8 15:32:25 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 8 Nov 2016 21:32:25 +0000 Subject: [Nek5000-users] A problem in Prenek Message-ID: Hi Saikat, I think this is what is expected. If we look at postpro.f in nek?s source code (subroutine gen_rea_bc), there are 4 different formats in which the boundary conditions will be written depending on the element count. In your case, since the element count is greater than 1000 but less than 100,000, we expect the format to be: first 4 character spaces for boundary condition, next 5 characters for element number, 1 character for edge/face number depending on 2d/3d and so on. As a result, your boundary condition line shows as: E 30724 2731.00 2.00000 0.00000 0.00000 0.00000 Thanks, Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 8 20:16:20 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Nov 2016 10:16:20 +0800 Subject: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py Message-ID: Hi, neks I tried to convert a 2D circular ring mesh generated by gambit to .rea file using the code mshconvert.py, but failed. I converted the example mesh file sirkel4.msh following the step in README, then I have a question that what command I should input when my mesh has more than one curved boundary just like a ring mesh. For sirkel4.msh the command "7:{..}" means that the zone 7 is curved, if I have two curved zones, for example, zone 3 and 4, should I input "3:{....},4:{....}" in one command line? Thank you in advance. Regards, Xu ---------------------------------------------------------------- Bolun Xu University of Science and Technology of Chnia Hefei, Anhui, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 9 06:45:32 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Nov 2016 13:45:32 +0100 Subject: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py In-Reply-To: References: Message-ID: Dear Bolun, Yes, you should specify the different curved zones separately. There is a bit of documentation at the end of the file "mshconvert.py". Here is what is said about the curves input: " curves = Dictionary of curve information. Keys are curve zones and value is either {'type': 'C', 'radius': radius, 'circle_center': (x, y), 'depth': depth} for a circle or {'type': 'm'} for midpoint with nek5000 or {'type': 'spline'} for a curved side with semtex. Here a .geom file containing the spline information will be created. The circle may provide the radius or the center of the circle through 'circle_center'. The curvature may also be used in the internal elements inside the surface through specifying the depth. depth=4 means that the curvature is used throughout the first four elements inside that surface. This is necessary to get good quality meshes in, e.g., a cylinder. The radius for an internal face is always computed as the distance to the circle_center. Not for FEniCS. " I hope that helps. Best, Nicolas Offermans On Wed, Nov 9, 2016 at 3:16 AM, wrote: > Hi, neks > > I tried to convert a 2D circular ring mesh generated by gambit to .rea > file using the code mshconvert.py, but failed. I converted the example mesh > file sirkel4.msh following the step in README, then I have a question that > what command I should input when my mesh has more than one curved boundary > just like a ring mesh. For sirkel4.msh the command ?7:{??}? means that the > zone 7 is curved, if I have two curved zones, for example, zone 3 and 4, > should I input ?3:{??..},4:{??..}? in one command line? > > Thank you in advance. > > Regards, > > Xu > > > > ---------------------------------------------------------------- > > Bolun Xu > > University of Science and Technology of Chnia > > Hefei, Anhui, China > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 9 06:50:59 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Nov 2016 13:50:59 +0100 Subject: [Nek5000-users] Read Nek output in Matlab In-Reply-To: References: Message-ID: Hi Alessandro, alternatively you can use the functions that I and a colleague of mine wrote. They can read and write nek's files. You can find them here https://github.com/nfabbiane/nekmatlab Cheers, Jacopo On 2016-11-02 15:20, nek5000-users at lists.mcs.anl.gov wrote: > Alessandro, > > Set, in usrdat2 in your .usr file the following lines: > > param(66)=0 > param(67)=0 > > this will give you an ascii file output. blah.fld01 blah.fld02 etc > > You can edit these files or write a short script to take off the header or > whatever and then load the data into matlab. > > Usual data lay out (for 2D) is: > > x y u v p T > > for fld01 > > and > > u v p T > > for all other fields. > > 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: Wednesday, November 02, 2016 7:44 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Read Nek output in Matlab > > Hi Neks, > > I would like to make some postprocessing with the Nek output. Can I read > that files in Matlab (or C)? > > Just to make it clear: If my .rea file is called whatever.rea and the > output is whatever0.f00**** > > I would like to read whatever0.f00**** and make some postprocessing. It > will be also very helpful to learn how to extrapolate the mesh so that I > can plot combinations of the solutions for instance. > > Thank you so much, > > 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 From nek5000-users at lists.mcs.anl.gov Wed Nov 9 09:27:12 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Nov 2016 16:27:12 +0100 Subject: [Nek5000-users] Name of the variable in userf and userq Message-ID: Hi Neks, I am trying to set volume forcing in my equations through userf and userq. However it is not for the baseflow but for perturbations. Does anyone know the name of the perturbations variables which are equivalent to ffx, ffy, ffz, and qvol? So I can write something like : ffxp = ... ffyp = ... ffzp = ... qvolp = ... Thank you for your time, Best wishes, Arnold From nek5000-users at lists.mcs.anl.gov Wed Nov 9 08:42:23 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Nov 2016 15:42:23 +0100 Subject: [Nek5000-users] PostDoc Position using NEK5000 Message-ID: Dear Nek5000 users, We have two immediate postdoc positions in our group in CORIA lab. (CNRS), Rouen, France. One of these position is on the use of Nek5000 software for converging and diverging pipe flows. We are looking for a talented young researcher who has a good knowledge of Nek5000 to join to our group for Jan./Feb. 2017. Please feel free to send your CV along with your references to me. More details about the position can be found in: http://www.cfd-online.com/Jobs/showjob.php?record_id=13809 Best, Mostafa -- Kind Regards, ****************************************** Mostafa SAFDARI SHADLOO Associate Professor, CNRS-University & INSA of Rouen 76800 St Etienne du Rouvray, France Office: (+33) 02 32 95 97 76 Emailto: msshadloo at coria.fr , mostafa at sabanciuniv.edu ****************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 9 20:11:56 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Nov 2016 10:11:56 +0800 Subject: [Nek5000-users] =?gb2312?b?tPC4tDogTmVrNTAwMC11c2VycyBEaWdlc3Qs?= =?gb2312?b?IFZvbCA5MywgSXNzdWUgNg==?= In-Reply-To: References: Message-ID: Hello, Nicolas I read the documentation again carefully and very happy that my problem has been solved. Thank you very much for advice. I would like to share the curve definition parts in my mesh converting commands for a ring below: Curves={4:{'type':'C','depth':4,'circle_center':(0,0), 'radius':1},3:{'type':'C','depth':4,'circle_center':(0,0),'radius':0.5}} For 4 and 3 are outer and inner circle. ---------------------------------------------------------------- Bolun Xu University of Science and Technology of China Hefei, Anhui, China -----????----- ???: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] ?? nek5000-users-request at lists.mcs.anl.gov ????: 2016?11?9? 23:27 ???: nek5000-users at lists.mcs.anl.gov ??: Nek5000-users Digest, Vol 93, Issue 6 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: A problem in Prenek (nek5000-users at lists.mcs.anl.gov) 2. 2D circular ring mesh converting by mshconvert.py (nek5000-users at lists.mcs.anl.gov) 3. Re: 2D circular ring mesh converting by mshconvert.py (nek5000-users at lists.mcs.anl.gov) 4. Re: Read Nek output in Matlab (nek5000-users at lists.mcs.anl.gov) 5. Name of the variable in userf and userq (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Nov 2016 21:32:25 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: Re: [Nek5000-users] A problem in Prenek Message-ID: Content-Type: text/plain; charset="utf-8" Hi Saikat, I think this is what is expected. If we look at postpro.f in nek?s source code (subroutine gen_rea_bc), there are 4 different formats in which the boundary conditions will be written depending on the element count. In your case, since the element count is greater than 1000 but less than 100,000, we expect the format to be: first 4 character spaces for boundary condition, next 5 characters for element number, 1 character for edge/face number depending on 2d/3d and so on. As a result, your boundary condition line shows as: E 30724 2731.00 2.00000 0.00000 0.00000 0.00000 Thanks, Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 9 Nov 2016 10:16:20 +0800 From: nek5000-users at lists.mcs.anl.gov To: Subject: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py Message-ID: Content-Type: text/plain; charset="us-ascii" Hi, neks I tried to convert a 2D circular ring mesh generated by gambit to .rea file using the code mshconvert.py, but failed. I converted the example mesh file sirkel4.msh following the step in README, then I have a question that what command I should input when my mesh has more than one curved boundary just like a ring mesh. For sirkel4.msh the command "7:{..}" means that the zone 7 is curved, if I have two curved zones, for example, zone 3 and 4, should I input "3:{....},4:{....}" in one command line? Thank you in advance. Regards, Xu ---------------------------------------------------------------- Bolun Xu University of Science and Technology of Chnia Hefei, Anhui, China -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 9 Nov 2016 13:45:32 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py Message-ID: Content-Type: text/plain; charset="utf-8" Dear Bolun, Yes, you should specify the different curved zones separately. There is a bit of documentation at the end of the file "mshconvert.py". Here is what is said about the curves input: " curves = Dictionary of curve information. Keys are curve zones and value is either {'type': 'C', 'radius': radius, 'circle_center': (x, y), 'depth': depth} for a circle or {'type': 'm'} for midpoint with nek5000 or {'type': 'spline'} for a curved side with semtex. Here a .geom file containing the spline information will be created. The circle may provide the radius or the center of the circle through 'circle_center'. The curvature may also be used in the internal elements inside the surface through specifying the depth. depth=4 means that the curvature is used throughout the first four elements inside that surface. This is necessary to get good quality meshes in, e.g., a cylinder. The radius for an internal face is always computed as the distance to the circle_center. Not for FEniCS. " I hope that helps. Best, Nicolas Offermans On Wed, Nov 9, 2016 at 3:16 AM, wrote: > Hi, neks > > I tried to convert a 2D circular ring mesh generated by gambit to .rea > file using the code mshconvert.py, but failed. I converted the example > mesh file sirkel4.msh following the step in README, then I have a > question that what command I should input when my mesh has more than > one curved boundary just like a ring mesh. For sirkel4.msh the command > ?7:{??}? means that the zone 7 is curved, if I have two curved zones, > for example, zone 3 and 4, should I input ?3:{??..},4:{??..}? in one command line? > > Thank you in advance. > > Regards, > > Xu > > > > ---------------------------------------------------------------- > > Bolun Xu > > University of Science and Technology of Chnia > > Hefei, Anhui, China > > > > > > _______________________________________________ > 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: ------------------------------ Message: 4 Date: Wed, 9 Nov 2016 13:50:59 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Read Nek output in Matlab Message-ID: Content-Type: text/plain; charset=windows-1252; format=flowed Hi Alessandro, alternatively you can use the functions that I and a colleague of mine wrote. They can read and write nek's files. You can find them here https://github.com/nfabbiane/nekmatlab Cheers, Jacopo On 2016-11-02 15:20, nek5000-users at lists.mcs.anl.gov wrote: > Alessandro, > > Set, in usrdat2 in your .usr file the following lines: > > param(66)=0 > param(67)=0 > > this will give you an ascii file output. blah.fld01 blah.fld02 etc > > You can edit these files or write a short script to take off the > header or whatever and then load the data into matlab. > > Usual data lay out (for 2D) is: > > x y u v p T > > for fld01 > > and > > u v p T > > for all other fields. > > 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: Wednesday, November 02, 2016 7:44 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Read Nek output in Matlab > > Hi Neks, > > I would like to make some postprocessing with the Nek output. Can I > read that files in Matlab (or C)? > > Just to make it clear: If my .rea file is called whatever.rea and the > output is whatever0.f00**** > > I would like to read whatever0.f00**** and make some postprocessing. > It will be also very helpful to learn how to extrapolate the mesh so > that I can plot combinations of the solutions for instance. > > Thank you so much, > > 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 ------------------------------ Message: 5 Date: Wed, 9 Nov 2016 16:27:12 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Name of the variable in userf and userq Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed Hi Neks, I am trying to set volume forcing in my equations through userf and userq. However it is not for the baseflow but for perturbations. Does anyone know the name of the perturbations variables which are equivalent to ffx, ffy, ffz, and qvol? So I can write something like : ffxp = ... ffyp = ... ffzp = ... qvolp = ... 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 End of Nek5000-users Digest, Vol 93, Issue 6 ******************************************** From nek5000-users at lists.mcs.anl.gov Fri Nov 11 01:54:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 11 Nov 2016 13:54:24 +0600 Subject: [Nek5000-users] Boundary condition on velocity Message-ID: Hi, neks. I am trying to simulate a 3d pipe, fluid flows along z. And I need an inflow boundary condition on velocity on forming of cylinder. How I can set a radial velocity in userbc (Vr = sqrt( vx**2+vy**2 ) ) ? I need to set Vr and dVr/dr. Thank you so mach Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 11 09:09:04 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 11 Nov 2016 15:09:04 +0000 Subject: [Nek5000-users] Boundary condition on velocity In-Reply-To: References: Message-ID: Hi Vatslav, Assuming your pipe is radius R, centered at x=y=0, then: rr = (x/R)**2 + (y/R)**2 uz = 1-rr should work for axial. For the radial that you prescribe, ux = x ! = r cos theta = sqrt(rr)*(x/r) = x uy = y 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, November 11, 2016 1:54 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Boundary condition on velocity Hi, neks. I am trying to simulate a 3d pipe, fluid flows along z. And I need an inflow boundary condition on velocity on forming of cylinder. How I can set a radial velocity in userbc (Vr = sqrt( vx**2+vy**2 ) ) ? I need to set Vr and dVr/dr. Thank you so mach Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 14 13:38:41 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 Nov 2016 19:38:41 +0000 Subject: [Nek5000-users] How to know if a solution if converged? Message-ID: Dear Nek users, I have a numerical solution for a turbulent flow and would like to know if my solution is well converged. My current method consists in monitoring the average velocity. I would like to know if there is a more advanced method/technique I could use in order to determine whether or not my solution is converged. Thanks, Marco From nek5000-users at lists.mcs.anl.gov Mon Nov 14 17:37:11 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 Nov 2016 18:37:11 -0500 Subject: [Nek5000-users] Linear Systems and Solvers in Nek5000 Message-ID: Hello Nek users, This could be a simple question to some, but any help would be great here. I am working on a project that is aiming to suggest appropriate solvers for the system Ax = b, using Machine Learning, given the matrix A. I know that there are many matrix datasets online, but for specific reasons, we want to extract matrices from Nek5000 (compute features from that) and note the solvers it uses for those linear systems. The Navier-Stokes equation is non-linear due to the advection term, but in certain cases, the governing equations reduce to being linear. I am trying to understand what those cases are and the solvers that Nek uses to handle those linear systems. Based on my reading from various sources, it looks like Nek handles the following linear system cases. Any comments on this would be very helpful: 1) *System:* Poisson equation for Pressure (incompressible case?) *Solvers:* Nek supports GMRES and PCG with Parameter P042 (from http://nek5000.github.io/NekDoc/Nek_usersch7.html#x9-750007.1) 2) https://www.mcs.anl.gov/~fischer/Nek5000/nek_tutorial_1.pdf - Page 44 What is the Helmholtz solve for velocity here? Is this the only "solver" for velocity? 3) http://nek5000.github.io/NekDoc/Nek_usersch1.html#x3-50001.1 *System*: Energy equation behaves as a transport equation for temperature right? *Solvers*: Helmholz, CVODE, CVODE with user-supplied Jacobian. 4) All Stokes flow cases with constant viscosity? Does this seem correct? If you need any other information, please let me know. Thanking You, K.N.Ramachandran (Ram) Ph: 814-441-4279 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 15 15:31:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Nov 2016 19:31:24 -0200 Subject: [Nek5000-users] Error Compiling Message-ID: Hi all, I'm ver new at nek5000. I'm trying to compiling a first example case (eddy) and I get a error. After ./makenek eddy_uv I get: ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file or directory make: makefile: No such file or directory make: *** No rule to make target 'makefile'. Stop. Can someone help me? -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 15 21:11:27 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 03:11:27 +0000 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: What does echo $PATH return for you? On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: Hi all, I'm ver new at nek5000. I'm trying to compiling a first example case (eddy) and I get a error. After ./makenek eddy_uv I get: ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file or directory make: makefile: No such file or directory make: *** No rule to make target 'makefile'. Stop. Can someone help me? -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 10:12:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 14:12:24 -0200 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: I realize my mistake. My PATH was wrong, now I can compile without problems. But now I have other problem. After compile with makenek and after run with nekb I can't vizualize the results with postx. My path is /bin, I type ./postx and I got a black window without a sidebar. Whats wrong? Thanks. 2016-11-16 1:11 GMT-02:00 : > What does echo $PATH return for you? > > On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi all, > > I'm ver new at nek5000. I'm trying to compiling a first example case > (eddy) and I get a error. > > After ./makenek eddy_uv > > I get: > > ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file > or directory > make: makefile: No such file or directory > make: *** No rule to make target 'makefile'. Stop. > > Can someone help me? > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > _______________________________________________ > 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 > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 10:27:07 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 14:27:07 -0200 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: I realize my mistake. My PATH was wrong, now I can compile without problems. But now I have other problem. After compile with makenek and after run with nekb I can't vizualize the results with postx. My path is /bin, I type ./postx and I got a black window without a sidebar. When I ran with ./nekb I got 2 errors: mv: cannot stat 'eddy_uv.log': No such file or directory mv: cannot stat 'eddy_uv.sch': No such file or directory nohup: redirecting stderr to stdout But the simulation still ran. Whats wrong? Thanks. 2016-11-16 1:11 GMT-02:00 : > What does echo $PATH return for you? > > On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi all, > > I'm ver new at nek5000. I'm trying to compiling a first example case > (eddy) and I get a error. > > After ./makenek eddy_uv > > I get: > > ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file > or directory > make: makefile: No such file or directory > make: *** No rule to make target 'makefile'. Stop. > > Can someone help me? > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > _______________________________________________ > 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 > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 10:34:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 16:34:24 +0000 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: I think you can ignore the error message you are getting. As for visualization of the solution, you can also use visit or paraview. You have to use visnek. Marco On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: I realize my mistake. My PATH was wrong, now I can compile without problems. But now I have other problem. After compile with makenek and after run with nekb I can't vizualize the results with postx. My path is /bin, I type ./postx and I got a black window without a sidebar. Whats wrong? Thanks. 2016-11-16 1:11 GMT-02:00 >: What does echo $PATH return for you? On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: Hi all, I'm ver new at nek5000. I'm trying to compiling a first example case (eddy) and I get a error. After ./makenek eddy_uv I get: ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file or directory make: makefile: No such file or directory make: *** No rule to make target 'makefile'. Stop. Can someone help me? -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ 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 -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 10:41:34 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 14:41:34 -0200 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: Thanks for the answer. I tried to use visnek. After type ./visnek eddy_uv I got these error: bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory Any ideia? Mateus. 2016-11-16 14:34 GMT-02:00 : > I think you can ignore the error message you are getting. > > As for visualization of the solution, you can also use visit or paraview. > You have to use visnek. > > Marco > > On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: > > I realize my mistake. My PATH was wrong, now I can compile without > problems. > > But now I have other problem. After compile with makenek and after run > with nekb I can't vizualize the results with postx. > My path is /bin, I type ./postx and I got a black window without a > sidebar. > > Whats wrong? > > Thanks. > > 2016-11-16 1:11 GMT-02:00 : > >> What does echo $PATH return for you? >> >> On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi all, >> >> I'm ver new at nek5000. I'm trying to compiling a first example case >> (eddy) and I get a error. >> >> After ./makenek eddy_uv >> >> I get: >> >> ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file >> or directory >> make: makefile: No such file or directory >> make: *** No rule to make target 'makefile'. Stop. >> >> Can someone help me? >> >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> *http://lattes.cnpq.br/1773896725783894 >> * >> _______________________________________________ >> 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 >> >> > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > _______________________________________________ > 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 > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 11:16:22 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 17:16:22 +0000 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: Try ?visnek eddy_uv? without the ?./' On Nov 16, 2016, at 11:41 AM, nek5000-users at lists.mcs.anl.gov wrote: Thanks for the answer. I tried to use visnek. After type ./visnek eddy_uv I got these error: bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory Any ideia? Mateus. 2016-11-16 14:34 GMT-02:00 >: I think you can ignore the error message you are getting. As for visualization of the solution, you can also use visit or paraview. You have to use visnek. Marco On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: I realize my mistake. My PATH was wrong, now I can compile without problems. But now I have other problem. After compile with makenek and after run with nekb I can't vizualize the results with postx. My path is /bin, I type ./postx and I got a black window without a sidebar. Whats wrong? Thanks. 2016-11-16 1:11 GMT-02:00 >: What does echo $PATH return for you? On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: Hi all, I'm ver new at nek5000. I'm trying to compiling a first example case (eddy) and I get a error. After ./makenek eddy_uv I get: ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file or directory make: makefile: No such file or directory make: *** No rule to make target 'makefile'. Stop. Can someone help me? -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ 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 -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ 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 -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 18:05:18 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 17:05:18 -0700 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: Also visnek requires tcsh shell. Try installing that as well. Best Regards, Tanmoy On Wed, Nov 16, 2016 at 10:16 AM, wrote: > Try ?visnek eddy_uv? without the ?./' > > On Nov 16, 2016, at 11:41 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Thanks for the answer. > > I tried to use visnek. After type ./visnek eddy_uv I got these error: > > bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory > > Any ideia? > > Mateus. > > 2016-11-16 14:34 GMT-02:00 : > >> I think you can ignore the error message you are getting. >> >> As for visualization of the solution, you can also use visit or paraview. >> You have to use visnek. >> >> Marco >> >> On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: >> >> I realize my mistake. My PATH was wrong, now I can compile without >> problems. >> >> But now I have other problem. After compile with makenek and after run >> with nekb I can't vizualize the results with postx. >> My path is /bin, I type ./postx and I got a black window without a >> sidebar. >> >> Whats wrong? >> >> Thanks. >> >> 2016-11-16 1:11 GMT-02:00 : >> >>> What does echo $PATH return for you? >>> >>> On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi all, >>> >>> I'm ver new at nek5000. I'm trying to compiling a first example case >>> (eddy) and I get a error. >>> >>> After ./makenek eddy_uv >>> >>> I get: >>> >>> ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file >>> or directory >>> make: makefile: No such file or directory >>> make: *** No rule to make target 'makefile'. Stop. >>> >>> Can someone help me? >>> >>> >>> -- >>> Mateus Peixoto Avanci >>> Engenheiro Mec?nico >>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>> Universidade Federal Fluminense >>> *http://lattes.cnpq.br/1773896725783894 >>> * >>> _______________________________________________ >>> 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 >>> >>> >> >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> *http://lattes.cnpq.br/1773896725783894 >> * >> _______________________________________________ >> 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 >> >> > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 18:48:10 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Nov 2016 22:48:10 -0200 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: I tried and I got "command not found". I copied visnek from /bin and paste at the eddy folder, is that right? 2016-11-16 15:16 GMT-02:00 : > Try ?visnek eddy_uv? without the ?./' > > On Nov 16, 2016, at 11:41 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Thanks for the answer. > > I tried to use visnek. After type ./visnek eddy_uv I got these error: > > bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory > > Any ideia? > > Mateus. > > 2016-11-16 14:34 GMT-02:00 : > >> I think you can ignore the error message you are getting. >> >> As for visualization of the solution, you can also use visit or paraview. >> You have to use visnek. >> >> Marco >> >> On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: >> >> I realize my mistake. My PATH was wrong, now I can compile without >> problems. >> >> But now I have other problem. After compile with makenek and after run >> with nekb I can't vizualize the results with postx. >> My path is /bin, I type ./postx and I got a black window without a >> sidebar. >> >> Whats wrong? >> >> Thanks. >> >> 2016-11-16 1:11 GMT-02:00 : >> >>> What does echo $PATH return for you? >>> >>> On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi all, >>> >>> I'm ver new at nek5000. I'm trying to compiling a first example case >>> (eddy) and I get a error. >>> >>> After ./makenek eddy_uv >>> >>> I get: >>> >>> ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file >>> or directory >>> make: makefile: No such file or directory >>> make: *** No rule to make target 'makefile'. Stop. >>> >>> Can someone help me? >>> >>> >>> -- >>> Mateus Peixoto Avanci >>> Engenheiro Mec?nico >>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>> Universidade Federal Fluminense >>> *http://lattes.cnpq.br/1773896725783894 >>> * >>> _______________________________________________ >>> 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 >>> >>> >> >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> *http://lattes.cnpq.br/1773896725783894 >> * >> _______________________________________________ >> 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 >> >> > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > _______________________________________________ > 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 > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 17 02:22:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Nov 2016 09:22:42 +0100 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: Sorry this mailing list is not about learning Linux. Don?t get me wrong but I would suggest you learn Linux and the command line first. Von: on behalf of Antworten an: Datum: Thursday, November 17, 2016 at 1:48 AM An: Betreff: Re: [Nek5000-users] Error Compiling I tried and I got "command not found". I copied visnek from /bin and paste at the eddy folder, is that right? 2016-11-16 15:16 GMT-02:00 : > Try ?visnek eddy_uv? without the ?./' >> On Nov 16, 2016, at 11:41 AM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Thanks for the answer. >> >> I tried to use visnek. After type ./visnek eddy_uv I got these error: >> >> bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory >> >> Any ideia? >> >> Mateus. >> >> 2016-11-16 14:34 GMT-02:00 : >>> I think you can ignore the error message you are getting. >>> >>> As for visualization of the solution, you can also use visit or paraview. >>> You have to use visnek. >>> >>> Marco >>> >>>> On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> I realize my mistake. My PATH was wrong, now I can compile without >>>> problems. >>>> >>>> But now I have other problem. After compile with makenek and after run with >>>> nekb I can't vizualize the results with postx. >>>> My path is /bin, I type ./postx and I got a black window without a sidebar. >>>> >>>> Whats wrong? >>>> >>>> Thanks. >>>> >>>> 2016-11-16 1:11 GMT-02:00 : >>>>> What does echo $PATH return for you? >>>>>> On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm ver new at nek5000. I'm trying to compiling a first example case >>>>>> (eddy) and I get a error. >>>>>> >>>>>> After ./makenek eddy_uv >>>>>> >>>>>> I get: >>>>>> >>>>>> ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such file >>>>>> or directory >>>>>> make: makefile: No such file or directory >>>>>> make: *** No rule to make target 'makefile'. Stop. >>>>>> >>>>>> Can someone help me? >>>>>> >>>>>> >>>>>> -- >>>>>> Mateus Peixoto Avanci >>>>>> Engenheiro Mec?nico >>>>>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>>>>> Universidade Federal Fluminense >>>>>> http://lattes.cnpq.br/1773896725783894 >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> Mateus Peixoto Avanci >>>> Engenheiro Mec?nico >>>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>>> Universidade Federal Fluminense >>>> http://lattes.cnpq.br/1773896725783894 >>>> _______________________________________________ >>>> 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 >>> >> >> >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> http://lattes.cnpq.br/1773896725783894 >> _______________________________________________ >> 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 > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense http://lattes.cnpq.br/1773896725783894 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 16 23:57:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Nov 2016 08:57:15 +0300 Subject: [Nek5000-users] =?utf-8?q?Autosphere=27s_radius?= Message-ID: Hi, Neks! I am trying to create an own mesh, based on expansion example. When I build a circle in pretex, it is always has radius = 0.5. Can I change it in the pretex directly? (Now I could vary only numbers of elements in inner and outer shells). Thanks in advance,? Jacob. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 17 10:09:09 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Nov 2016 16:09:09 +0000 Subject: [Nek5000-users] Autosphere's radius In-Reply-To: References: Message-ID: Hi Jacob, Yes - you can change the radius. I find it best to convert mid-side node defs to circles first, before doing any modifications. It seems that some of preneks operations are not fully compatible with the mid side node definitions at present. Here is a script that resizes and otherwise modifies a circle. Note that "one2d.rea" should be any 2D .rea file with a single element. (I've attached one here.) pretex << EOF c3 1 READ PREVIOUS PARAMETERS one2d 1 BUILD FROM FILE one2d 5 DELETE ELEMENT 4 CURVE SIDES 5 Autosphere 2 3 Enter number of elements in core and shell: 0.66 Enter ratio in outer shell: 8 Convert Midside to Circle 1000 Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 11 STRETCH 5 Stretch R 3 Input expansion factor ( =< 0 to abort): 1 UP MENU 8 OCT/Multi-SPLIT q quad or multi-split? (q/m) y Are you sure you want to split (y/n)? 1 END GLOBAL REFINE 4 CURVE SIDES 8 Convert Midside to Circle 1000 Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 7 REPLICATE/ROTATE 3 Rep. (1), Rot. (2), Rep/Rot (3) Template (4)? (0=abort) 90 Input rotation angle (deg): 3 Input number of reps (e.g., 1 --> double mesh size) 13 Clean up vertices 1 END GLOBAL REFINE 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF echo c3 > SESSION.NAME postx ________________________________ 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: Wednesday, November 16, 2016 11:57 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Autosphere's radius Hi, Neks! I am trying to create an own mesh, based on expansion example. When I build a circle in pretex, it is always has radius = 0.5. Can I change it in the pretex directly? (Now I could vary only numbers of elements in inner and outer shells). Thanks in advance, Jacob. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: one2d.rea Type: application/octet-stream Size: 6440 bytes Desc: one2d.rea URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 18 06:56:27 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Nov 2016 10:56:27 -0200 Subject: [Nek5000-users] Error Compiling In-Reply-To: References: Message-ID: Thanks Tanmoy! I installed tcsh shell and everything is fine. Thanks a lot! I'm very new at nek and I have a lot to learn about ^^ Thanks again! Mateus. 2016-11-16 22:05 GMT-02:00 : > Also visnek requires tcsh shell. Try installing that as well. > > Best Regards, > Tanmoy > > On Wed, Nov 16, 2016 at 10:16 AM, wrote: > >> Try ?visnek eddy_uv? without the ?./' >> >> On Nov 16, 2016, at 11:41 AM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Thanks for the answer. >> >> I tried to use visnek. After type ./visnek eddy_uv I got these error: >> >> bash: ./visnek: /bin/tcsh: bad interpreter: No such file or directory >> >> Any ideia? >> >> Mateus. >> >> 2016-11-16 14:34 GMT-02:00 : >> >>> I think you can ignore the error message you are getting. >>> >>> As for visualization of the solution, you can also use visit or >>> paraview. You have to use visnek. >>> >>> Marco >>> >>> On Nov 16, 2016, at 11:12 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> I realize my mistake. My PATH was wrong, now I can compile without >>> problems. >>> >>> But now I have other problem. After compile with makenek and after run >>> with nekb I can't vizualize the results with postx. >>> My path is /bin, I type ./postx and I got a black window without a >>> sidebar. >>> >>> Whats wrong? >>> >>> Thanks. >>> >>> 2016-11-16 1:11 GMT-02:00 : >>> >>>> What does echo $PATH return for you? >>>> >>>> On Nov 15, 2016, at 4:31 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> Hi all, >>>> >>>> I'm ver new at nek5000. I'm trying to compiling a first example case >>>> (eddy) and I get a error. >>>> >>>> After ./makenek eddy_uv >>>> >>>> I get: >>>> >>>> ./makenek: line 92: /home/mateus/nek5000/core/makenek.inc: No such >>>> file or directory >>>> make: makefile: No such file or directory >>>> make: *** No rule to make target 'makefile'. Stop. >>>> >>>> Can someone help me? >>>> >>>> >>>> -- >>>> Mateus Peixoto Avanci >>>> Engenheiro Mec?nico >>>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>>> Universidade Federal Fluminense >>>> *http://lattes.cnpq.br/1773896725783894 >>>> * >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> >>> >>> -- >>> Mateus Peixoto Avanci >>> Engenheiro Mec?nico >>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>> Universidade Federal Fluminense >>> *http://lattes.cnpq.br/1773896725783894 >>> * >>> _______________________________________________ >>> 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 >>> >>> >> >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> *http://lattes.cnpq.br/1773896725783894 >> * >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 20 11:12:21 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Nov 2016 15:12:21 -0200 Subject: [Nek5000-users] Laminar Flow Poiseuille Message-ID: Hi neks! I just want to simulate a laminar flow case like a Poiseuille flow. What case example I can use? Sorry for the question, I'm very new at nek. Thanks. Mateus. -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 20 11:23:03 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Nov 2016 10:23:03 -0700 Subject: [Nek5000-users] Laminar Flow Poiseuille In-Reply-To: References: Message-ID: You can start with the nek example : helix. Make necessary modifications to helix.usr and helix.rea as needed. On Sun, Nov 20, 2016 at 10:12 AM, wrote: > Hi neks! > > I just want to simulate a laminar flow case like a Poiseuille flow. What > case example I can use? > > Sorry for the question, I'm very new at nek. > > Thanks. > Mateus. > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > > _______________________________________________ > 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 Nov 20 16:49:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Nov 2016 22:49:36 +0000 Subject: [Nek5000-users] Error Compiling Message-ID: Hi, I think it might be helpful to familiarize yourself with the Nek?s user guide first: http://nek5000.github.io/NekDoc/Nek_users.pdf Specifically chapter 2 which talks about setting up your path. Using Visit might be a better option if you are just starting with Nek since there is a lot more documentation for it. Let?s say you have result files for your case (let?s say a1) - a10.f0000* or a10.fld0* formats. To visualize using Visit, type "visnek a1? which will generate a file a1.nek5000. Now you are ready to visualize.. open Visit (I have visit 2.9.1), and click ?Open? and navigate to the folder where you ran your calculation. Once you are there double click on a1.nek5000. It should open fine and you can then use the options (open - pseudocolor - velocity) to visualize velocity results etc? If you really want to use postx, type in postx to get started. This will pop up a black window. Depending on your display settings, the text at the bottom of the window might not be visible. If you don?t see any text, you will have to use the terminal to read the text (the text is duplicated there). I usually move the black window to the right side of the screen and terminal to the left side of the screen. Once you have done that, click on the black window and answer the question that you read on terminal window ?Enter Session Name?. Type in a1 and hit enter. The postx window should populate with a plot of the mesh and a bunch of options on the right side which are self descriptive. Thanks, Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 21 02:08:41 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Nov 2016 16:08:41 +0800 Subject: [Nek5000-users] Nek5000-users Digest, Vol 93, Issue 6 Message-ID: HI, all I would like to make a supplementary that for an inner circle (or other curved boundary) the 'radius' in your commend should be a minus value, say, -0.5. ---------------------------------------------------------------- Bolun Xu University of Science and Technology of China Hefei, Anhui, China -----????----- ???: Xu Bolun [mailto:xblkid at mail.ustc.edu.cn] ????: 2016?11?10? 10:12 ???: 'nek5000-users at lists.mcs.anl.gov' ??: ??: Nek5000-users Digest, Vol 93, Issue 6 Hello, Nicolas I read the documentation again carefully and very happy that my problem has been solved. Thank you very much for advice. I would like to share the curve definition parts in my mesh converting commands for a ring below: Curves={4:{'type':'C','depth':4,'circle_center':(0,0), 'radius':1},3:{'type':'C','depth':4,'circle_center':(0,0),'radius':0.5}} For 4 and 3 are outer and inner circle. ---------------------------------------------------------------- Bolun Xu University of Science and Technology of China Hefei, Anhui, China -----????----- ???: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] ?? nek5000-users-request at lists.mcs.anl.gov ????: 2016?11?9? 23:27 ???: nek5000-users at lists.mcs.anl.gov ??: Nek5000-users Digest, Vol 93, Issue 6 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: A problem in Prenek (nek5000-users at lists.mcs.anl.gov) 2. 2D circular ring mesh converting by mshconvert.py (nek5000-users at lists.mcs.anl.gov) 3. Re: 2D circular ring mesh converting by mshconvert.py (nek5000-users at lists.mcs.anl.gov) 4. Re: Read Nek output in Matlab (nek5000-users at lists.mcs.anl.gov) 5. Name of the variable in userf and userq (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Nov 2016 21:32:25 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: Re: [Nek5000-users] A problem in Prenek Message-ID: Content-Type: text/plain; charset="utf-8" Hi Saikat, I think this is what is expected. If we look at postpro.f in nek?s source code (subroutine gen_rea_bc), there are 4 different formats in which the boundary conditions will be written depending on the element count. In your case, since the element count is greater than 1000 but less than 100,000, we expect the format to be: first 4 character spaces for boundary condition, next 5 characters for element number, 1 character for edge/face number depending on 2d/3d and so on. As a result, your boundary condition line shows as: E 30724 2731.00 2.00000 0.00000 0.00000 0.00000 Thanks, Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 9 Nov 2016 10:16:20 +0800 From: nek5000-users at lists.mcs.anl.gov To: Subject: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py Message-ID: Content-Type: text/plain; charset="us-ascii" Hi, neks I tried to convert a 2D circular ring mesh generated by gambit to .rea file using the code mshconvert.py, but failed. I converted the example mesh file sirkel4.msh following the step in README, then I have a question that what command I should input when my mesh has more than one curved boundary just like a ring mesh. For sirkel4.msh the command "7:{..}" means that the zone 7 is curved, if I have two curved zones, for example, zone 3 and 4, should I input "3:{....},4:{....}" in one command line? Thank you in advance. Regards, Xu ---------------------------------------------------------------- Bolun Xu University of Science and Technology of Chnia Hefei, Anhui, China -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 9 Nov 2016 13:45:32 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] 2D circular ring mesh converting by mshconvert.py Message-ID: Content-Type: text/plain; charset="utf-8" Dear Bolun, Yes, you should specify the different curved zones separately. There is a bit of documentation at the end of the file "mshconvert.py". Here is what is said about the curves input: " curves = Dictionary of curve information. Keys are curve zones and value is either {'type': 'C', 'radius': radius, 'circle_center': (x, y), 'depth': depth} for a circle or {'type': 'm'} for midpoint with nek5000 or {'type': 'spline'} for a curved side with semtex. Here a .geom file containing the spline information will be created. The circle may provide the radius or the center of the circle through 'circle_center'. The curvature may also be used in the internal elements inside the surface through specifying the depth. depth=4 means that the curvature is used throughout the first four elements inside that surface. This is necessary to get good quality meshes in, e.g., a cylinder. The radius for an internal face is always computed as the distance to the circle_center. Not for FEniCS. " I hope that helps. Best, Nicolas Offermans On Wed, Nov 9, 2016 at 3:16 AM, wrote: > Hi, neks > > I tried to convert a 2D circular ring mesh generated by gambit to .rea > file using the code mshconvert.py, but failed. I converted the example > mesh file sirkel4.msh following the step in README, then I have a > question that what command I should input when my mesh has more than > one curved boundary just like a ring mesh. For sirkel4.msh the command > ?7:{??}? means that the zone 7 is curved, if I have two curved zones, > for example, zone 3 and 4, should I input ?3:{??..},4:{??..}? in one command line? > > Thank you in advance. > > Regards, > > Xu > > > > ---------------------------------------------------------------- > > Bolun Xu > > University of Science and Technology of Chnia > > Hefei, Anhui, China > > > > > > _______________________________________________ > 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: ------------------------------ Message: 4 Date: Wed, 9 Nov 2016 13:50:59 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Read Nek output in Matlab Message-ID: Content-Type: text/plain; charset=windows-1252; format=flowed Hi Alessandro, alternatively you can use the functions that I and a colleague of mine wrote. They can read and write nek's files. You can find them here https://github.com/nfabbiane/nekmatlab Cheers, Jacopo On 2016-11-02 15:20, nek5000-users at lists.mcs.anl.gov wrote: > Alessandro, > > Set, in usrdat2 in your .usr file the following lines: > > param(66)=0 > param(67)=0 > > this will give you an ascii file output. blah.fld01 blah.fld02 etc > > You can edit these files or write a short script to take off the > header or whatever and then load the data into matlab. > > Usual data lay out (for 2D) is: > > x y u v p T > > for fld01 > > and > > u v p T > > for all other fields. > > 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: Wednesday, November 02, 2016 7:44 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Read Nek output in Matlab > > Hi Neks, > > I would like to make some postprocessing with the Nek output. Can I > read that files in Matlab (or C)? > > Just to make it clear: If my .rea file is called whatever.rea and the > output is whatever0.f00**** > > I would like to read whatever0.f00**** and make some postprocessing. > It will be also very helpful to learn how to extrapolate the mesh so > that I can plot combinations of the solutions for instance. > > Thank you so much, > > 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 ------------------------------ Message: 5 Date: Wed, 9 Nov 2016 16:27:12 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Name of the variable in userf and userq Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed Hi Neks, I am trying to set volume forcing in my equations through userf and userq. However it is not for the baseflow but for perturbations. Does anyone know the name of the perturbations variables which are equivalent to ffx, ffy, ffz, and qvol? So I can write something like : ffxp = ... ffyp = ... ffzp = ... qvolp = ... 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 End of Nek5000-users Digest, Vol 93, Issue 6 ******************************************** From nek5000-users at lists.mcs.anl.gov Mon Nov 21 05:53:40 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Nov 2016 12:53:40 +0100 (CET) Subject: [Nek5000-users] Mantle Convection (infinite Prandtl, variable viscosity) with Nek5000 Message-ID: Hi Neks, I'm trying to use Nek to simulate convection in planetary mantles (infinite Prandtl-number, variable viscosity...) in the way Jan has requested a few months ago: >> Hi all, >> I was wondering if it is possible to use Nek5000 for simulations in >> the infinite Prandtlnumber regime (e.g. planetary mantles). This >> would require to solve the NS Stokes equation without the time >> derivative and advection term and the heat equation for T: >> >> 1) Solve visc * laplace u - grad p + buoyancy = 0 and div u = 0, >> where bouyancy depends on a given T field and a Rayleigh number >> 2) Update T by solving dT/dt + u grad T = diff * laplace T (+ other >> sources) >> 3) go back to 1 with the new T field, repeat >> >> More realistic models would then use a varying viscosity. >> I looked at the steady state example (kov_st_state), but this is >> missing the time depencence via the Temperature. Any hints on the >> possibility would be much appreciated. >> >> Thanks, >> Jan Initially I tried the whole thing with a simple 2D rectangular geometry and a fluid with temperature-dependent viscosity ([udiff=param(2)*exp(-log(param(70))*temp)] were param(70) is the viscosity contrast between temp=1 and temp=0) cooled from above (T=0) and heated from below (T=1) . At first I tried the way Paul suggested: >> Hi Jan, >> I just saw this and the follow-on posts. (Apologies - have been on the road for >> several weeks.) >> >> I've not tried this, but it appears to me that you simply will set IFNAV = F in the .rea >> file and can set param(1) [ rho ] to be a very small number. Param(2) is the dynamic >> viscosity, so you can set that independently of param(1). This will have the affect >> of forcing the velocity to relax very quickly (its inertia is negligible compared to the >> other terms in the momentum equation). So, you could conceivably set param(1) >> to be 1.e-30, say. >> >> Note that, on the same line where IFNAV is set, you would set IFADV to be "T" for >> the second field. It should look something like: >> >> F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) >> Also, you might find it of value in this scenario to try the Pn-Pn-2 formulation with >> plan1 ... In this case, you would indeed want to edit the source --- specifically: >> change the call to plan3() to call plan1() in drive2.f ... As I say, I've not experimented >> with this flow regime so am only making suggestions to try, rather than firm >> recommendations based on experience. >> Paul but I got the problem that Nek worked well only for one condition, either for an infinite Prandtlnumber (i.e. density=1.e-30) or variable viscosity. As I wanted Nek to solve both, I got some strange results... for a sufficient resolution very thin boundary layers evolve (they should be much thicker with for instance Rayleigh numbers like 10^4 and a viscosity contrast of 1000) and the boundary layers had a rough structure, but they should be quite smooth. For lower resolution I got no or completely wrong results, either the temperature was oscillating very strong (with values higher than the maximum temperature of 1) or Nek crashed at all. Maybe someone has an idea how to fix it?! However, after that I also tried the way lailai suggested: > Hello, Jan, > > We have in fact solved a similar problem as you face now. In our case, > we have steady Stokes equation at each time step, > in the absence of time derivative and convection term. However we have > time-dependent volume forcing and boundary > conditions, as we solve for fluid-structure interactions in the Stokes > regime. > > You only need to change the source code for one thing. By changing the > flags in the .rea file, you can easily turn > off the two terms. However, the code only runs for 1 time step even if > you specify for example 10 total time steps, which makes sense > as NEK realizes this is a steady problem. NEK5000 does not see that > the next time step, BCs and forcing will be changed, and so > as the flow. > > So I remember I only commented two lines of the source code to achieve > this, in the file 'connect2.f', subroutine 'rdparam', > this is what I have done (i am using a quite old version of the NEK, > so...) > > IF (.NOT.IFTRAN) THEN > c PARAM(11) = 1.0 !lailai comment for steady stokes > c PARAM(12) = 1.0 !lailai comment for steady stokes > PARAM(19) = 0.0 > ENDIF > > Of course you need to set the flags right in .rea file, which you can > find the details on the webpage. You also need to > solve for heat equations to get T. Then in the userchk subroutine, you > calculate the T-dependent buoyancy forcing at each time step. > Solve the flow with new forcing terms. This should be all manageable. > > cheers and good luck, > > lailai where I've included Jan's advice as well: > Hi, > thanks for the advice. I found that one also has to comment the line > IF (.NOT.IFTRAN) NSTEPS=1 > in setvar in drive2.f and use a fixed timestep so that the timeloop does > not stop too soon. > > Thanks again, > Jan Using this method I got more satisfying results, at least for the tested parameters (Ra=10^4, viscosity contrast of 1000), but to achieve a statistically steady state it took a very long time (non-dimensional) of t>1 (independent of the maximum stepsize dt) and therefore very much iteration steps (~10^6) and CPU-time. For comparison other mantle convection codes need a non-dimensional time of t<0.1 and less than 10000 steps (with a comparable maximum stepsize). Unfortunately I've no idea why it takes that much time using Nek... I would be vary grateful for any hints or suggestions to make at least one method work (either Paul's or lailai's way). Thanks, Philipp ---------------------- Philipp Hellenkamp Institut f?r Geophysik Corrensstr. 24 D-48149 M?nster From nek5000-users at lists.mcs.anl.gov Mon Nov 21 09:16:19 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Nov 2016 16:16:19 +0100 Subject: [Nek5000-users] Impose/change velocity in userchk Message-ID: Dear Neks, I am using the MHD example for kinematic Dynamo. In the example gpf, the force is added as f=-Nabla^2 u - partial u/partial t, where u is ux = -sys uy = -cxc uz = sxc + cys I want to do it the straight forward approach i.e. directly imposing the velocity in userchk and switching off the iteration Navier-Stokes equation. For this I set the IFNAV to False F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F F T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) IC being the same as imposed velocity and in userchk added the following if (ifield.eq.1) then ! velocity omega = 1. do i=1,nx1*ny1*nz1*nelv x = xm1(i,1,1,1); y = ym1(i,1,1,1); z = zm1(i,1,1,1) st = sin(omega*time) ct = cos(omega*time) c argxc = x + ct argyc = y + ct argxs = x + st argys = y + st c visc = param(2) s = 3./2. s = sqrt(s) c cxc = s*cos(argxc) cys = s*cos(argys) sxc = s*sin(argxc) sys = s*sin(argys) c vx(i,1,1,1) = -sys vy(i,1,1,1) = -cxc vz(i,1,1,1) = sxc + cys enddo endif ibstep = iostep if (istep.gt.0.and.mod(istep,ibstep).eq.0) $ call outpost(bx,by,bz,pm,t,' ') ! odd blah.fld/.f for B-field c $ call outpost(bx,by,bz,pm,t,'mag') ! magblah.fld/.f for B-field if (ifxyo.and.istep.gt.istep) ifxyo = .false. kinerg2 = 0.5*(glsc3(vx,bm1,vx,m) $ +glsc3(vy,bm1,vy,m) $ +glsc3(vz,bm1,vz,m))/volvm1 n = nx1*ny1*nz1*nelfld(ifldmhd) ! Magnetic energy !?nelb energy0 = energy energy = glsc3(bx,bm1,bx,n) $ + glsc3(by,bm1,by,n) $ + glsc3(bz,bm1,bz,n) energy = 0.5*energy/volfld(ifldmhd) if (istep.gt.1) then ratio = energy/energy0 growth = 0.5*log(ratio)/dt ! 1/2 of magnetic energy growth rate if (nid.eq.0) write(6,1) istep,time,growth,energy, $ kinerg1,kinerg2 1 format(i8,1p5e15.6,' growth') nstepag = param(120) ! p121 < t_avg < p120 nstepsa = param(121) if (istep.lt.nstepag) call $ runtimeavg(Emga,growth,1,nstepsa,1,'gr_Em') ! avg. growth endif When I calculate the energy of the system, it is decaying. Is there anyway I can tamper with / change the velocity field array in nek5000 from userchk? Thanking you in advance. Cheers, Sandeep PS: Attached are the .usr and .rea files -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: gpf.usr Type: application/octet-stream Size: 12212 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: gpf.rea Type: application/octet-stream Size: 5891 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 22 03:22:02 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 Nov 2016 10:22:02 +0100 (CET) Subject: [Nek5000-users] Mantle convection (infinite Prandtl, variable viscosity) with Nek5000 Message-ID: Hi Neks, I'm trying to use Nek to simulate convection in planetary mantles (infinite Prandtl-number, variable viscosity...) in the way Jan has requested a few months ago: >> Hi all, >> I was wondering if it is possible to use Nek5000 for simulations in >> the infinite Prandtlnumber regime (e.g. planetary mantles). This >> would require to solve the NS Stokes equation without the time >> derivative and advection term and the heat equation for T: >> >> 1) Solve visc * laplace u - grad p + buoyancy = 0 and div u = 0, >> where bouyancy depends on a given T field and a Rayleigh number >> 2) Update T by solving dT/dt + u grad T = diff * laplace T (+ other >> sources) >> 3) go back to 1 with the new T field, repeat >> >> More realistic models would then use a varying viscosity. >> I looked at the steady state example (kov_st_state), but this is >> missing the time depencence via the Temperature. Any hints on the >> possibility would be much appreciated. >> >> Thanks, >> Jan Initially I tried the whole thing with a simple 2D rectangular geometry and a fluid with temperature-dependent viscosity ([udiff=param(2)*exp(-log(param(70))*temp)] were param(70) is the viscosity contrast between temp=1 and temp=0) cooled from above (T=0) and heated from below (T=1) . At first I tried the way Paul suggested: >> Hi Jan, >> I just saw this and the follow-on posts. (Apologies - have been on the road for >> several weeks.) >> >> I've not tried this, but it appears to me that you simply will set IFNAV = F in the .rea >> file and can set param(1) [ rho ] to be a very small number. Param(2) is the dynamic >> viscosity, so you can set that independently of param(1). This will have the affect >> of forcing the velocity to relax very quickly (its inertia is negligible compared to the >> other terms in the momentum equation). So, you could conceivably set param(1) >> to be 1.e-30, say. >> >> Note that, on the same line where IFNAV is set, you would set IFADV to be "T" for >> the second field. It should look something like: >> >> F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) >> Also, you might find it of value in this scenario to try the Pn-Pn-2 formulation with >> plan1 ... In this case, you would indeed want to edit the source --- specifically: >> change the call to plan3() to call plan1() in drive2.f ... As I say, I've not experimented >> with this flow regime so am only making suggestions to try, rather than firm >> recommendations based on experience. >> Paul but I got the problem that Nek worked well only for one condition, either for an infinite Prandtlnumber (i.e. density=1.e-30) or variable viscosity. As I wanted Nek to solve both, I got some strange results... for a sufficient resolution very thin boundary layers evolve (they should be much thicker with for instance Rayleigh numbers like 10^4 and a viscosity contrast of 1000) and the boundary layers had a rough structure, but they should be quite smooth. For lower resolution I got no or completely wrong results, either the temperature was oscillating very strong (with values higher than the maximum temperature of 1) or Nek crashed at all. Maybe someone has an idea how to fix it?! However, after that I also tried the way lailai suggested: > Hello, Jan, > > We have in fact solved a similar problem as you face now. In our case, > we have steady Stokes equation at each time step, > in the absence of time derivative and convection term. However we have > time-dependent volume forcing and boundary > conditions, as we solve for fluid-structure interactions in the Stokes > regime. > > You only need to change the source code for one thing. By changing the > flags in the .rea file, you can easily turn > off the two terms. However, the code only runs for 1 time step even if > you specify for example 10 total time steps, which makes sense > as NEK realizes this is a steady problem. NEK5000 does not see that > the next time step, BCs and forcing will be changed, and so > as the flow. > > So I remember I only commented two lines of the source code to achieve > this, in the file 'connect2.f', subroutine 'rdparam', > this is what I have done (i am using a quite old version of the NEK, > so...) > > IF (.NOT.IFTRAN) THEN > c PARAM(11) = 1.0 !lailai comment for steady stokes > c PARAM(12) = 1.0 !lailai comment for steady stokes > PARAM(19) = 0.0 > ENDIF > > Of course you need to set the flags right in .rea file, which you can > find the details on the webpage. You also need to > solve for heat equations to get T. Then in the userchk subroutine, you > calculate the T-dependent buoyancy forcing at each time step. > Solve the flow with new forcing terms. This should be all manageable. > > cheers and good luck, > > lailai where I've included Jan's advice as well: > Hi, > thanks for the advice. I found that one also has to comment the line > IF (.NOT.IFTRAN) NSTEPS=1 > in setvar in drive2.f and use a fixed timestep so that the timeloop does > not stop too soon. > > Thanks again, > Jan Using this method I got more satisfying results, at least for the tested parameters (Ra=10^4, viscosity contrast of 1000), but to achieve a statistically steady state it took a very long time (non-dimensional) of t>1 (independent of the maximum stepsize dt) and therefore very much iteration steps (~10^6) and CPU-time. For comparison other mantle convection codes need a non-dimensional time of t<0.1 and less than 10000 steps (with a comparable maximum stepsize). Unfortunately I've no idea why it takes that much time using Nek... I would be vary grateful for any hints or suggestions to make at least one method work (either Paul's or lailai's way). Thanks, Philipp ---------------------- Philipp Hellenkamp Institut f?r Geophysik Corrensstr. 24 D-48149 M?nster From nek5000-users at lists.mcs.anl.gov Tue Nov 22 13:34:43 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 Nov 2016 17:34:43 -0200 Subject: [Nek5000-users] Laminar Flow Poiseuille In-Reply-To: References: Message-ID: Helix example is a 3D Poiseiulle flow with flow in the z direction. I want to simulate a plane Poiseuille flow, in which a fluid is moving laterally between two plates whose length and width is much greater than the distance separating them. I don't know how to modify helix for my case. Can you help me? 2016-11-20 15:23 GMT-02:00 : > You can start with the nek example : helix. Make necessary modifications > to helix.usr and helix.rea as needed. > > On Sun, Nov 20, 2016 at 10:12 AM, wrote: > >> Hi neks! >> >> I just want to simulate a laminar flow case like a Poiseuille flow. What >> case example I can use? >> >> Sorry for the question, I'm very new at nek. >> >> Thanks. >> Mateus. >> >> -- >> Mateus Peixoto Avanci >> Engenheiro Mec?nico >> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >> Universidade Federal Fluminense >> *http://lattes.cnpq.br/1773896725783894 >> * >> >> _______________________________________________ >> 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 > > -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 22 22:59:57 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 Nov 2016 21:59:57 -0700 Subject: [Nek5000-users] Laminar Flow Poiseuille In-Reply-To: References: Message-ID: Ok, if you are looking for plane-poiseuille flow you can look into the turbChannel example. It is designed for turbulent channel flow, but you can reduce the Reynolds number to generate a desired 3D Laminar flow. Also it is periodic boundary conditions, you can modify BC's like inflow/outflow according to your wish. Best Regards, Tanmoy On Tue, Nov 22, 2016 at 12:34 PM, wrote: > Helix example is a 3D Poiseiulle flow with flow in the z direction. > > I want to simulate a plane Poiseuille flow, in which a fluid > is moving laterally between two plates whose length and width is much > greater than the distance separating them. > > I don't know how to modify helix for my case. Can you help me? > > 2016-11-20 15:23 GMT-02:00 : > >> You can start with the nek example : helix. Make necessary modifications >> to helix.usr and helix.rea as needed. >> >> On Sun, Nov 20, 2016 at 10:12 AM, >> wrote: >> >>> Hi neks! >>> >>> I just want to simulate a laminar flow case like a Poiseuille flow. What >>> case example I can use? >>> >>> Sorry for the question, I'm very new at nek. >>> >>> Thanks. >>> Mateus. >>> >>> -- >>> Mateus Peixoto Avanci >>> Engenheiro Mec?nico >>> Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica >>> Universidade Federal Fluminense >>> *http://lattes.cnpq.br/1773896725783894 >>> * >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Mateus Peixoto Avanci > Engenheiro Mec?nico > Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica > Universidade Federal Fluminense > *http://lattes.cnpq.br/1773896725783894 > * > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 23 10:33:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Nov 2016 14:33:42 -0200 Subject: [Nek5000-users] postx black window Message-ID: Hi neks, After enter "postx" at terminal I got a black window with any sidebar. At terminal I got: ------------------------------------------------------------------------ Beginning Session renaming SESSION.NAME SESSION.NAME~ Session name: ** ERROR ** Can't open file .rea Enter Session Name ------------------------------------------------------------------------ What I have to do for plot the results? Thanks, Mateus. -- Mateus Peixoto Avanci Engenheiro Mec?nico Aluno do Programa de P?s-Gradua??o em Engenharia Mec?nica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 23 14:13:37 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Nov 2016 20:13:37 +0000 Subject: [Nek5000-users] postx black window Message-ID: Hi Mateus, This post might help: http://lists.mcs.anl.gov/pipermail/nek5000-users/2016-November/004007.html Ketan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 29 06:19:33 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Nov 2016 14:19:33 +0200 Subject: [Nek5000-users] srun error Message-ID: Hi Neks, I am trying to run a job using SLURM Job script. The batch script job suggested for MPI uses the srun command. My job submission failed and I got the following error: ???????????????????????????? srun: error: Application launch failed: Job credential revoked ???????????????????????????? Has anybody faced similar difficulties? SP From nek5000-users at lists.mcs.anl.gov Tue Nov 29 09:50:31 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Nov 2016 15:50:31 +0000 Subject: [Nek5000-users] srun error In-Reply-To: References: Message-ID: Hi SP, This is a script modified from nekbmpi that I used to run with srun awhile ago echo $1 > SESSION.NAME echo $1 > SESSION.NAME echo `pwd`'/' >> SESSION.NAME touch $1.rea rm ioinfo mv $1.log.$2 $1.log1.$2 mv $1.his $1.his1 mv $1.sch $1.sch1 rm -f logfile nohup srun -p scx-comp -n $2 -N $3 nek5000 > $1.log.$2 & sleep 2 ln $1.log.$2 logfile where $2 & $3 command line arguments are the numbers of MPI ranks and compute node, respectively. Also make sure that you could run any MPI job first using, e.g., "Hello world" printout from ranks or something similar. 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: Tuesday, November 29, 2016 6:19 AM To: Nek5000 Users Subject: [Nek5000-users] srun error Hi Neks, I am trying to run a job using SLURM Job script. The batch script job suggested for MPI uses the srun command. My job submission failed and I got the following error: ???????????????????????????? srun: error: Application launch failed: Job credential revoked ???????????????????????????? Has anybody faced similar difficulties? SP _______________________________________________ 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 Nov 29 14:30:14 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Nov 2016 22:30:14 +0200 Subject: [Nek5000-users] srun error In-Reply-To: References: Message-ID: Thanks Aleks, I will try this. SP On Tue, 29 Nov 2016 15:50:31 +0000, nek5000-users at lists.mcs.anl.gov wrote: > Hi SP, > > This is a script modified from nekbmpi that I used to run with srun > awhile ago > > echo $1 > SESSION.NAME > echo $1 > SESSION.NAME > echo `pwd`'/' >> SESSION.NAME > touch $1.rea > rm ioinfo > mv $1.log.$2 $1.log1.$2 > mv $1.his $1.his1 > mv $1.sch $1.sch1 > rm -f logfile > nohup srun -p scx-comp -n $2 -N $3 nek5000 > $1.log.$2 & > sleep 2 > ln $1.log.$2 logfile > > where $2 & $3 command line arguments are the numbers of MPI ranks and > compute node, respectively. > > Also make sure that you could run any MPI job first using, e.g., > "Hello world" printout from ranks or something similar. > > 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: Tuesday, November 29, 2016 6:19 AM > To: Nek5000 Users > Subject: [Nek5000-users] srun error > > Hi Neks, > I am trying to run a job using SLURM Job script. The batch script > job > suggested for MPI uses the srun command. > My job submission failed and I got the following error: > ???????????????????????????? > srun: error: Application launch failed: Job credential revoked > ???????????????????????????? > > Has anybody faced similar difficulties? > > SP > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Nov 30 02:51:41 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Nov 2016 03:51:41 -0500 Subject: [Nek5000-users] Error reading domains with 3072 elements in Postnek Message-ID: Hi Neks, I have been having trouble reading my domain with 3 Scalars, having 3072 elements in Postnek. The same domain can be however read without the Scalars. Also the same domain with lesser elements, like 768, can be read fine with/without scalars. I am getting this kind of an error 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 Any help is appreciated. 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 Nov 30 08:56:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Nov 2016 14:56:39 +0000 Subject: [Nek5000-users] Questions on turbChannel Message-ID: Hello, I have a few questions on the turbChannel example. 1) the ?eddy viscosity ? is computed in the function eddy_visc and called in a loop over the elements of mesh 1. Inside the function eddy_visc there is the following piece of code: if (e.eq.nelv) then ! planar avg and define nu_tau ? ntot = nx1*ny1*nz1*nelv do i=1,ntot cdyn = 0 if (den(i,1).gt.0) cdyn = 0.5*num(i,1)/den(i,1) cdyn = 0.16*0.16 ! max(cdyn,0.) ! AS ALTERNATIVE, could clip ediff ediff(i,1) = param(2)+cdyn*dg2(i,1)*snrm(i,1) enddo endif eddy that stores the eddy viscosity is updated when the last element of mesh 1 is called. Is there any reason why it should be done in this manner? 2) I am still confused over the differences between ?ifsplit?, ?ifexplvis? and ?ifstrs?. From the archive and the documentation I understand the following (please correct me if I am wrong): * ?ifexplvis? is set to true when the user specified the viscosity coefficient in uservp. It does not required, however, the stress formation meaning the the diffusive term in the NS equations looks like \mu(x,t) \nabla^2 \vec{u}. * when ?ifsplit? is set to true, the viscosity is split in a explicit part and an implicit part. If this correct, how and where are defined the explicit and implicit parts? * ?ifstrs?: when set to true, ?ifexplvis? and ?if split? do not have any effect. 3) could someone shed some light on the subroutine ?set_ds_filt? in turbChannel.usr, please? It seems to compute some sort of filter that is then used to compute M_{i,j} and L_{i,j} Thanks, Marco -------------- next part -------------- An HTML attachment was scrubbed... URL: