From nek5000-users at lists.mcs.anl.gov Thu Mar 1 10:56:07 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 1 Mar 2018 16:56:07 +0000 Subject: [Nek5000-users] Sponge layer in Nek5000 Message-ID: Hi all, I'm trying to implement outflow boundary conditions for a turbulent plume using a sponge layer to absorb the energy of the flow and prevent reflections back into the domain. I was wondering whether there is anything set up in Nek already to construct this sponge layer or if it's something I need to do myself, and if so whether anybody could help with something they've done before - I've read a couple of other threads here that mention a sponge layer but not its implementation. I look forward to hearing from you. Best, Daniel Ward -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 1 13:24:45 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 1 Mar 2018 12:24:45 -0700 Subject: [Nek5000-users] Sponge layer in Nek5000 In-Reply-To: References: Message-ID: Hi Daniel, We did implement the Sponge layer a couple of years back in nek5000 at the outflow boundary condition. We used a Smagorinsky type of eddy-viscosity closure where the Smagorinsky coefficient quadratically varies in the x direction (where is the direction of dominant flow), close to a few elements near the outflow. You can set it up with uservp in nek5000. However, the stabilized natural outflow boundary conditions by Dong et al. (2014) behaves much better than the sponge layer in my opinion. For my type of problem the sponge layer actually creates artificial diffusive structures close to the boundary, even when they are applied very smoothly, and you need to chop off the near-outflow region for data analysis. On Thu, Mar 1, 2018 at 9:56 AM, wrote: > Hi all, > > > I'm trying to implement outflow boundary conditions for a turbulent plume > using a sponge layer to absorb the energy of the flow and prevent > reflections back into the domain. I was wondering whether there is > anything set up in Nek already to construct this sponge layer or if it's > something I need to do myself, and if so whether anybody could help with > something they've done before - I've read a couple of other threads here > that mention a sponge layer but not its implementation. > > > I look forward to hearing from you. > > > Best, > > > Daniel Ward > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 1 15:05:45 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 1 Mar 2018 22:05:45 +0100 Subject: [Nek5000-users] Sponge layer in Nek5000 In-Reply-To: References: Message-ID: Hi, we have also implemented various sponges and other boundary conditions, including the Dong condition and convective conditions. The sponge we typically base on a "direct" forcing approach as e.g. described in the paper by Appelquist (JFM 2015); the implementation of that type of forcing is in userf. The Dong condition is essentially a modified "o" condition (where one has to change a few lines here and there in the code, but I could send you our code), and the convective condition, which behaved the best (see e.g. the Master's thesis by Erik Bostr?m) can be implemented in usercheck. The latter condition did create the least upstream disturbances. Philipp On 2018-03-01 20:24, nek5000-users at lists.mcs.anl.gov wrote: > Hi Daniel, > > We did implement the Sponge layer a couple of years back in nek5000 at > the outflow boundary condition. We used a Smagorinsky type of > eddy-viscosity closure where the Smagorinsky coefficient quadratically > varies in the x direction (where is the direction of dominant flow), > close to a few elements near the outflow. You can set it up with uservp > in nek5000. However, the stabilized natural outflow boundary conditions > by Dong et al. (2014) behaves much better than the sponge layer in my > opinion. For my type of problem the sponge layer actually creates > artificial diffusive structures close to the boundary, even when they > are applied very smoothly, and you need to chop off the near-outflow > region for data analysis. > > On Thu, Mar 1, 2018 at 9:56 AM, > wrote: > > Hi all, > > > I'm trying to implement outflow boundary conditions for a turbulent > plume using a sponge layer to absorb the energy of the flow and > prevent reflections back into the domain.? I was wondering whether > there is anything set up in Nek already to construct this sponge > layer or if it's something I need to do myself, and if so whether > anybody could help with something they've done before - I've read a > couple of other threads here that mention a sponge layer but not its > implementation. > > > I look forward to hearing from you. > > > Best, > > > Daniel Ward > > > _______________________________________________ > 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 Sun Mar 4 06:11:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 4 Mar 2018 13:11:15 +0100 Subject: [Nek5000-users] gmsh and nek5000 Message-ID: Dear all, For a different project (with OpenFOAM), we have started to use gmsh for meshing, and it seems to be quite powerful for our purposes, and also provide high-order meshing capabilities, which come in handy for Nek5000. I have seen the tool by Praveen Chandrashekar on bitbucket, but it appears to only handle 2D geometries so far: https://bitbucket.org/cpraveen/nek5000 Is there any other converted being developed perhaps which could handle 3D? Thanks, Philipp From nek5000-users at lists.mcs.anl.gov Tue Mar 6 01:33:29 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 08:33:29 +0100 Subject: [Nek5000-users] Outflow boundary conditions Message-ID: Dear all, are outflow advective boundary conditions available in nek5000? Or is there any work around in order to impose outflow boundary conditions (for the velocity and the passive scalars) that can grantee that there is no flow coming back from the outflow boundary? Thanks, Dante -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 07:21:23 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 13:21:23 +0000 Subject: [Nek5000-users] Outflow boundary conditions In-Reply-To: References: Message-ID: Dear Dante, I typically use the turb_outflow boundary condition that is in navier5.f (see below). It will guarantee no inflow. Sometimes you need to set "uin" to get the correct scale if your inlet and outlet areas are disparate in one way or another, but I've rarely found a case where this does not work. Other groups use some form of convective outflow treatment. There were comments on this just last week. hth, Paul c . Set div U > 0 in elements with 'O ' bc. c c . rq is nominally the ratio of Qout/Qin and is typically 1.5 c c . uin is normally zero, unless your flow is zero everywhere c c . d and m1 are work arrays of size (lx1,ly1,lz1,lelt), assumed persistant c c This routine may or may not work with multiple outlets --- it has c not been tested for this case. c c c TYPICAL USAGE -- ADD THESE LINES TO userchk() in your .usr file: c (uncommented) c c common /myoutflow/ d(lx1,ly1,lz1,lelt),m1(lx1*ly1*lz1,lelt) c real m1 c rq = 2. c uin = 0. c call turb_outflow(d,m1,rq,uin) c ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 6, 2018 1:33:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Outflow boundary conditions Dear all, are outflow advective boundary conditions available in nek5000? Or is there any work around in order to impose outflow boundary conditions (for the velocity and the passive scalars) that can grantee that there is no flow coming back from the outflow boundary? Thanks, Dante -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 09:47:13 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 15:47:13 +0000 Subject: [Nek5000-users] Generating Turbulence Message-ID: Dear Nek5000-users, Could you please help me to solve my problem? My geometry is axisymmetric with the following dimensions (R=0.01 m, L=10 R). Well, I did DNS and got something indicating turbulence which is consistent with experiments. However, once I increase either the spatial and/or temporal resolution even a little bit, the flow is laminarized completely. Any help would be greatly appreciated Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 10:09:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 16:09:35 +0000 Subject: [Nek5000-users] Small random perturbations Message-ID: Thank you for responding. It is axisymmetric with periodic conditions at the ends. what geometry are you interested in? Philipp On 2018-02-20 15:20, nek5000-users at lists.mcs.anl.gov wrote: > > Hello everyone, > > I am just wondering about the validity of my way to initiate > turbulence. My question is that instead of introducing random > disturbances to the initial velocity, can I introduce them to the > pressure gradient? Hint, I am using Nek5000 to simulate statistically > non-stationary turbulent flow. > > Thank you in advance > Ali > Embry-Riddle Aeronautical University -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 11:37:05 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 17:37:05 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Dear Ali, I've had good luck for rapid transition to turbulence in pipes with the attached i.c. routine. In addition to random perturbations, it has a significant amount stream wise vorticity near the pipe wall that is rapidly stretched by the mean shear profile, so it generally takes off fairly quickly (e.g., within 10 convective time units). Alternatively or in conjunction with this, you can start with a high Reynolds number and then reduce the Re once turbulence has set in. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 6, 2018 10:09:35 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Thank you for responding. It is axisymmetric with periodic conditions at the ends. what geometry are you interested in? Philipp On 2018-02-20 15:20, nek5000-users at lists.mcs.anl.gov wrote: > > Hello everyone, > > I am just wondering about the validity of my way to initiate > turbulence. My question is that instead of introducing random > disturbances to the initial velocity, can I introduce them to the > pressure gradient? Hint, I am using Nek5000 to simulate statistically > non-stationary turbulent flow. > > Thank you in advance > Ali > Embry-Riddle Aeronautical University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turb_pipe_ic.f Type: application/octet-stream Size: 1493 bytes Desc: turb_pipe_ic.f URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 13:00:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 20:00:24 +0100 (CET) Subject: [Nek5000-users] Complex number as mesh velocity Message-ID: Hi Neks, I was doing pitching and plunging simulation of airfoil. I could successfully rotate the foil with smoothing function. Thank to you all who helped me. Now as a part of validation, I have to impose a forced motion. For that, I found a good paper where a complex exponential function( e^ iwt ) as the velocity of the foil. My question is, is it possible to give a complex number to give as an input to the mesh velocity ? Sorry if its a foolish question. Thanks Sijo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 6 17:14:36 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Mar 2018 23:14:36 +0000 Subject: [Nek5000-users] Complex number as mesh velocity In-Reply-To: References: Message-ID: Hi Sijo, You'll have to convert this to sin(omega t) and perhaps addition of cos(omega t) Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, March 6, 2018 1:00:24 PM To: nek5000-users Subject: [Nek5000-users] Complex number as mesh velocity Hi Neks, I was doing pitching and plunging simulation of airfoil. I could successfully rotate the foil with smoothing function. Thank to you all who helped me. Now as a part of validation, I have to impose a forced motion. For that, I found a good paper where a complex exponential function( e^ iwt ) as the velocity of the foil. My question is, is it possible to give a complex number to give as an input to the mesh velocity ? Sorry if its a foolish question. Thanks Sijo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 7 00:10:34 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Mar 2018 07:10:34 +0100 Subject: [Nek5000-users] Outflow boundary conditions In-Reply-To: References: Message-ID: Hi, indeed, we typically use the stabilised outflow condition based on the paper by Dong et al. (2014, JCP), and have experimented with convective outflow conditions as well. The former is very easy as there are not many parameters to be chosen; for the latter one needs to have an estimate for the convection velocity which can be obtained in different ways. Perhaps one should collect all options at some point and perhaps do a comparative study for a few canonical cases. That could be helpful. Best regards, Philipp On 2018-03-06 14:21, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Dante, > > > I typically use the turb_outflow boundary condition that is in navier5.f > (see below). It will guarantee no inflow. > > > Sometimes you need to set "uin" to get the correct scale if your inlet > and outlet areas are disparate in one way or another, but I've rarely > found a case where this does not work. ?Other groups use some form of > convective outflow treatment. ?There were comments on this just last week. > > > hth, > > > Paul > > > > > c ? ? . Set div U > 0 in elements with 'O? ' bc. > > c > > c ? ? . rq is nominally the ratio of Qout/Qin and is typically 1.5 > > c > > c ? ? . uin is normally zero, unless your flow is zero everywhere > > c > > c ? ? . d and m1 are work arrays of size (lx1,ly1,lz1,lelt), assumed > persistant > > c > > c ? ? This routine may or may not work with multiple outlets --- it has > > c ? ? not been tested for this case. > > c > > c > > c ? ? TYPICAL USAGE -- ADD THESE LINES TO userchk() in your .usr file: > > c? ? ? ? ? ? ? ? ? ? ? (uncommented) > > c > > c ? ? common /myoutflow/ d(lx1,ly1,lz1,lelt),m1(lx1*ly1*lz1,lelt) > > c ? ? real m1 > > c ? ? rq? = 2. > > c ? ? uin = 0. > > c ? ? call turb_outflow(d,m1,rq,uin) > > c > > > ------------------------------------------------------------------------ > *From:* Nek5000-users on > behalf of nek5000-users at lists.mcs.anl.gov > *Sent:* Tuesday, March 6, 2018 1:33:29 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Outflow boundary conditions > Dear all, > > are outflow advective boundary conditions available in nek5000? > > Or is there any work around in order to impose outflow boundary conditions > (for the velocity and the passive scalars) that can grantee that there > is no flow coming > back from the outflow boundary? > > Thanks, > Dante > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Mar 7 00:10:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Mar 2018 07:10:49 +0100 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Hi, indeed, the suggestions by Paul are probably the best way to get started! What we have experimented with was to use tripping also for periodic flows (i.e. a near-wall wall-normal focing); this way you do not really need to care about the divergence of the initial velocity field. This was quite useful for both pipes and ducts. Philipp On 2018-03-06 18:37, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Ali, > > > I've had good luck for rapid transition to turbulence in pipes?with the > attached i.c. routine. > > > In addition to random perturbations, it has a significant amount stream > wise vorticity near the pipe wall that is rapidly stretched by the mean > shear profile, so it generally takes off fairly quickly (e.g., within 10 > convective time units). > > > Alternatively or in conjunction with this, you can start with a high > Reynolds number and then reduce the Re once turbulence has set in. > > > hth, > > Paul > > > ------------------------------------------------------------------------ > *From:* Nek5000-users on > behalf of nek5000-users at lists.mcs.anl.gov > *Sent:* Tuesday, March 6, 2018 10:09:35 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Small random perturbations > > Thank you for responding. It is axisymmetric with periodic conditions at > the ends. > > > what geometry are you interested in? > Philipp > > On 2018-02-20 15:20,nek5000-users at lists.mcs.anl.gov > wrote: >>//>/Hello everyone, />//>/ ? ?I am just wondering about the validity of my way to initiate />/turbulence. My question is that instead of introducing random />/disturbances to the initial velocity, can I introduce them to the />/pressure gradient? Hint, I am using Nek5000 to simulate statistically />/non-stationary turbulent flow. />//>/Thank you in advance />/Ali />/Embry-Riddle Aeronautical University/ > > > > > _______________________________________________ > 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 Mar 7 10:26:32 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Mar 2018 17:26:32 +0100 Subject: [Nek5000-users] Non-uniform mesh Message-ID: Dear Neks, I'm simulating the flow in a 90 degree bent pipe. I am trying to build a non-uniform mesh which is finer in the bent section and coarser in the straight sections. For this purpose I am writing this code in the subroutine usrdat2: do i = 1, nelv iel=lglel(i) if (iel.le.960) then z = 0.8*z elseif ((iel.gt.960).and.(iel.le.1728)) then z = 3.*z elseif (iel.gt.1728) then z = 0.5*z endif enddo The idea is to dilate the coordinates in the straight sections and to shrink them in the bent section so that the mesh would be non-uniform. However, this doesn't work. Is this the correct procedure? Thanks. Best regards. From nek5000-users at lists.mcs.anl.gov Thu Mar 8 09:18:02 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 15:18:02 +0000 Subject: [Nek5000-users] Small random perturbations Message-ID: Dear all First, many thanks for your response. I couldn't be more thankful. Either by starting with high Reynolds number or by using initial noise is working now. However, once I increase the resolution the turbulence decays and disappears completely, and I don't know why? I just wanted to make grid independence and my geometry is very small, 10 cm in axial direction & 1 cm along the radius. Any idea is greatly appreciable. Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005126.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 8 10:47:16 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 16:47:16 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Dear Ali, This is definitely strange and not usual behavior. How are you increasing your resolution? Are you moving to a new mesh? Are you simply changing lx1 in the SIZE file? How many elements are you using now and what order lx1 ? What is your Re? Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, March 8, 2018 9:18:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Dear all First, many thanks for your response. I couldn't be more thankful. Either by starting with high Reynolds number or by using initial noise is working now. However, once I increase the resolution the turbulence decays and disappears completely, and I don't know why? I just wanted to make grid independence and my geometry is very small, 10 cm in axial direction & 1 cm along the radius. Any idea is greatly appreciable. Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005126.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 8 11:16:05 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 17:16:05 +0000 Subject: [Nek5000-users] Small random perturbations Message-ID: Dear Dr.Fischer, Thank you for your time. I simply change lx1 in the SIZE from 7 to 9 in order to increase the resolution and I am not moving to a new mesh. Also, I just started with 40 elements with lx1 =7, clustered to the wall, and my Re is around 6000. Best Regards, Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005129.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 8 14:13:06 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 20:13:06 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Dear Ali, How long is your pipe (in terms of number of diameters) ? 40 elements - is that the number in the x-y plane? Or the total number? Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, March 8, 2018 11:16:05 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Dear Dr.Fischer, Thank you for your time. I simply change lx1 in the SIZE from 7 to 9 in order to increase the resolution and I am not moving to a new mesh. Also, I just started with 40 elements with lx1 =7, clustered to the wall, and my Re is around 6000. Best Regards, Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005129.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 8 14:28:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 20:28:42 +0000 Subject: [Nek5000-users] Small random perturbations Message-ID: Yes, the length is 5D and 40 elements are in the x-y plane only. sincerely, Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 8 15:59:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Mar 2018 21:59:30 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: How many elements in z? (If you'd like, you can send a gzippd tar file with SIZE, usr, rea, etc. to me off-list.) Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, March 8, 2018 2:28:42 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Yes, the length is 5D and 40 elements are in the x-y plane only. sincerely, Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 9 08:11:09 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 9 Mar 2018 15:11:09 +0100 Subject: [Nek5000-users] comp_vort3, conj_ht Message-ID: Hello Nek team, In conj_ht example, I compute curl using common /myvort/ b1(lx1,ly1,lz1,lelt,3), call comp_vort3(b1,work1,work2,t(1,1,1,1,1), $ t(1,1,1,1,2),t(1,1,1,1,3)) b1 is being computed correctly in the fluid domain, but in the solid domain it is showing zero. Can you please correct it to compute the curl in the solid domain? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 9 11:21:46 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 9 Mar 2018 17:21:46 +0000 Subject: [Nek5000-users] Small random perturbations Message-ID: Dear Dr.Fischer, Actually, I am doing 2-D simulation, at least for now, so no z-dimension is up there. Am I wrong to do DNS in 2-D? Also, I just started doing so, and I think my files are not useful at this point. Let me try more, maybe I am missing something. Thank you for your awesome free code and your continuous support. Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005133.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 9 13:10:28 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 9 Mar 2018 19:10:28 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Hi Ali, Two questions: 1) How are you forcing your flow? (Do you have periodic boundary conditions in x ? Are you using constant flow rate? (p54 = -1; p55=1 would be recommended for periodic bcs with ffx=0 in the .usr file). 2) If your Reynolds number is Re = Ubar H / nu , where H=channel half height and Re > (2/3) * 5772 then you should find that you have sustained unsteadiness. That is, you should have linear instabilities that will grow and saturate to some truly nonlinear (unsteady) state. [ The 2/3 is because Re=5772 is the transition point for 2D plane channel flow based on U_max, when the background profile is U=(1-y*y)*Umax and H=1. In this case, Ubar = 2/3 * Umax .] In general, you won't have turbulence in 2D. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, March 9, 2018 11:21:46 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Dear Dr.Fischer, Actually, I am doing 2-D simulation, at least for now, so no z-dimension is up there. Am I wrong to do DNS in 2-D? Also, I just started doing so, and I think my files are not useful at this point. Let me try more, maybe I am missing something. Thank you for your awesome free code and your continuous support. Ali https://lists.mcs.anl.gov/pipermail/nek5000-users/2018-March/005133.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 10 05:30:28 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 10 Mar 2018 12:30:28 +0100 Subject: [Nek5000-users] comp_vort3, conj_ht In-Reply-To: References: Message-ID: I guess the routine is hardwired to to compute the curl of a field defined on the velocity mesh. On 9 Mar 2018, at 15:11, "nek5000-users at lists.mcs.anl.gov " > wrote: Hello Nek team, In conj_ht example, I compute curl using common /myvort/ b1(lx1,ly1,lz1,lelt,3), call comp_vort3(b1,work1,work2,t(1,1,1,1,1), $ t(1,1,1,1,2),t(1,1,1,1,3)) b1 is being computed correctly in the fluid domain, but in the solid domain it is showing zero. Can you please correct it to compute the curl in the solid domain? Thanks in advance. _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 12 11:17:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 12 Mar 2018 16:17:20 +0000 Subject: [Nek5000-users] Sponge/Dong boundary condition: Nek5000-users Digest, Vol 109, Issue 2 In-Reply-To: References: Message-ID: Hi Phillip, Apologies for the delayed reply, seeing your code and implementation of the Dong boundary condition would be very useful. I may also have a look at the Appelquist paper but at this point I would just like something that allows my flow to leave the domain without crashing the simulation. Thanks for your help. Best, Daniel ________________________________ From: Nek5000-users on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: 02 March 2018 18:00 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 109, Issue 2 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: Sponge layer in Nek5000 (nek5000-users at lists.mcs.anl.gov) 2. Re: Sponge layer in Nek5000 (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 1 Mar 2018 12:24:45 -0700 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Sponge layer in Nek5000 Message-ID: Content-Type: text/plain; charset="utf-8" Hi Daniel, We did implement the Sponge layer a couple of years back in nek5000 at the outflow boundary condition. We used a Smagorinsky type of eddy-viscosity closure where the Smagorinsky coefficient quadratically varies in the x direction (where is the direction of dominant flow), close to a few elements near the outflow. You can set it up with uservp in nek5000. However, the stabilized natural outflow boundary conditions by Dong et al. (2014) behaves much better than the sponge layer in my opinion. For my type of problem the sponge layer actually creates artificial diffusive structures close to the boundary, even when they are applied very smoothly, and you need to chop off the near-outflow region for data analysis. On Thu, Mar 1, 2018 at 9:56 AM, wrote: > Hi all, > > > I'm trying to implement outflow boundary conditions for a turbulent plume > using a sponge layer to absorb the energy of the flow and prevent > reflections back into the domain. I was wondering whether there is > anything set up in Nek already to construct this sponge layer or if it's > something I need to do myself, and if so whether anybody could help with > something they've done before - I've read a couple of other threads here > that mention a sponge layer but not its implementation. > > > I look forward to hearing from you. > > > Best, > > > Daniel Ward > > _______________________________________________ > 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: 2 Date: Thu, 1 Mar 2018 22:05:45 +0100 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Sponge layer in Nek5000 Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed Hi, we have also implemented various sponges and other boundary conditions, including the Dong condition and convective conditions. The sponge we typically base on a "direct" forcing approach as e.g. described in the paper by Appelquist (JFM 2015); the implementation of that type of forcing is in userf. The Dong condition is essentially a modified "o" condition (where one has to change a few lines here and there in the code, but I could send you our code), and the convective condition, which behaved the best (see e.g. the Master's thesis by Erik Bostr?m) can be implemented in usercheck. The latter condition did create the least upstream disturbances. Philipp On 2018-03-01 20:24, nek5000-users at lists.mcs.anl.gov wrote: > Hi Daniel, > > We did implement the Sponge layer a couple of years back in nek5000 at > the outflow boundary condition. We used a Smagorinsky type of > eddy-viscosity closure where the Smagorinsky coefficient quadratically > varies in the x direction (where is the direction of dominant flow), > close to a few elements near the outflow. You can set it up with uservp > in nek5000. However, the stabilized natural outflow boundary conditions > by Dong et al. (2014) behaves much better than the sponge layer in my > opinion. For my type of problem the sponge layer actually creates > artificial diffusive structures close to the boundary, even when they > are applied very smoothly, and you need to chop off the near-outflow > region for data analysis. > > On Thu, Mar 1, 2018 at 9:56 AM, > wrote: > > Hi all, > > > I'm trying to implement outflow boundary conditions for a turbulent > plume using a sponge layer to absorb the energy of the flow and > prevent reflections back into the domain.? I was wondering whether > there is anything set up in Nek already to construct this sponge > layer or if it's something I need to do myself, and if so whether > anybody could help with something they've done before - I've read a > couple of other threads here that mention a sponge layer but not its > implementation. > > > I look forward to hearing from you. > > > Best, > > > Daniel Ward > > > _______________________________________________ > 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 > ------------------------------ Subject: Digest Footer _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ------------------------------ End of Nek5000-users Digest, Vol 109, Issue 2 ********************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 12 12:39:55 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 12 Mar 2018 18:39:55 +0100 Subject: [Nek5000-users] Sponge/Dong boundary condition: Nek5000-users Digest, Vol 109, Issue 2 In-Reply-To: References: Message-ID: Hi Daniel, I can send you the code if you contact me by email. Unfortunately, I haven't had the time to prepare a proper example that works with newer versions. PHilipp On 2018-03-12 17:17, nek5000-users at lists.mcs.anl.gov wrote: > Hi Phillip, > > > Apologies for the delayed reply, seeing your code and implementation of > the Dong boundary condition would be very useful.? I may also have a > look at the Appelquist paper but at this point I would just like > something that allows my flow to leave the domain without crashing the > simulation. > > > Thanks for your help. > > > Best, > > > Daniel > > > > ------------------------------------------------------------------------ > *From:* Nek5000-users on > behalf of nek5000-users-request at lists.mcs.anl.gov > > *Sent:* 02 March 2018 18:00 > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Nek5000-users Digest, Vol 109, Issue 2 > 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: Sponge layer in Nek5000 (nek5000-users at lists.mcs.anl.gov) > ?? 2. Re: Sponge layer in Nek5000 (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Mar 2018 12:24:45 -0700 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Sponge layer in Nek5000 > Message-ID: > ??????? > Content-Type: text/plain; charset="utf-8" > > Hi Daniel, > > We did implement the Sponge layer a couple of years back in nek5000 at the > outflow boundary condition. We used a Smagorinsky type of eddy-viscosity > closure where the Smagorinsky coefficient quadratically varies in the x > direction (where is the direction of dominant flow), close to a few > elements near the outflow. You can set it up with uservp in nek5000. > However, the stabilized natural outflow boundary conditions by Dong et al. > (2014) behaves much better than the sponge layer in my opinion. For my type > of problem the sponge layer actually creates artificial diffusive > structures close to the boundary, even when they are applied very smoothly, > and you need to chop off the near-outflow region for data analysis. > > On Thu, Mar 1, 2018 at 9:56 AM, wrote: > >> Hi all, >> >> >> I'm trying to implement outflow boundary conditions for a turbulent plume >> using a sponge layer to absorb the energy of the flow and prevent >> reflections back into the domain.? I was wondering whether there is >> anything set up in Nek already to construct this sponge layer or if it's >> something I need to do myself, and if so whether anybody could help with >> something they've done before - I've read a couple of other threads here >> that mention a sponge layer but not its implementation. >> >> >> I look forward to hearing from you. >> >> >> Best, >> >> >> Daniel Ward >> >> _______________________________________________ >> 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: 2 > Date: Thu, 1 Mar 2018 22:05:45 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Sponge layer in Nek5000 > Message-ID: > ??????? > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi, > we have also implemented various sponges and other boundary conditions, > including the Dong condition and convective conditions. The sponge we > typically base on a "direct" forcing approach as e.g. described in the > paper by Appelquist (JFM 2015); the implementation of that type of > forcing is in userf. > > The Dong condition is essentially a modified "o" condition (where one > has to change a few lines here and there in the code, but I could send > you our code), and the convective condition, which behaved the best (see > e.g. the Master's thesis by Erik Bostr?m) can be implemented in > usercheck. The latter condition did create the least upstream disturbances. > > Philipp > > On 2018-03-01 20:24, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Daniel, >> >> We did implement the Sponge layer a couple of years back in nek5000 at >> the outflow boundary condition. We used a Smagorinsky type of >> eddy-viscosity closure where the Smagorinsky coefficient quadratically >> varies in the x direction (where is the direction of dominant flow), >> close to a few elements near the outflow. You can set it up with uservp >> in nek5000. However, the stabilized natural outflow boundary conditions >> by Dong et al. (2014) behaves much better than the sponge layer in my >> opinion. For my type of problem the sponge layer actually creates >> artificial diffusive structures close to the boundary, even when they >> are applied very smoothly, and you need to chop off the near-outflow >> region for data analysis. >> >> On Thu, Mar 1, 2018 at 9:56 AM, > > wrote: >> >>???? Hi all, >> >> >>???? I'm trying to implement outflow boundary conditions for a turbulent >>???? plume using a sponge layer to absorb the energy of the flow and >>???? prevent reflections back into the domain.? I was wondering whether >>???? there is anything set up in Nek already to construct this sponge >>???? layer or if it's something I need to do myself, and if so whether >>???? anybody could help with something they've done before - I've read a >>???? couple of other threads here that mention a sponge layer but not its >>???? implementation. >> >> >>???? I look forward to hearing from you. >> >> >>???? Best, >> >> >>???? Daniel Ward >> >> >>???? _______________________________________________ >>???? 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 >> > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > End of Nek5000-users Digest, Vol 109, Issue 2 > ********************************************* > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Mar 14 08:37:18 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 13:37:18 +0000 Subject: [Nek5000-users] Nek Developer/User Meeting, April 17-18, 2018, Tampa, Florida In-Reply-To: References: , Message-ID: Dear All, A reminder to register for the upcoming Developer/User Meeting in Tampa, just one month away. http://reg.conferences.dce.ufl.edu/SSP/1400066876 Conference rates for the Renaissance Tampa International Plaza Hotel are available till this Friday (March 16). We will start to put the program together next week, so an accurate assessment of the number of attendees will be important. Looking forward to seeing you in Tampa! The Nek Team ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, January 29, 2018 9:46 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Nek Developer/User Meeting, April 17-18, 2018, Tampa, Florida Dear Neks, We are pleased to announce that the 6th Nek5000 User/Developer meeting will be held in Tampa, Florida, at the Renaissance Tampa International Plaza Hotel on April 17 (Tuesday) and April 18 (Wednesday) 2018. This meeting is being organized by the Center for Compressible Multiphase Flow (CCMT) at the University of Florida and will bring together a group of experts in high-order numerical methods, high-performance computing, and a wide spectrum of application areas in physics and fluid/thermal sciences to discuss new developments and uses of the open-source solvers, Nek5000, NekCEM, and CMT-nek. We expect that there will be several invited speakers at the meeting who made significant contributions to the theory and development of high-order methods, as well as some of the principal user/developers who have pushed these methods to the limit in important application areas on the world's fastest computers. The presentations will feature our standard User/Developer Meeting format, with 15-minute talks by each participant along with a handful of more extended presentations. The meeting is not limited to past users and developers only. We welcome potential new users from the national laboratories, universities, and industry who are interested in knowing more about Nek5000 family of codes. This year, there will be a meeting registration fee to cover coffee breaks, lunch on both days, and well as dinner on Tuesday, 4/17. The registration site is here: http://reg.conferences.dce.ufl.edu/SSP/1400066876 Hotel and registration deadlines will be posted shortly along with abstract submission information, but we ask that you please register early so that we may estimate the attendance. Also, please help us to connect with existing Nek5000 users and potential users of the new capabilities. We look forward to seeing you in April! Sincerely, The Nek development team. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 14 10:24:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 16:24:14 +0100 (CET) Subject: [Nek5000-users] Nodal points using face and element number Message-ID: Hi Neks, Could you please tell me, if i give the face number and element number, can i get the nodal co ordinates? My problem is I have a body in fluid domain and I have the element number and face number of elements which is in contact with the surface of the body. I need to get the x cordinates of the Nodes which are on the body. Regards Sijo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 14 10:42:22 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 16:42:22 +0100 Subject: [Nek5000-users] Nodal points using face and element number In-Reply-To: References: Message-ID: Hi Sijo, Given element iel and face iface, the corresponding nodal points can be accessed as follows: c Identify the start and end indices of the face call facind(kx1,kx2,ky1,ky2,kz1,kz2,nx1,ny1,nz1,iface) c Loop through the nodes of the face do iz = kz1,kz2 do iy = ky1,ky2 do ix = kx1,kx2 myarray(ix,iy,iz,iel) = ... ! accessing the points on face iface enddo enddo enddo Best, Nicolas On Wed, Mar 14, 2018 at 4:24 PM, wrote: > Hi Neks, > > Could you please tell me, if i give the face number and element number, > can i get the nodal co ordinates? My problem is I have a body in fluid > domain and I have the element number and face number of elements which is > in contact with the surface of the body. I need to get the x cordinates of > the Nodes which are on the body. > > > Regards > > Sijo > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 14 10:48:37 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 16:48:37 +0100 (CET) Subject: [Nek5000-users] Nodal points using face and element number In-Reply-To: References: Message-ID: Thank you Nicolas i will give a try. De: "nek5000-users" ?: "nek5000-users" Envoy?: Mercredi 14 Mars 2018 16:42:22 Objet: Re: [Nek5000-users] Nodal points using face and element number Hi Sijo, Given element iel and face iface, the corresponding nodal points can be accessed as follows: c Identify the start and end indices of the face call facind(kx1,kx2,ky1,ky2,kz1,kz2,nx1,ny1,nz1,iface) c Loop through the nodes of the face do iz = kz1,kz2 do iy = ky1,ky2 do ix = kx1,kx2 myarray(ix,iy,iz,iel) = ... ! accessing the points on face iface enddo enddo enddo Best, Nicolas On Wed, Mar 14, 2018 at 4:24 PM, < [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] > wrote: Hi Neks, Could you please tell me, if i give the face number and element number, can i get the nodal co ordinates? My problem is I have a body in fluid domain and I have the element number and face number of elements which is in contact with the surface of the body. I need to get the x cordinates of the Nodes which are on the body. Regards Sijo _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list 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 Mar 14 10:35:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 15:35:20 +0000 Subject: [Nek5000-users] Nodal points using face and element number In-Reply-To: References: Message-ID: Hi Sijo, You can use the function "facind" to obtain a set of index ranges on one face, denoted by the input argument "iface". Then, to obtain the x-coordinates you just access entries in array xm1. call facind (kx1,kx2,ky1,ky2,kz1,kz2,nx,ny,nz,iface) do 100 iz=kz1,kz2 do 100 iy=ky1,ky2 do 100 ix=kx1,kx2 write(6,*) xm1(ix,iy,iz,ie) 100 continue Hope this helps, Li From: Nek5000-users [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, March 14, 2018 10:24 To: nek5000-users Subject: [Nek5000-users] Nodal points using face and element number Hi Neks, Could you please tell me, if i give the face number and element number, can i get the nodal co ordinates? My problem is I have a body in fluid domain and I have the element number and face number of elements which is in contact with the surface of the body. I need to get the x cordinates of the Nodes which are on the body. Regards Sijo From nek5000-users at lists.mcs.anl.gov Wed Mar 14 15:29:21 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 21:29:21 +0100 (CET) Subject: [Nek5000-users] Nodal points using face and element number In-Reply-To: References: Message-ID: Thank you Li. I had tried a similar method with the help of Nicolas and it worked. Thanks again ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Mercredi 14 Mars 2018 16:35:20 Objet: Re: [Nek5000-users] Nodal points using face and element number Hi Sijo, You can use the function "facind" to obtain a set of index ranges on one face, denoted by the input argument "iface". Then, to obtain the x-coordinates you just access entries in array xm1. call facind (kx1,kx2,ky1,ky2,kz1,kz2,nx,ny,nz,iface) do 100 iz=kz1,kz2 do 100 iy=ky1,ky2 do 100 ix=kx1,kx2 write(6,*) xm1(ix,iy,iz,ie) 100 continue Hope this helps, Li From: Nek5000-users [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, March 14, 2018 10:24 To: nek5000-users Subject: [Nek5000-users] Nodal points using face and element number Hi Neks, Could you please tell me, if i give the face number and element number, can i get the nodal co ordinates? My problem is I have a body in fluid domain and I have the element number and face number of elements which is in contact with the surface of the body. I need to get the x cordinates of the Nodes which are on the body. Regards Sijo _______________________________________________ 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 Mar 14 20:46:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 14 Mar 2018 20:46:15 -0500 Subject: [Nek5000-users] Balancing heat flux BCs in periodic domain Message-ID: Hello Nek Users, I have a periodic fluid domain with heat flux BCs at my walls. To prevent my temperatures from increasing indefinitely, I am prescribing a sink within userq using qvol which is equal to "user_flux * wall_surface_area / fluid_volume". This works in theory. The issue is that due to round-off errors, my temperatures still increases (although extremely slowly). I would like my average temperature be the same regardless of run time. What would be the most efficient method to balance the temperature in my domain? Best, Jon -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 08:20:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 14:20:14 +0100 (CET) Subject: [Nek5000-users] Filtering in the turbChannel, it that possible to use another filter, such as top-hat filter or Gaussian filter? Message-ID: Hello everyone, I have been working on the turbulent channel case for some time. But I am quite confused with the filtering technique in the turbChannel.usr. I understand well the filtering technique for improving stability (p101 and p103), thanks to the discussion on the forum. However, is the same technique used in the build_1d_filt ? basically, partly removing the high wavenumber spectral in the expansion ? I have a question about transfer function also: diag(nx-0) = 0.05 diag(nx-1) = 0.50 diag(nx-2) = 0.95 It seems to me that the diag(:) would determine how much energy will be removed for the high wave number spectral? but what are the variables fh, fht in the subroutine build_1d_filt (fh,fht,diag,nx,nid) ? it seems quite difficult to apply the more traditional filters like top-hat filter or Gaussian filter in the Nek5000. Lastly, removing high wave number parts of Legendre expansion seems makes no sense physically. After all, the energy spectral of turbulence is represented in Fourier series. Does anyone has any idea on these puzzles? Any discussion is greatly appreciated. Best regards Bien cordialement Zhenrong JING Doctorant (Doctor Candidate) LHEEA Ecole Centrale de Nantes 1 Rue de la No?, 44321 Nantes, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 09:07:51 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 21:07:51 +0700 Subject: [Nek5000-users] Subscribe In-Reply-To: References: Message-ID: Hello everybody! Can you tell me how this function work? !----------------------------------------------------------------------- subroutine particle_advect_std(x,vh,partv,npart) ! Lagrangian particle advection include 'SIZE' include 'TOTAL' real x(ldim,lpart),vh(ldim,2:3,lpart),partv(lpart) common /scruz/ u1(ldim,lpart) common /padvc/ xmx(3,0:2) if (istep.eq.0) then ! AB1 call rzero(vh,3*ndim*npart) c1 = 1. c2 = 0. c3 = 0. elseif (istep.eq.1) then ! AB2 c1 = 3 c2 = -1. c3 = 0 c1 = c1/2. c2 = c2/2. else ! AB3 c1 = 23. c2 = -16. c3 = 5. c1 = c1/12. c2 = c2/12. c3 = c3/12 endif call interp_v(u1,x,npart) do i=1,npart do k=1,ndim ! Update particle position and history x(k,i) = x(k,i) $ + dt*(c1*u1(k,i) + c2*vh(k,2,i) + c3*vh(k,3,i)) ! Update particle and fluid velocity history vh(k,3,i) = vh(k,2,i) vh(k,2,i) = u1(k,i) enddo enddo return end !---------------------------------------------------------------------- I understood how works function interp_v. Also, I know what is ldim, lpart, x, u1. I think that vh is lagged velocity. Can I give vh? What is partv? I have no idea( And scruz? Ilya -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 12:47:12 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 12:47:12 -0500 Subject: [Nek5000-users] Balancing heat flux BCs in periodic domain In-Reply-To: References: Message-ID: Hi Jon, You can manually force the average temperature to be a certain value. If you add the following code in userchk, the average temperature should be constant: include 'TOTAL' real tw(lx1*ly1*lz1*lelt) offset = 1. ! desired average value n = lx1*ly1*lz1*nelt call col3(tw,t,bm1,n) tave = glsum(tw,n) / voltm1 call cadd(t,offset-tave,n) If you just want to check the average temperature value, you can add the following lines: call col3(tw,t,bm1,n) tave = glsum(tw,n) / voltm1 write (6,*) 'tave=', tave Kento > On Mar 14, 2018, at 20:46, nek5000-users at lists.mcs.anl.gov wrote: > > Hello Nek Users, > > I have a periodic fluid domain with heat flux BCs at my walls. To prevent my temperatures from increasing indefinitely, I am prescribing a sink within userq using qvol which is equal to "user_flux * wall_surface_area / fluid_volume". > > This works in theory. The issue is that due to round-off errors, my temperatures still increases (although extremely slowly). > > I would like my average temperature be the same regardless of run time. What would be the most efficient method to balance the temperature in my domain? > > Best, > Jon > _______________________________________________ > 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 Mar 15 12:58:43 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 10:58:43 -0700 Subject: [Nek5000-users] Filtering in the turbChannel, it that possible to use another filter, such as top-hat filter or Gaussian filter? In-Reply-To: References: Message-ID: Hello Zhenrong, fh is the 1D filter transformation matrix i.e. applied by kronecker product transformation for 3D. So, for 3D case, is u_ijk is the velocity data at each element, fh X fh X fh . u_ijk is the filtered variable, where X denotes the kronecker multiplication and . denotes the matrix multiplication. fht is the transpose of fh. You can look into the tens3d1() routine in postpro.f for more details. If you denote fh as *F* in matrix notation, then *F* =* V D V^*-1, where *V *is the transformation matrix from nodal to modal (Legendre) space, and V ^-1, the inverse transformation. Now, D is the diagonal transfer function, which is referred to as diag in the routine. You can design your diag() in any way you want. diag is a nx X nx matrix, with non-zero diagonal. The first two entries of the diagonal needs to be 1, probably to maintain C0 continuity of u (I need to check that), and you can design the shape of the diagonal entries, in any way you want, (.i.e. as a function of cut-off modes.) You can look into the appendix of the paper https://aip.scitation.org/doi/pdf/10.1063/1.4994603 for details regarding the filtering operation. On Thu, Mar 15, 2018 at 6:20 AM, wrote: > Hello everyone, > > I have been working on the turbulent channel case for some time. But I am > quite confused with the filtering technique in the turbChannel.usr. > I understand well the filtering technique for improving stability (p101 > and p103), thanks to the discussion on the forum. However, is the same > technique used in the build_1d_filt ? basically, partly removing the high > wavenumber spectral in the expansion ? > > I have a question about transfer function also: > > diag(nx-0) = 0.05 > diag(nx-1) = 0.50 > diag(nx-2) = 0.95 > > It seems to me that the diag(:) would determine how much energy will be > removed for the high wave number spectral? but what are the variables fh, > fht in the subroutine > build_1d_filt (fh,fht,diag,nx,nid) ? > > it seems quite difficult to apply the more traditional filters like > top-hat filter or Gaussian filter in the Nek5000. > > Lastly, removing high wave number parts of Legendre expansion seems makes > no sense physically. After all, the energy spectral of turbulence is > represented in Fourier series. > > Does anyone has any idea on these puzzles? Any discussion is greatly > appreciated. > > Best regards > > Bien cordialement > > Zhenrong JING > > Doctorant (Doctor Candidate) > > LHEEA > > Ecole Centrale de Nantes > > 1 Rue de la No?, 44321 Nantes, France > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 13:05:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 11:05:35 -0700 Subject: [Nek5000-users] Filtering in the turbChannel, it that possible to use another filter, such as top-hat filter or Gaussian filter? In-Reply-To: References: Message-ID: PS: Additionally, to answer your question " *Lastly, removing high wave number parts of Legendre expansion seems makes no sense physically. After all, the energy spectral of turbulence is represented in Fourier series.* *Does anyone has any idea on these puzzles*?" -- Within each element, every variable is expanded as a function of Legendre polynomials. Note, that higher the order (mode) of the polynomial the more frequent oscillations it has. So in this sense, the highly frequent oscillations are somewhat very similar to the frequency/wavenumber in a classical Fourier series. A relation between mode and frequency would be worth a derivation, but the idea is just as a function can be thought of as a series of different frequency/wave number content sine/cosine oscillations, similarly an aperiodic function can be thought of as a series of Legendre polynomials of different modes. In this sense, removing/ filtering a highest modes of the transfer function, is equivalent to removing the high frequency content of the flow variables. It would have a similar effect in removing the high frequency content of a turbulent flow field. HTH, Tanmoy On Thu, Mar 15, 2018 at 10:58 AM, wrote: > Hello Zhenrong, > > fh is the 1D filter transformation matrix i.e. applied by kronecker > product transformation for 3D. So, for 3D case, is u_ijk is the velocity > data at each element, fh X fh X fh . u_ijk is the filtered variable, where > X denotes the kronecker multiplication and . denotes the matrix > multiplication. fht is the transpose of fh. You can look into the tens3d1() > routine in postpro.f for more details. > > If you denote fh as *F* in matrix notation, then > > *F* =* V D V^*-1, where *V *is the transformation matrix from nodal to > modal (Legendre) space, and V ^-1, the inverse transformation. Now, D is > the diagonal transfer function, which is referred to as diag in the > routine. You can design your diag() in any way you want. diag is a nx X nx > matrix, with non-zero diagonal. The first two entries of the diagonal needs > to be 1, probably to maintain C0 continuity of u (I need to check that), > and you can design the shape of the diagonal entries, in any way you want, > (.i.e. as a function of cut-off modes.) You can look into the appendix of > the paper https://aip.scitation.org/doi/pdf/10.1063/1.4994603 for details > regarding the filtering operation. > > On Thu, Mar 15, 2018 at 6:20 AM, wrote: > >> Hello everyone, >> >> I have been working on the turbulent channel case for some time. But I am >> quite confused with the filtering technique in the turbChannel.usr. >> I understand well the filtering technique for improving stability (p101 >> and p103), thanks to the discussion on the forum. However, is the same >> technique used in the build_1d_filt ? basically, partly removing the high >> wavenumber spectral in the expansion ? >> >> I have a question about transfer function also: >> >> diag(nx-0) = 0.05 >> diag(nx-1) = 0.50 >> diag(nx-2) = 0.95 >> >> It seems to me that the diag(:) would determine how much energy will be >> removed for the high wave number spectral? but what are the variables fh, >> fht in the subroutine >> build_1d_filt (fh,fht,diag,nx,nid) ? >> >> it seems quite difficult to apply the more traditional filters like >> top-hat filter or Gaussian filter in the Nek5000. >> >> Lastly, removing high wave number parts of Legendre expansion seems makes >> no sense physically. After all, the energy spectral of turbulence is >> represented in Fourier series. >> >> Does anyone has any idea on these puzzles? Any discussion is greatly >> appreciated. >> >> Best regards >> >> Bien cordialement >> >> Zhenrong JING >> >> Doctorant (Doctor Candidate) >> >> LHEEA >> >> Ecole Centrale de Nantes >> >> 1 Rue de la No?, 44321 Nantes, France >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 13:07:23 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 13:07:23 -0500 Subject: [Nek5000-users] Balancing heat flux BCs in periodic domain In-Reply-To: References: Message-ID: P.S. The write line should be: if (nio.eq.0) write (6,*) ?tave=?, tave Sorry about that > On Mar 15, 2018, at 12:47, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Jon, > > You can manually force the average temperature to be a certain value. If you add the following code in userchk, the average temperature should be constant: > > include 'TOTAL' > > real tw(lx1*ly1*lz1*lelt) > > offset = 1. ! desired average value > > n = lx1*ly1*lz1*nelt > > call col3(tw,t,bm1,n) > tave = glsum(tw,n) / voltm1 > > call cadd(t,offset-tave,n) > > If you just want to check the average temperature value, you can add the following lines: > > call col3(tw,t,bm1,n) > tave = glsum(tw,n) / voltm1 > write (6,*) 'tave=', tave > > Kento > >> On Mar 14, 2018, at 20:46, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hello Nek Users, >> >> I have a periodic fluid domain with heat flux BCs at my walls. To prevent my temperatures from increasing indefinitely, I am prescribing a sink within userq using qvol which is equal to "user_flux * wall_surface_area / fluid_volume". >> >> This works in theory. The issue is that due to round-off errors, my temperatures still increases (although extremely slowly). >> >> I would like my average temperature be the same regardless of run time. What would be the most efficient method to balance the temperature in my domain? >> >> Best, >> Jon >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Mar 15 13:49:21 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 18:49:21 +0000 Subject: [Nek5000-users] Subscribe In-Reply-To: References: , Message-ID: Dear Ilya, Given a list of points, x, which can be and _should_ be distinct on each mpi process, interp_v() returns the fluid velocity at each of those points, x_i, i=1,...,npart. Here, npart can be zero on some processors, but each process _must_ call interp_v. Particle positions are then updated using 3rd-order Adams Bashforth (AB3). x^n = x^{n-1} + dt*(23/12 v^{n-1} - 16/12 v^{n-2} + 5/12 v^{n-3} Each mpi rank is responsible for updating it's list of particle positions. interp_v handles all of the interpolation and data movement required to find the velocity at any point x_i in the list. (Communication would be required, for example, if a particle on a given mpi rank was in an element that is on a difference processor.) Communication cost is ~ M * log_2 P, where M is the maximum of npart (or perhaps the average of npart). ndim is the number of space dimensions (2 or 3). hth Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, March 15, 2018 9:07:51 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Subscribe Hello everybody! Can you tell me how this function work? !----------------------------------------------------------------------- subroutine particle_advect_std(x,vh,partv,npart) ! Lagrangian particle advection include 'SIZE' include 'TOTAL' real x(ldim,lpart),vh(ldim,2:3,lpart),partv(lpart) common /scruz/ u1(ldim,lpart) common /padvc/ xmx(3,0:2) if (istep.eq.0) then ! AB1 call rzero(vh,3*ndim*npart) c1 = 1. c2 = 0. c3 = 0. elseif (istep.eq.1) then ! AB2 c1 = 3 c2 = -1. c3 = 0 c1 = c1/2. c2 = c2/2. else ! AB3 c1 = 23. c2 = -16. c3 = 5. c1 = c1/12. c2 = c2/12. c3 = c3/12 endif call interp_v(u1,x,npart) do i=1,npart do k=1,ndim ! Update particle position and history x(k,i) = x(k,i) $ + dt*(c1*u1(k,i) + c2*vh(k,2,i) + c3*vh(k,3,i)) ! Update particle and fluid velocity history vh(k,3,i) = vh(k,2,i) vh(k,2,i) = u1(k,i) enddo enddo return end !---------------------------------------------------------------------- I understood how works function interp_v. Also, I know what is ldim, lpart, x, u1. I think that vh is lagged velocity. Can I give vh? What is partv? I have no idea( And scruz? Ilya -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 17:42:10 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 23:42:10 +0100 (CET) Subject: [Nek5000-users] Output files reading by python Message-ID: HI Neks, I was trying to read the output files of NEK5000 using some python files which are available in internet. But when I tried an old which is attached in this email, it throws some error. But the same code was working for other files. The attached file looks also bit different from other files. I assume that the standard of construction for this file is quite different from others. Could you please help me, to find a way to read the NEK5000 output files by using python scripts? Or anyway to make the standard output files? Thanks Sijo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 17:43:46 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 23:43:46 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Hi, you can check the python library by Jacopo and Nicolo: https://github.com/jcanton/pymech There are also matlab routines around. Perhpas Adam can send you a link to these. Philipp On 2018-03-15 23:42, nek5000-users at lists.mcs.anl.gov wrote: > HI Neks, > > I was trying to read the output files of NEK5000 using some python files > which are available in internet. But when I tried an old which is > attached in this email, it throws some error. But the same code was > working for other files. The attached file looks also bit different from > other files. I assume that the standard of construction for this file is > quite different from others. Could you please help me, to find a way to > read the NEK5000 output files by using python scripts? Or anyway to make > the standard output files? > > Thanks > > Sijo > > > _______________________________________________ > 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 Mar 15 17:50:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 23:50:24 +0100 (CET) Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? Thank you ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Jeudi 15 Mars 2018 23:43:46 Objet: Re: [Nek5000-users] Output files reading by python Hi, you can check the python library by Jacopo and Nicolo: https://github.com/jcanton/pymech There are also matlab routines around. Perhpas Adam can send you a link to these. Philipp On 2018-03-15 23:42, nek5000-users at lists.mcs.anl.gov wrote: > HI Neks, > > I was trying to read the output files of NEK5000 using some python files > which are available in internet. But when I tried an old which is > attached in this email, it throws some error. But the same code was > working for other files. The attached file looks also bit different from > other files. I assume that the standard of construction for this file is > quite different from others. Could you please help me, to find a way to > read the NEK5000 output files by using python scripts? Or anyway to make > the standard output files? > > Thanks > > Sijo > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 16 03:47:46 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 09:47:46 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Hi Sijo, what format are you trying to read? The files created by Nicolo (using python) are ONLY for *0.f0* files. Best regards, AW Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit : > Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? > > Thank you > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 15 Mars 2018 23:43:46 > Objet: Re: [Nek5000-users] Output files reading by python > > Hi, > you can check the python library by Jacopo and Nicolo: > > https://github.com/jcanton/pymech > > There are also matlab routines around. Perhpas Adam can send you a link > to these. > > Philipp > > On 2018-03-15 23:42, nek5000-users at lists.mcs.anl.gov wrote: >> HI Neks, >> >> I was trying to read the output files of NEK5000 using some python files >> which are available in internet. But when I tried an old which is >> attached in this email, it throws some error. But the same code was >> working for other files. The attached file looks also bit different from >> other files. I assume that the standard of construction for this file is >> quite different from others. Could you please help me, to find a way to >> read the NEK5000 output files by using python scripts? Or anyway to make >> the standard output files? >> >> Thanks >> >> Sijo >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: onihdfppfgfkggfp.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:29:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:29:24 +0100 (CET) Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Hi Arnold, I was trying to read .fld format. Is there any scripts I can read this? thank you sijo De: "nek5000-users" ?: "nek5000-users" Envoy?: Vendredi 16 Mars 2018 09:47:46 Objet: Re: [Nek5000-users] Output files reading by python Hi Sijo, what format are you trying to read? The files created by Nicolo (using python) are ONLY for *0.f0* files. Best regards, AW Le 15/03/2018 ? 23:50, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] a ?crit : Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? Thank you ----- Mail original ----- De: "nek5000-users" [ mailto:nek5000-users at lists.mcs.anl.gov | ] ?: "nek5000-users" [ mailto:nek5000-users at lists.mcs.anl.gov | ] Envoy?: Jeudi 15 Mars 2018 23:43:46 Objet: Re: [Nek5000-users] Output files reading by python Hi, you can check the python library by Jacopo and Nicolo: [ https://github.com/jcanton/pymech | https://github.com/jcanton/pymech ] There are also matlab routines around. Perhpas Adam can send you a link to these. Philipp On 2018-03-15 23:42, [ mailto:nek5000-users at lists.mcs.anl.gov | nek5000-users at lists.mcs.anl.gov ] wrote: BQ_BEGIN HI Neks, I was trying to read the output files of NEK5000 using some python files which are available in internet. But when I tried an old which is attached in this email, it throws some error. But the same code was working for other files. The attached file looks also bit different from other files. I assume that the standard of construction for this file is quite different from others. Could you please help me, to find a way to read the NEK5000 output files by using python scripts? Or anyway to make the standard output files? Thanks Sijo _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] _______________________________________________ Nek5000-users mailing list [ mailto:Nek5000-users at lists.mcs.anl.gov | Nek5000-users at lists.mcs.anl.gov ] [ https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users | https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ] BQ_END -- Arnold Wakim Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : [ http://www.onera.fr/ | www.onera.fr ] | [ http://www.twitter.com/@onera_fr | Twitter ] | [ http://www.linkedin.com/company/onera | LinkedIn ] | [ http://www.facebook.fr/thefrenchaerospacelab | Facebook ] Avertissement/disclaimer [ http://www.onera.fr/onera-en/emails-terms | http://www.onera.fr/onera-en/emails-terms ] _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: onihdfppfgfkggfp.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:33:00 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:33:00 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: I recommend to convert to f* format. On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: > Hi Arnold, > > I was trying to read .fld format. > Is there any scripts I can read this? > > > thank you > sijo > > ------------------------------------------------------------------------ > *De: *"nek5000-users" > *?: *"nek5000-users" > *Envoy?: *Vendredi 16 Mars 2018 09:47:46 > *Objet: *Re: [Nek5000-users] Output files reading by python > > Hi Sijo, what format are you trying to read? > The files created by Nicolo (using python) are ONLY for *0.f0* files. > > Best regards, > > AW > > Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: > > Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? > > Thank you > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 15 Mars 2018 23:43:46 > Objet: Re: [Nek5000-users] Output files reading by python > > Hi, > you can check the python library by Jacopo and Nicolo: > > https://github.com/jcanton/pymech > > There are also matlab routines around. Perhpas Adam can send you a link > to these. > > Philipp > > On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: > > HI Neks, > > I was trying to read the output files of NEK5000 using some python files > which are available in internet. But when I tried an old which is > attached in this email, it throws some error. But the same code was > working for other files. The attached file looks also bit different from > other files. I assume that the standard of construction for this file is > quite different from others. Could you please help me, to find a way to > read the NEK5000 output files by using python scripts? Or anyway to make > the standard output files? > > Thanks > > Sijo > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > -- > *Arnold Wakim* > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur : www.onera.fr ?| Twitter > ?| LinkedIn > ?| Facebook > > > > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:36:53 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:36:53 +0100 (CET) Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: I am sorry . I don't have much experience in that. Could you please tell me how can I convert? Thanks ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Vendredi 16 Mars 2018 10:33:00 Objet: Re: [Nek5000-users] Output files reading by python I recommend to convert to f* format. On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: > Hi Arnold, > > I was trying to read .fld format. > Is there any scripts I can read this? > > > thank you > sijo > > ------------------------------------------------------------------------ > *De: *"nek5000-users" > *?: *"nek5000-users" > *Envoy?: *Vendredi 16 Mars 2018 09:47:46 > *Objet: *Re: [Nek5000-users] Output files reading by python > > Hi Sijo, what format are you trying to read? > The files created by Nicolo (using python) are ONLY for *0.f0* files. > > Best regards, > > AW > > Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: > > Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? > > Thank you > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Jeudi 15 Mars 2018 23:43:46 > Objet: Re: [Nek5000-users] Output files reading by python > > Hi, > you can check the python library by Jacopo and Nicolo: > > https://github.com/jcanton/pymech > > There are also matlab routines around. Perhpas Adam can send you a link > to these. > > Philipp > > On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: > > HI Neks, > > I was trying to read the output files of NEK5000 using some python files > which are available in internet. But when I tried an old which is > attached in this email, it throws some error. But the same code was > working for other files. The attached file looks also bit different from > other files. I assume that the standard of construction for this file is > quite different from others. Could you please help me, to find a way to > read the NEK5000 output files by using python scripts? Or anyway to make > the standard output files? > > Thanks > > Sijo > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > -- > *Arnold Wakim* > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur : www.onera.fr ?| Twitter > ?| LinkedIn > ?| Facebook > > > > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:37:59 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:37:59 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: load as fld, save as f* On 2018-03-16 10:36, nek5000-users at lists.mcs.anl.gov wrote: > I am sorry . I don't have much experience in that. > Could you please tell me how can I convert? > > Thanks > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Vendredi 16 Mars 2018 10:33:00 > Objet: Re: [Nek5000-users] Output files reading by python > > I recommend to convert to f* format. > > > On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Arnold, >> >> I was trying to read .fld format. >> Is there any scripts I can read this? >> >> >> thank you >> sijo >> >> ------------------------------------------------------------------------ >> *De: *"nek5000-users" >> *?: *"nek5000-users" >> *Envoy?: *Vendredi 16 Mars 2018 09:47:46 >> *Objet: *Re: [Nek5000-users] Output files reading by python >> >> Hi Sijo, what format are you trying to read? >> The files created by Nicolo (using python) are ONLY for *0.f0* files. >> >> Best regards, >> >> AW >> >> Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: >> >> Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? >> >> Thank you >> >> ----- Mail original ----- >> De: "nek5000-users" >> ?: "nek5000-users" >> Envoy?: Jeudi 15 Mars 2018 23:43:46 >> Objet: Re: [Nek5000-users] Output files reading by python >> >> Hi, >> you can check the python library by Jacopo and Nicolo: >> >> https://github.com/jcanton/pymech >> >> There are also matlab routines around. Perhpas Adam can send you a link >> to these. >> >> Philipp >> >> On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: >> >> HI Neks, >> >> I was trying to read the output files of NEK5000 using some python files >> which are available in internet. But when I tried an old which is >> attached in this email, it throws some error. But the same code was >> working for other files. The attached file looks also bit different from >> other files. I assume that the standard of construction for this file is >> quite different from others. Could you please help me, to find a way to >> read the NEK5000 output files by using python scripts? Or anyway to make >> the standard output files? >> >> Thanks >> >> Sijo >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> -- >> *Arnold Wakim* >> Ph.D. Student >> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >> INST >> T?l: +33 1 46 23 51 83 >> >> >> ONERA?-?The French Aerospace Lab?-?Centre de Meudon >> 8, rue des Vertugadins - 92190 MEUDON >> >> Nous suivre sur : www.onera.fr ?| Twitter >> ?| LinkedIn >> ?| Facebook >> >> >> >> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:40:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:40:15 +0100 (CET) Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: sorry for silly questions..I am sorry I didn't get you load as fld? where? thanks silo ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Vendredi 16 Mars 2018 10:37:59 Objet: Re: [Nek5000-users] Output files reading by python load as fld, save as f* On 2018-03-16 10:36, nek5000-users at lists.mcs.anl.gov wrote: > I am sorry . I don't have much experience in that. > Could you please tell me how can I convert? > > Thanks > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Vendredi 16 Mars 2018 10:33:00 > Objet: Re: [Nek5000-users] Output files reading by python > > I recommend to convert to f* format. > > > On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Arnold, >> >> I was trying to read .fld format. >> Is there any scripts I can read this? >> >> >> thank you >> sijo >> >> ------------------------------------------------------------------------ >> *De: *"nek5000-users" >> *?: *"nek5000-users" >> *Envoy?: *Vendredi 16 Mars 2018 09:47:46 >> *Objet: *Re: [Nek5000-users] Output files reading by python >> >> Hi Sijo, what format are you trying to read? >> The files created by Nicolo (using python) are ONLY for *0.f0* files. >> >> Best regards, >> >> AW >> >> Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: >> >> Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? >> >> Thank you >> >> ----- Mail original ----- >> De: "nek5000-users" >> ?: "nek5000-users" >> Envoy?: Jeudi 15 Mars 2018 23:43:46 >> Objet: Re: [Nek5000-users] Output files reading by python >> >> Hi, >> you can check the python library by Jacopo and Nicolo: >> >> https://github.com/jcanton/pymech >> >> There are also matlab routines around. Perhpas Adam can send you a link >> to these. >> >> Philipp >> >> On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: >> >> HI Neks, >> >> I was trying to read the output files of NEK5000 using some python files >> which are available in internet. But when I tried an old which is >> attached in this email, it throws some error. But the same code was >> working for other files. The attached file looks also bit different from >> other files. I assume that the standard of construction for this file is >> quite different from others. Could you please help me, to find a way to >> read the NEK5000 output files by using python scripts? Or anyway to make >> the standard output files? >> >> Thanks >> >> Sijo >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> -- >> *Arnold Wakim* >> Ph.D. Student >> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >> INST >> T?l: +33 1 46 23 51 83 >> >> >> ONERA?-?The French Aerospace Lab?-?Centre de Meudon >> 8, rue des Vertugadins - 92190 MEUDON >> >> Nous suivre sur : www.onera.fr ?| Twitter >> ?| LinkedIn >> ?| Facebook >> >> >> >> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:42:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:42:20 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: you start your simulation by loading an fld file, and then you write it out directly as f file. This can be done by changing some of the parameters, see the documentation. On 2018-03-16 10:40, nek5000-users at lists.mcs.anl.gov wrote: > > sorry for silly questions..I am sorry I didn't get you > > load as fld? > where? > > thanks > silo > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Vendredi 16 Mars 2018 10:37:59 > Objet: Re: [Nek5000-users] Output files reading by python > > load as fld, save as f* > > On 2018-03-16 10:36, nek5000-users at lists.mcs.anl.gov wrote: >> I am sorry . I don't have much experience in that. >> Could you please tell me how can I convert? >> >> Thanks >> >> ----- Mail original ----- >> De: "nek5000-users" >> ?: "nek5000-users" >> Envoy?: Vendredi 16 Mars 2018 10:33:00 >> Objet: Re: [Nek5000-users] Output files reading by python >> >> I recommend to convert to f* format. >> >> >> On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Arnold, >>> >>> I was trying to read .fld format. >>> Is there any scripts I can read this? >>> >>> >>> thank you >>> sijo >>> >>> ------------------------------------------------------------------------ >>> *De: *"nek5000-users" >>> *?: *"nek5000-users" >>> *Envoy?: *Vendredi 16 Mars 2018 09:47:46 >>> *Objet: *Re: [Nek5000-users] Output files reading by python >>> >>> Hi Sijo, what format are you trying to read? >>> The files created by Nicolo (using python) are ONLY for *0.f0* files. >>> >>> Best regards, >>> >>> AW >>> >>> Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: >>> >>> Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? >>> >>> Thank you >>> >>> ----- Mail original ----- >>> De: "nek5000-users" >>> ?: "nek5000-users" >>> Envoy?: Jeudi 15 Mars 2018 23:43:46 >>> Objet: Re: [Nek5000-users] Output files reading by python >>> >>> Hi, >>> you can check the python library by Jacopo and Nicolo: >>> >>> https://github.com/jcanton/pymech >>> >>> There are also matlab routines around. Perhpas Adam can send you a link >>> to these. >>> >>> Philipp >>> >>> On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: >>> >>> HI Neks, >>> >>> I was trying to read the output files of NEK5000 using some python files >>> which are available in internet. But when I tried an old which is >>> attached in this email, it throws some error. But the same code was >>> working for other files. The attached file looks also bit different from >>> other files. I assume that the standard of construction for this file is >>> quite different from others. Could you please help me, to find a way to >>> read the NEK5000 output files by using python scripts? Or anyway to make >>> the standard output files? >>> >>> Thanks >>> >>> Sijo >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> -- >>> *Arnold Wakim* >>> Ph.D. Student >>> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >>> INST >>> T?l: +33 1 46 23 51 83 >>> >>> >>> ONERA?-?The French Aerospace Lab?-?Centre de Meudon >>> 8, rue des Vertugadins - 92190 MEUDON >>> >>> Nous suivre sur : www.onera.fr ?| Twitter >>> ?| LinkedIn >>> ?| Facebook >>> >>> >>> >>> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 16 04:46:18 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 10:46:18 +0100 (CET) Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Thank you very much.. I will give a try. Regards Sijo ----- Mail original ----- De: "nek5000-users" ?: "nek5000-users" Envoy?: Vendredi 16 Mars 2018 10:42:20 Objet: Re: [Nek5000-users] Output files reading by python you start your simulation by loading an fld file, and then you write it out directly as f file. This can be done by changing some of the parameters, see the documentation. On 2018-03-16 10:40, nek5000-users at lists.mcs.anl.gov wrote: > > sorry for silly questions..I am sorry I didn't get you > > load as fld? > where? > > thanks > silo > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Vendredi 16 Mars 2018 10:37:59 > Objet: Re: [Nek5000-users] Output files reading by python > > load as fld, save as f* > > On 2018-03-16 10:36, nek5000-users at lists.mcs.anl.gov wrote: >> I am sorry . I don't have much experience in that. >> Could you please tell me how can I convert? >> >> Thanks >> >> ----- Mail original ----- >> De: "nek5000-users" >> ?: "nek5000-users" >> Envoy?: Vendredi 16 Mars 2018 10:33:00 >> Objet: Re: [Nek5000-users] Output files reading by python >> >> I recommend to convert to f* format. >> >> >> On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Arnold, >>> >>> I was trying to read .fld format. >>> Is there any scripts I can read this? >>> >>> >>> thank you >>> sijo >>> >>> ------------------------------------------------------------------------ >>> *De: *"nek5000-users" >>> *?: *"nek5000-users" >>> *Envoy?: *Vendredi 16 Mars 2018 09:47:46 >>> *Objet: *Re: [Nek5000-users] Output files reading by python >>> >>> Hi Sijo, what format are you trying to read? >>> The files created by Nicolo (using python) are ONLY for *0.f0* files. >>> >>> Best regards, >>> >>> AW >>> >>> Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit?: >>> >>> Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? >>> >>> Thank you >>> >>> ----- Mail original ----- >>> De: "nek5000-users" >>> ?: "nek5000-users" >>> Envoy?: Jeudi 15 Mars 2018 23:43:46 >>> Objet: Re: [Nek5000-users] Output files reading by python >>> >>> Hi, >>> you can check the python library by Jacopo and Nicolo: >>> >>> https://github.com/jcanton/pymech >>> >>> There are also matlab routines around. Perhpas Adam can send you a link >>> to these. >>> >>> Philipp >>> >>> On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: >>> >>> HI Neks, >>> >>> I was trying to read the output files of NEK5000 using some python files >>> which are available in internet. But when I tried an old which is >>> attached in this email, it throws some error. But the same code was >>> working for other files. The attached file looks also bit different from >>> other files. I assume that the standard of construction for this file is >>> quite different from others. Could you please help me, to find a way to >>> read the NEK5000 output files by using python scripts? Or anyway to make >>> the standard output files? >>> >>> Thanks >>> >>> Sijo >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> -- >>> *Arnold Wakim* >>> Ph.D. Student >>> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >>> INST >>> T?l: +33 1 46 23 51 83 >>> >>> >>> ONERA?-?The French Aerospace Lab?-?Centre de Meudon >>> 8, rue des Vertugadins - 92190 MEUDON >>> >>> Nous suivre sur : www.onera.fr ?| Twitter >>> ?| LinkedIn >>> ?| Facebook >>> >>> >>> >>> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 16 05:07:00 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 11:07:00 +0100 Subject: [Nek5000-users] Output files reading by python In-Reply-To: References: Message-ID: Hi Sijo, So you can use, rea file : param(66)=66 param(67)=4 usr file: load_fld(filename) call outpost(... Arnold Le 16/03/2018 ? 10:46, nek5000-users at lists.mcs.anl.gov a ?crit : > Thank you very much.. > I will give a try. > > Regards > > Sijo > > ----- Mail original ----- > De: "nek5000-users" > ?: "nek5000-users" > Envoy?: Vendredi 16 Mars 2018 10:42:20 > Objet: Re: [Nek5000-users] Output files reading by python > > you start your simulation by loading an fld file, and then you write it > out directly as f file. This can be done by changing some of the > parameters, see the documentation. > > > On 2018-03-16 10:40, nek5000-users at lists.mcs.anl.gov wrote: >> sorry for silly questions..I am sorry I didn't get you >> >> load as fld? >> where? >> >> thanks >> silo >> >> ----- Mail original ----- >> De: "nek5000-users" >> ?: "nek5000-users" >> Envoy?: Vendredi 16 Mars 2018 10:37:59 >> Objet: Re: [Nek5000-users] Output files reading by python >> >> load as fld, save as f* >> >> On 2018-03-16 10:36, nek5000-users at lists.mcs.anl.gov wrote: >>> I am sorry . I don't have much experience in that. >>> Could you please tell me how can I convert? >>> >>> Thanks >>> >>> ----- Mail original ----- >>> De: "nek5000-users" >>> ?: "nek5000-users" >>> Envoy?: Vendredi 16 Mars 2018 10:33:00 >>> Objet: Re: [Nek5000-users] Output files reading by python >>> >>> I recommend to convert to f* format. >>> >>> >>> On 2018-03-16 10:29, nek5000-users at lists.mcs.anl.gov wrote: >>>> Hi Arnold, >>>> >>>> I was trying to read .fld format. >>>> Is there any scripts I can read this? >>>> >>>> >>>> thank you >>>> sijo >>>> >>>> ------------------------------------------------------------------------ >>>> *De: *"nek5000-users" >>>> *?: *"nek5000-users" >>>> *Envoy?: *Vendredi 16 Mars 2018 09:47:46 >>>> *Objet: *Re: [Nek5000-users] Output files reading by python >>>> >>>> Hi Sijo, what format are you trying to read? >>>> The files created by Nicolo (using python) are ONLY for *0.f0* files. >>>> >>>> Best regards, >>>> >>>> AW >>>> >>>> Le 15/03/2018 ? 23:50, nek5000-users at lists.mcs.anl.gov a ?crit : >>>> >>>> Yes in fact I was using these codes. It was working for me with some cases and not with the file which I had attached. The header itself looks bit different. Could you please have look into that ? >>>> >>>> Thank you >>>> >>>> ----- Mail original ----- >>>> De: "nek5000-users" >>>> ?: "nek5000-users" >>>> Envoy?: Jeudi 15 Mars 2018 23:43:46 >>>> Objet: Re: [Nek5000-users] Output files reading by python >>>> >>>> Hi, >>>> you can check the python library by Jacopo and Nicolo: >>>> >>>> https://github.com/jcanton/pymech >>>> >>>> There are also matlab routines around. Perhpas Adam can send you a link >>>> to these. >>>> >>>> Philipp >>>> >>>> On 2018-03-15 23:42,nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> HI Neks, >>>> >>>> I was trying to read the output files of NEK5000 using some python files >>>> which are available in internet. But when I tried an old which is >>>> attached in this email, it throws some error. But the same code was >>>> working for other files. The attached file looks also bit different from >>>> other files. I assume that the standard of construction for this file is >>>> quite different from others. Could you please help me, to find a way to >>>> read the NEK5000 output files by using python scripts? Or anyway to make >>>> the standard output files? >>>> >>>> Thanks >>>> >>>> Sijo >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> >>>> -- >>>> *Arnold Wakim* >>>> Ph.D. Student >>>> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >>>> INST >>>> T?l: +33 1 46 23 51 83 >>>> >>>> >>>> ONERA - The French Aerospace Lab - Centre de Meudon >>>> 8, rue des Vertugadins - 92190 MEUDON >>>> >>>> Nous suivre sur : www.onera.fr | Twitter >>>> | LinkedIn >>>> | Facebook >>>> >>>> >>>> >>>> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dcjjkiamjbdeegpo.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 15 13:48:41 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Mar 2018 19:48:41 +0100 (CET) Subject: [Nek5000-users] Filtering in the turbChannel, it that possible to use another filter, such as top-hat filter or Gaussian filter Message-ID: Hi Thanks for your reply, which shed a lot light on my problem. I will have a careful study of what you said later. Thanks again. Bien cordialement Zhenrong JING Doctorant (Doctor Candidate) LHEEA Ecole Centrale de Nantes 1 Rue de la No?, 44321 Nantes, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 16 03:22:07 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 16 Mar 2018 09:22:07 +0100 (CET) Subject: [Nek5000-users] Small random perturbations Message-ID: Hello everyone I have been troubled by the exactly same problem with Ali for the last two months with the turbulent channel case. When I increase elements, the flow is laminarized even though the Re is quite big (10000). I tried many different ways. Even added a constant random forcing, but the disturbance just disappear. (because the disturbance shape is not the same as that in linear stability theory, it is possible that the disturbance just decay. ) How I finally solve this problem is running a coarse mesh calculation first, and then interpolating the result to fine mesh. Then I got a sustaining turbulence and the result is quite satisfying. I hope this could solve Ali's problem. However, I still cannot understand why increasing resolution would laminarize flow. hoping someone else could explain the problem. Regards Bien cordialement Zhenrong JING Doctorant (Doctor Candidate) LHEEA Ecole Centrale de Nantes 1 Rue de la No?, 44321 Nantes, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 17 11:07:16 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 17 Mar 2018 16:07:16 +0000 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Dear Zhenrong, Please send me your case files off-list, along with an explanation of how you start the case that re-laminarizes. I'll try to sort this out. Thanks! Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, March 16, 2018 3:22:07 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Small random perturbations Hello everyone I have been troubled by the exactly same problem with Ali for the last two months with the turbulent channel case. When I increase elements, the flow is laminarized even though the Re is quite big (10000). I tried many different ways. Even added a constant random forcing, but the disturbance just disappear. (because the disturbance shape is not the same as that in linear stability theory, it is possible that the disturbance just decay. ) How I finally solve this problem is running a coarse mesh calculation first, and then interpolating the result to fine mesh. Then I got a sustaining turbulence and the result is quite satisfying. I hope this could solve Ali's problem. However, I still cannot understand why increasing resolution would laminarize flow. hoping someone else could explain the problem. Regards Bien cordialement Zhenrong JING Doctorant (Doctor Candidate) LHEEA Ecole Centrale de Nantes 1 Rue de la No?, 44321 Nantes, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 17 11:42:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 17 Mar 2018 17:42:49 +0100 Subject: [Nek5000-users] Small random perturbations In-Reply-To: References: Message-ID: Hi, to circumvent the problem of specifying initial conditions (which should even be divergence free) we have made good experience with a physics-inspired tripping (i.e. a small vertical force which then amplifies due to lift-up). This has really solved our problems with getting a flow turbulent. The fact that a flow relaminarises when going from low to high resolution I have seen before, in particular for marginally turbulent cases. The recommendation is to increase the resolution in small steps, and making sure that you let the flow adapt at the intermediate resolutions. Best regards, Philipp On 2018-03-16 09:22, nek5000-users at lists.mcs.anl.gov wrote: > Hello everyone > > I have been troubled by the exactly same problem with Ali for the last > two months with the turbulent channel case. When I increase elements, > the flow is laminarized even though the Re is quite big (10000). I tried > many different ways. Even added a constant random forcing, but the > disturbance just disappear. (because the disturbance shape is not the > same as that in linear stability theory, it is possible that the > disturbance just decay. ) > > How I finally solve this problem is running a coarse mesh calculation > first, and then interpolating the result to fine mesh. Then I got a > sustaining turbulence and the result is quite satisfying. I hope this > could solve Ali's problem. > > However, I still cannot understand why increasing resolution would > laminarize flow. hoping someone else could explain the problem. > > Regards > > Bien cordialement > > Zhenrong JING > > Doctorant (Doctor Candidate) > > LHEEA > > Ecole Centrale de Nantes > > 1 Rue de la No?, 44321 Nantes, France > > > _______________________________________________ > 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 Mar 21 11:45:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 21 Mar 2018 16:45:35 +0000 Subject: [Nek5000-users] Significant computational time increase from 2D to 3D runs Message-ID: Hello, I am running a DNS cross-flow, two density fluid, turbulent duct simulation and I see a significant increase in computation time going from 2D to 3D that cannot be attributed to a simple increase in grid points. I believe I am at the small end of simulation size for Nek5000, as I am only running on average 4-500k grid points and running on 1-32 cores. Keeping all other things the same (i.e., parameters, physical set-up, etc), I?ve run a 2D simulation of 100x4 elements and a 3D simulation with 100x4x4 elements, both with 9 grid points per element and on 4 cores, and found a increase in computational time of more than 100 fold. I?ve also run 2D simulations of 200x16 elements on 4 cores (again everything else the same) and found it still ran ~100 times faster than the 3D simulations that had half the amount of grid points. This doesn?t make sense to me and implies that this issue would not be simply resolved by following the ?Performance and Memory Considerations? advice in the Nek5000 Docs as it is not just about an increase in grid points. It seems to be linked to going from 2D to 3D, rather than due to an increase in grid points. I feel that I am missing something fundamental here. Is there something one should do when switching from 2D to 3D in Nek5000 that I am not aware of? I have searched through old email threads but could not find anything that mentions something like this. Thanks! - Kat From nek5000-users at lists.mcs.anl.gov Wed Mar 21 16:47:12 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 21 Mar 2018 22:47:12 +0100 Subject: [Nek5000-users] Significant computational time increase from 2D to 3D runs In-Reply-To: References: Message-ID: Just calculating grid points, the difference between the mentioned 2D and 3D case is 36 (9*4, i.e. the 36 spanwise planes). So I guess to a large extent you see just the increase in grid points. or? Philipp On 2018-03-21 17:45, nek5000-users at lists.mcs.anl.gov wrote: > Hello, > > I am running a DNS cross-flow, two density fluid, turbulent duct simulation and I see a significant increase in computation time going from 2D to 3D that cannot be attributed to a simple increase in grid points. I believe I am at the small end of simulation size for Nek5000, as I am only running on average 4-500k grid points and running on 1-32 cores. Keeping all other things the same (i.e., parameters, physical set-up, etc), I?ve run a 2D simulation of 100x4 elements and a 3D simulation with 100x4x4 elements, both with 9 grid points per element and on 4 cores, and found a increase in computational time of more than 100 fold. I?ve also run 2D simulations of 200x16 elements on 4 cores (again everything else the same) and found it still ran ~100 times faster than the 3D simulations that had half the amount of grid points. This doesn?t make sense to me and implies that this issue would not be simply resolved by following the ?Performance and Memory Considerations? advice in the Nek5000 Docs as it is not just about an increase in grid points. It seems to be linked to going from 2D to 3D, rather than due to an increase in grid points. > > I feel that I am missing something fundamental here. Is there something one should do when switching from 2D to 3D in Nek5000 that I am not aware of? I have searched through old email threads but could not find anything that mentions something like this. > > Thanks! > - Kat > _______________________________________________ > 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 Mar 21 16:52:29 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 21 Mar 2018 21:52:29 +0000 Subject: [Nek5000-users] Significant computational time increase from 2D to 3D runs In-Reply-To: References: Message-ID: Dear Kat, When you say 9-points per element, are you running with lx1=3? Let me state that this is really suboptimal for Nek, which was designed for lx1 = 8-20, with lx1=5 about as low as I would go for any reasonable calculation. That being said, your analysis is somewhat correct, but there are a few other things to be concerned with in going from 2D to 3D. You start with 2D on a 4x100 mesh, 9 points per element. Going to 3D, you have 4x4x100, 3x9 points per element, so an increase of 12x. In addition, many of the operations go from 2x2 to 3x3, which is a ratio of 2.25. (e.g., the Laplacian now involves more work as you have derivatives with respect to r,s, and t in the local coordinates and their transposes, etc.). In addition to each operation being more expensive per gridpiont, you now have 3 velocity components instead of 2, so there is another multiplier there. Moreover, there are more surface points, 6 x 3^2, instead of 4 x 3, so 54 instead of 12, for each element. My suggestion would be to first rethink your 2D and 3D problems in terms of 8x8 = 64 or 8x8x8=512 points per element, at the target resolution. Then, start the calculation with lx1=5 or 6 to converge to a reasonable solution and restart with at the target value. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, March 21, 2018 11:45:35 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Significant computational time increase from 2D to 3D runs Hello, I am running a DNS cross-flow, two density fluid, turbulent duct simulation and I see a significant increase in computation time going from 2D to 3D that cannot be attributed to a simple increase in grid points. I believe I am at the small end of simulation size for Nek5000, as I am only running on average 4-500k grid points and running on 1-32 cores. Keeping all other things the same (i.e., parameters, physical set-up, etc), I?ve run a 2D simulation of 100x4 elements and a 3D simulation with 100x4x4 elements, both with 9 grid points per element and on 4 cores, and found a increase in computational time of more than 100 fold. I?ve also run 2D simulations of 200x16 elements on 4 cores (again everything else the same) and found it still ran ~100 times faster than the 3D simulations that had half the amount of grid points. This doesn?t make sense to me and implies that this issue would not be simply resolved by following the ?Performance and Memory Considerations? advice in the Nek5000 Docs as it is not just about an increase in grid points. It seems to be linked to going from 2D to 3D, rather than due to an increase in grid points. I feel that I am missing something fundamental here. Is there something one should do when switching from 2D to 3D in Nek5000 that I am not aware of? I have searched through old email threads but could not find anything that mentions something like this. Thanks! - Kat _______________________________________________ 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 Mar 21 16:54:05 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 21 Mar 2018 22:54:05 +0100 Subject: [Nek5000-users] Significant computational time increase from 2D to 3D runs In-Reply-To: References: Message-ID: ok, I assumed lx1=9... sorry about that. Philipp On 2018-03-21 22:52, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Kat, > > > When you say 9-points per element, are you running with lx1=3? > > > Let me state that this is really suboptimal for Nek, which was designed > for lx1 = 8-20, with lx1=5 about as low as I would go for any reasonable > calculation. > > > That being said, your analysis is somewhat correct, but there are a few > other things to be concerned with in going from 2D to 3D. > > > You start with 2D on a 4x100 mesh, 9 points per element. > > > Going to 3D, you have 4x4x100, 3x9 points per element, so an increase of > 12x. > > > In addition, many of the operations go from 2x2 to 3x3, which is a ratio > of 2.25. ?(e.g., the Laplacian now involves more work as you have > derivatives with respect to r,s, and t in the local coordinates and > their transposes, etc.). ?In addition to each operation being more > expensive per gridpiont, you now have 3 velocity components instead of > 2, so there is another multiplier there. ? Moreover, there are more > surface points, 6 x 3^2, instead of 4 x 3, so 54 instead of 12, for each > element. > > > My suggestion would be to first rethink your 2D and 3D problems in terms > of 8x8 = 64 or 8x8x8=512 points per element, ?at the target resolution. > ? Then, start the calculation with lx1=5 or 6 to converge to a > reasonable solution and restart with at the target value. > > > hth, > > > Paul > > > ------------------------------------------------------------------------ > *From:* Nek5000-users on > behalf of nek5000-users at lists.mcs.anl.gov > *Sent:* Wednesday, March 21, 2018 11:45:35 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Significant computational time increase from > 2D to 3D runs > Hello, > > I am running a DNS cross-flow, two density fluid, turbulent duct > simulation and I see a significant increase in computation time going > from 2D to 3D that cannot be attributed to a simple increase in grid > points. I believe I am at the small end of simulation size for Nek5000, > as I am only running on average 4-500k grid points and running on 1-32 > cores. Keeping all other things the same (i.e., parameters, physical > set-up, etc), I?ve run a 2D simulation of 100x4 elements and a 3D > simulation with 100x4x4 elements, both with 9 grid points per element > and on 4 cores, and found a increase in computational time of more than > 100 fold. I?ve also run 2D simulations of 200x16 elements on 4 cores > (again everything else the same) and found it still ran ~100 times > faster than the 3D simulations that had half the amount of grid points. > This doesn?t make sense to me and implies that this issue would not be > simply resolved by following the ?Performance and Memory Considerations? > advice in the Nek5000 Docs as it is not just about an increase in grid > points. It seems to be linked to going from 2D to 3D, rather than due to > an increase in grid points. > > I feel that I am missing something fundamental here. Is there something > one should do when switching from 2D to 3D in Nek5000 that I am not > aware of? I have searched through old email threads but could not find > anything that mentions something like this. > > Thanks! > - Kat > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 23 08:40:03 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 23 Mar 2018 14:40:03 +0100 (CET) Subject: [Nek5000-users] runtime statistics, cannot find time used by userchk Message-ID: Hello everyone I saw there is a summary about the time used by different subroutines when the calculation is finished. I can see the runtime of uservp, userbc , However, I cannot find the time used by userchk. I added a interpolation operation in the userchk, which takes a lots of time. I want to see how much time is increased by userchk . Is it included in somewhere else? It is quite strange for me if one could have uservp, userbc's statistics but not userchk. Thanks in advance. total time 447.89117082532829 mxmf time 0 0.0000000000000000 0.0000000000000000 tgop time 2643 9.9580898643471301 2.2233280120251924E-002 inv3 time 230 0.98762099850864615 2.2050468123512206E-003 invc time 120 0.38182595738908276 8.5249717400209682E-004 mltd time 690 8.8917919600353343 1.9852572542679161E-002 cdtp time 750 12.148632817334146 2.7124073008512047E-002 eslv time 20 44.806365604032180 0.10003851051912357 pres time 20 54.221211027994286 0.12105889680316974 crsl time 179 0.38399919478979427 8.5734932903946200E-004 crsl min 0.38399919478979427 crsl max 0.41605458219419234 crsl avg 3.1121358200866859E-003 hmhz time 0 0.0000000000000000 0.0000000000000000 proj time 0 0.0000000000000000 0.0000000000000000 usvp time 21 1.6338681453635218 3.6479132695399997E-003 usfq time 0 0.0000000000000000 0.0000000000000000 usbc time 21 1.6406853507214691 3.6631339432259429E-003 usbc min 1.6165314224344911 usbc max 1.6937481226777891 usb avg 1.2943636483095721E-002 axhm time 0 0.0000000000000000 0.0000000000000000 advc time 60 6.0429743653076002 1.3492059587091708E-002 vdss time 625 20.775962491126847 4.6386184511838034E-002 vdss min 19.829680008784635 vdss max 21.383793186410912 vdss avg 0.16122654504807607 dsum time 720 8.1395189651229884 1.8172983740948299E-002 dsum min 7.5462320667429594 dsum max 8.3177108413365204 dsum avg 6.1515564823741695E-002 dadd time 0 1.9019991281093098 4.2465653533747929E-003 ddsl time 179 12.773915659927297 2.8520132773300320E-002 solv time 179 2.7990334107162198 6.2493605434517626E-003 prep time 20 0.22789684135932475 5.0882191077662828E-004 Bien cordialement Zhenrong JING Doctorant (Doctor Candidate) LHEEA Ecole Centrale de Nantes 1 Rue de la No?, 44321 Nantes, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 23 13:25:00 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 23 Mar 2018 18:25:00 +0000 Subject: [Nek5000-users] Further to ffx, ffy and ffz Message-ID: Hi Paul, Thanks for your reply regarding on the questions of ''Further to the issue of ffx, ffy and ffz''. May I ask you if I keep p54=-3, p55=1, will the fluid be changed if ffx not eqauls to 0 (supposed x is streamwise direction) in the same time? And dear Philipp, May I know what you ususally set for the pipe flow if p54 and p55 are not used, fixing flow rate or fixing pressure gradient? and how you do you set if the flow considering the interaction between fluid and particles for the two-phase flow? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 23 14:41:59 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 23 Mar 2018 20:41:59 +0100 Subject: [Nek5000-users] Further to ffx, ffy and ffz In-Reply-To: References: Message-ID: On 2018-03-23 19:25, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, > > Thanks for your reply regarding on the questions of? ''Further to the > issue of ffx, ffy and ffz''. May I ask you if I keep p54=-3, p55=1, will > the fluid be changed if ffx not eqauls to 0 (supposed x is streamwise > direction) in the same time? > > And dear Philipp, > > May I know what you ususally set for the pipe flow if p54 and p55 are > not used, fixing flow rate or fixing pressure gradient? and how you do > you set if the flow considering the interaction between fluid and > particles for the two-phase flow? Hi, we typically set fixed mass flux, using p54 and p55; sometimes with some variants of it when the geometry requires it. Fixed pressure gradient is typically quite slow in adapting to a given value for the friction (Reynolds number). For two-phase flow we usually do not change anything. Philipp > > Kind regards, > > Zhai > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 24 01:33:01 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 24 Mar 2018 14:33:01 +0800 Subject: [Nek5000-users] How to use Nek5000 to solve equations similar to NS Message-ID: Dear Neks, I would like to numerically solve some 2D equations which come from 3D Navier-Stokes equations after our modeling. The new 2D equations are very similar to 2D Navier-Stokes equations but there are some extra numerical coefficients in advection term and pressure term, and there is an extra source term in momentum equations. Is it possible to use Nek5000 to solve this kind of equations? Thank you very much! Best regards, Wei XU -------- Wei XU Ph.D. Candidate Nano Science and Technology Program The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 24 11:11:18 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 24 Mar 2018 16:11:18 +0000 Subject: [Nek5000-users] Further to ffx, ffy and ffz In-Reply-To: References: Message-ID: Dear Zhai, p54 = -3 ( implies fixed flow rate in z, with Wbar=p55 ) p55 = 1 ( implies Wbar = 1 ) would be appropriate for a fixed flow rate in the z-direction. If you have ffx nonzero, then one of two things can happen. If you also have periodicity in x, then you will have flow in the x direction. Otherwise, you will simply have a pressure gradient in x. If, on the other hand, you have ffz nonzero, then the flow will be unchanged, but the apparent z pressure drop will be different. Paul PS - Normally, I would run with p54 = -1 p55 = 1 ffx = 0 which would be fixed axial flow rate (assuming "x" is the axial direction), with Ubar = 1. Then, "grep volf logfile" would reveal the pressure drop as a function of time. ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, March 23, 2018 1:25:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Further to ffx, ffy and ffz Hi Paul, Thanks for your reply regarding on the questions of ''Further to the issue of ffx, ffy and ffz''. May I ask you if I keep p54=-3, p55=1, will the fluid be changed if ffx not eqauls to 0 (supposed x is streamwise direction) in the same time? And dear Philipp, May I know what you ususally set for the pipe flow if p54 and p55 are not used, fixing flow rate or fixing pressure gradient? and how you do you set if the flow considering the interaction between fluid and particles for the two-phase flow? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 24 18:49:40 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 24 Mar 2018 19:49:40 -0400 Subject: [Nek5000-users] 'comp_vort3' in 2D Message-ID: Hello neks, I am using 'comp_vort3' for a 2D flow, with a forcing in x direction, call comp_vort3 (vort, w1, w2, vx, vy, vz) call outpost (vort(1,1), vort(1,2), vort(1,3), pr, t, 'vrt') In this case, the x and y component of vorticity should be trivial, and only z component should remain. However I am getting a non-zero component of x-component, vort(1,1) while vort(1,2) and vort(1,3) are zero. However if I add a z-direction, comp_vort3 returns a non-zero value of vort(1,3) and the x and y-components are zero, which should be the case. So my question is, in 2D, does comp_vort3 return only one value which is in vort(1,1)? The vorticity fields in both cases look sort of similar. 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 Sun Mar 25 03:40:14 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 25 Mar 2018 10:40:14 +0200 Subject: [Nek5000-users] 'comp_vort3' in 2D In-Reply-To: References: Message-ID: Hi, if you look into the code you see that for 2D cases the result it stored in vort(:,1), even though it is of course the z-vorticity. 00791 if (if3d) then 00792 c work1=dw/dy ; work2=dv/dz 00793 call dudxyz(work1,w,rym1,sym1,tym1,jacm1,1,2) 00794 call dudxyz(work2,v,rzm1,szm1,tzm1,jacm1,1,3) 00795 call sub3(vort(1,1),work1,work2,ntot) 00796 c work1=du/dz ; work2=dw/dx 00797 call dudxyz(work1,u,rzm1,szm1,tzm1,jacm1,1,3) 00798 call dudxyz(work2,w,rxm1,sxm1,txm1,jacm1,1,1) 00799 call sub3(vort(1,2),work1,work2,ntot) 00800 c work1=dv/dx ; work2=du/dy 00801 call dudxyz(work1,v,rxm1,sxm1,txm1,jacm1,1,1) 00802 call dudxyz(work2,u,rym1,sym1,tym1,jacm1,1,2) 00803 call sub3(vort(1,3),work1,work2,ntot) 00804 else 00805 c work1=dv/dx ; work2=du/dy 00806 call dudxyz(work1,v,rxm1,sxm1,txm1,jacm1,1,1) 00807 call dudxyz(work2,u,rym1,sym1,tym1,jacm1,1,2) 00808 call sub3(vort,work1,work2,ntot) 00809 endif Philipp On 2018-03-25 00:49, nek5000-users at lists.mcs.anl.gov wrote: > Hello neks, > > I am using 'comp_vort3' for a 2D flow, with a forcing in x direction, > > call comp_vort3 (vort, w1, w2, vx, vy, vz) > > call outpost (vort(1,1), vort(1,2), vort(1,3), pr, t, 'vrt') > > > In this case, the x and y component of vorticity should be trivial, and > only z component should remain. However I am getting a non-zero > component of x-component, vort(1,1) while vort(1,2) and vort(1,3) are zero. > > However if I add a z-direction, comp_vort3 returns a non-zero value of > vort(1,3) and the x and y-components are zero, which should be the case. > > So my question is, in 2D, does comp_vort3 return only one value which is > in vort(1,1)? The vorticity fields in both cases look sort of similar. > > Thanks, > Saikat > > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Mar 25 08:47:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 25 Mar 2018 09:47:39 -0400 Subject: [Nek5000-users] 'comp_vort3' in 2D In-Reply-To: References: Message-ID: Thanks for the clarification. Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Sun, Mar 25, 2018 at 4:40 AM, wrote: > Hi, > if you look into the code you see that for 2D cases the result it stored > in vort(:,1), even though it is of course the z-vorticity. > > 00791 if (if3d) then > 00792 c work1=dw/dy ; work2=dv/dz > 00793 call dudxyz(work1,w,rym1,sym1,tym1,jacm1,1,2) > 00794 call dudxyz(work2,v,rzm1,szm1,tzm1,jacm1,1,3) > 00795 call sub3(vort(1,1),work1,work2,ntot) > 00796 c work1=du/dz ; work2=dw/dx > 00797 call dudxyz(work1,u,rzm1,szm1,tzm1,jacm1,1,3) > 00798 call dudxyz(work2,w,rxm1,sxm1,txm1,jacm1,1,1) > 00799 call sub3(vort(1,2),work1,work2,ntot) > 00800 c work1=dv/dx ; work2=du/dy > 00801 call dudxyz(work1,v,rxm1,sxm1,txm1,jacm1,1,1) > 00802 call dudxyz(work2,u,rym1,sym1,tym1,jacm1,1,2) > 00803 call sub3(vort(1,3),work1,work2,ntot) > 00804 else > 00805 c work1=dv/dx ; work2=du/dy > 00806 call dudxyz(work1,v,rxm1,sxm1,txm1,jacm1,1,1) > 00807 call dudxyz(work2,u,rym1,sym1,tym1,jacm1,1,2) > 00808 call sub3(vort,work1,work2,ntot) > 00809 endif > > Philipp > > > > On 2018-03-25 00:49, nek5000-users at lists.mcs.anl.gov wrote: > >> Hello neks, >> >> I am using 'comp_vort3' for a 2D flow, with a forcing in x direction, >> >> call comp_vort3 (vort, w1, w2, vx, vy, vz) >> >> call outpost (vort(1,1), vort(1,2), vort(1,3), pr, t, 'vrt') >> >> >> In this case, the x and y component of vorticity should be trivial, and >> only z component should remain. However I am getting a non-zero component >> of x-component, vort(1,1) while vort(1,2) and vort(1,3) are zero. >> >> However if I add a z-direction, comp_vort3 returns a non-zero value of >> vort(1,3) and the x and y-components are zero, which should be the case. >> >> So my question is, in 2D, does comp_vort3 return only one value which is >> in vort(1,1)? The vorticity fields in both cases look sort of similar. >> >> Thanks, >> Saikat >> >> >> Saikat Mukherjee, >> PhD Student, >> Paul Research Group - http://www.me.vt.edu/mpaul/ >> Engineering Science and Mechanics, >> Virginia Tech. >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 26 10:39:52 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 26 Mar 2018 16:39:52 +0100 Subject: [Nek5000-users] Further to ffx, ffy and ffz Message-ID: Dear Paul and Phillip, Thanks for your reply. Paul, I am sorry say that I made an mistake for my question last time. I intended to ask if I set P54=-1 P55=1 ffx: non-zero (x is streamwise) Will the fluid be changed by the effect of non-zero ffx which I am thinking can be considered as the effect of the particles acting on the fluid while I am doing the lagrangian paticle tracking. By the way, can I fix the pressure gradient as (Re_t/Re_b)^2 for the pipe as well? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 26 12:16:37 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 26 Mar 2018 17:16:37 +0000 Subject: [Nek5000-users] Further to ffx, ffy and ffz In-Reply-To: References: Message-ID: Dear Zhai, ffx will have no impact on the flow if you set p54=-1, p55=1. The code fixes the flow rate by adding an auxiliary solution, (U0,p0) such that = Ubar, where a is a constant determined by the equation the requirement that =Ubar. The velocity pressure pair (U0,p0) is the solution to the linear unsteady Stokes problem: (1/dt) U0 - 1/Re \nabla^2 U0 = -grad p0 + F0 div U0 = 0 where F0=[1 , 0 , 0 ] is a unit forcing in the x direction. If you add your own ffx, then the net forcing will be: ffx + a*1 If you don't, it will be "a*1 = a". Note that if you add your own forcing, then "a" will be smaller because the preliminary solution, U, will be closer to the target Ubar value, assuming your ffx value is reasonably close to the actual mean pressure drop in your system. Note that because these equations are _linear_ it really doesn't matter how you satisfy the condition = Ubar. Also, note that, in the above, I've been using "U" to represent the solution computed by Nek5000 _prior_ to the addition of the auxiliary solution U0. The real solution that is returned at the end of the tilmestep is: U := U + a*U0 p := p + a*p0 (Of course, like U, p and p0 are periodic --- so, the "true" pressure is p + a linear term corresponding to the mean pressure drop...) The reason I prefer p54/p55 to adjusting ffx via a feedback loop is that the feedback loop introduces its own timescale -- i.e., the response time that you find in any feedback system. Since we already have multiple timescales in a turbulent flow, I prefer to not add an additional one that is not well characterized. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, March 26, 2018 10:39:52 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Further to ffx, ffy and ffz Dear Paul and Phillip, Thanks for your reply. Paul, I am sorry say that I made an mistake for my question last time. I intended to ask if I set P54=-1 P55=1 ffx: non-zero (x is streamwise) Will the fluid be changed by the effect of non-zero ffx which I am thinking can be considered as the effect of the particles acting on the fluid while I am doing the lagrangian paticle tracking. By the way, can I fix the pressure gradient as (Re_t/Re_b)^2 for the pipe as well? Kind regards, Zhai -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 26 12:45:44 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 26 Mar 2018 20:45:44 +0300 Subject: [Nek5000-users] How to Restart ? Message-ID: ** *Im trying to solve some basic cases on Nek5000. I have been struggling with a restart problem for a few days and i couldnt solve it on my own. So i wonder is there a easy way for restart from a .f0000n file ?* * Or should i change the output format. When i try to restart from a .fnn file that i got from first run with that restart option in .rea file, it gives me ctarg error and case stops after a few steps. I dont know if there is some settings that i should do on .usr file. I have readed some things about that but i couldnt make any properly working save code in .usr file. So if you could help me i would really apperciate it. Thanks and gooddays. * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 26 15:45:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 26 Mar 2018 22:45:49 +0200 Subject: [Nek5000-users] Further to ffx, ffy and ffz In-Reply-To: References: Message-ID: Hi, I guess in addition to Paul's answer (correct me if I am wrong): you can still add some forcing in ffx,ffy,ffz while having p54/p55 active. The latter settings just make sure that the mass flux is constant, irrespective of what the spatially invariant part of ffx... is. Indeed, using p54/p55 is certainly much better than a feedback loop for ffx, precisely because there is not time lag as Paul describes. Alternatively, one can set a constant pressure gradient in ffx..., which effectively sets the (averaged) friction to a predetermined value. What you want is dependent on your flow case. Note that for very large cases (large domains) there should be no difference between the two forcing mechanisms. Best regards, Philipp On 2018-03-26 19:16, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Zhai, > > > ffx will have no impact on the flow if you set p54=-1, p55=1. > > > The code fixes the flow rate by adding an auxiliary solution, > > (U0,p0) such that = Ubar, where a is a constant > > determined by the equation the requirement that =Ubar. > > > The velocity pressure pair (U0,p0) is the solution to the linear > > unsteady Stokes problem: > > > ? ? ? (1/dt) U0 - 1/Re \nabla^2 U0 = -grad p0 ?+ F0 > > ? ? ? ? ?div U0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 0 > > > where F0=[1 , 0 , 0 ] is a unit forcing in the x direction. > > > If you add your own ffx, then the net forcing will be: > > > ? ? ?ffx + a*1 > > > If you don't, it will be "a*1 = a". > > > Note that if you add your own forcing, then "a" will be smaller > > because the preliminary solution, U, will be closer to the target > > Ubar value, assuming your ffx value is reasonably close to the > > actual mean pressure drop in your system. > > > Note that because these equations are _linear_ it really doesn't > > matter how you satisfy the condition = Ubar. > > > Also, note that, in the above, I've been using "U" to represent the > > solution computed by Nek5000 ?_prior_ to the addition of the auxiliary > solution U0. > > > The real solution that is returned at the end of the tilmestep is: > > > ? ? U := U + a*U0 > > > ? ? p := ?p + a*p0 > > > (Of course, like U, p and p0 are periodic --- so, the "true" pressure is > p + a linear term corresponding to the mean pressure drop...) > > > The reason I prefer p54/p55 to adjusting ffx via a feedback loop is that > the feedback loop introduces its own timescale -- i.e., the response > time that you find in any feedback system. ? Since we already have > multiple timescales in a turbulent flow, I prefer to not add an > additional one that is not well characterized. > > > hth, > > > Paul > > > ------------------------------------------------------------------------ > *From:* Nek5000-users on > behalf of nek5000-users at lists.mcs.anl.gov > *Sent:* Monday, March 26, 2018 10:39:52 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Further to ffx, ffy and ffz > Dear Paul and Phillip, > > Thanks for your reply. > > Paul, I am sorry say that I made an mistake for my question last time. > > I intended to ask if I set > P54=-1 > P55=1 > ffx: non-zero (x is streamwise) > > Will the fluid be changed by the effect of non-zero ffx which I am > thinking can be considered as the effect of the particles acting on the > fluid while I am doing the lagrangian paticle tracking. > > By the way, can I fix the pressure gradient as (Re_t/Re_b)^2 for the > pipe as well? > > Kind regards, > > Zhai > > > _______________________________________________ > 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 Mar 28 06:29:43 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 28 Mar 2018 13:29:43 +0200 (CEST) Subject: [Nek5000-users] skin friction on air foil Message-ID: Hello Neks, Here I have a problem whie caluclating the skin friction on airfoil. Could you please help me with this? I used a piece of your code to extract the viscous the stress applied on the object by using subroutine drgtrq ( dgtq ,xm0,ym0,zm0, sij ,pm1, visc ,f,e) . Here is what I have done, else ! 2D i = 0 a = 0 do j2=js2,jf2,jskip2 do j1=js1,jf1,jskip1 i = i+1 n1 = unx(i,1,f,e) ! I removed area to avoid getting Force since I need stress n2 = uny(i,1,f,e) ! I removed area to avoid getting Force since I need stress a = a + area(i,1,f,e) v = visc(j1,j2,1,e) s11 = sij(j1,j2,1,1,e) s12 = sij(j1,j2,1,3,e) s21 = sij(j1,j2,1,3,e) s22 = sij(j1,j2,1,2,e) dg(1,1) = pm1(j1,j2,1,e)*n1 ! pressure drag dg(2,1) = pm1(j1,j2,1,e)*n2 dg(3,1) = 0 dg(1,2) = -v*(s11*n1 + s12*n2) ! viscous drag dg(2,2) = -v*(s21*n1 + s22*n2) dg(3,2) = 0. r1 = xm0(j1,j2,1,e) r2 = ym0(j1,j2,1,e) r3 = 0. do l=1,2 do k=1,3 dgtq(k,l) = dgtq(k,l) + dg(k,l) enddo enddo enddo enddo endif Then I add dgtq(1,2) + dgtq(2,2) to get the total skin friction stress acting on the wall at each faces. Since I know the face number and element number I extract the x cordinates of the corrrespoinding wall elements. Do you think Am i doing right? I have some questions 1 )Since the equation for skin frcition is : tau_w = -mu*du/dy ( at wall) C_f = 2 * nu * du/dy In our code it is written like : dg(1,2) = -v*(s11*n1 + s12*n2) That is , stress is again muliplied with a normal velocity, and there are two components of stress in each dg. could you please tell me why? 2) The loopshown below muliplies my answer by 4 at the end. (Its getting added each time, I didnt understand the concept behind it, I thought its just way to store all the values into a single array) Could you please tell me why? do l=1,2 do k=1,3 dgtq(k,l) = dgtq(k,l) + dg(k,l) enddo enddo Thanks in advance Sijo GEORGE -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 28 23:56:05 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 11:56:05 +0700 Subject: [Nek5000-users] genmap for 130k elements Message-ID: Hi all, Now I am trying to build the mesh with more than 130k elements, so I find out that genmap can not process properly the mesh. I catch the errors like: ' not connected 1 4 5 0 '. But when I reduce the number of elements to ~ 129k it works great. Is it a bug or I must use some flag ? Regards, Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 29 06:25:57 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 11:25:57 +0000 Subject: [Nek5000-users] genmap for 130k elements In-Reply-To: References: Message-ID: Dear Vatslav, Genmap uses recursive spectral bisection to partition the mesh into successively smaller subsets. In principle, each cut should have minimally-sized separators so that communication is small. In addition, the load should be balanced, meaning that the number of elements in each of the two newly-generated subsets should differ by at most 1. A consequence of the first of these aims is that each newly-created subdomain should be connected. (In other words, the cut generates at most 2 separated subgraphs.) It's easy to show that there are some small subgraphs where all of these conditions cannot be met. It can also happen on larger subgraphs---which is where it become problematic because the communication overhead can then start to be quite large. So, we have genmap flag cases whenever one of the new subgraphs is not connected. In your case, the small integers indicate that the cut in question is near the bottom of the partition tree--in effect at the leaves--so all is ok. There will be no adverse consequences. hth Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, March 28, 2018 11:56:05 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] genmap for 130k elements Hi all, Now I am trying to build the mesh with more than 130k elements, so I find out that genmap can not process properly the mesh. I catch the errors like: ' not connected 1 4 5 0 '. But when I reduce the number of elements to ~ 129k it works great. Is it a bug or I must use some flag ? Regards, Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 29 09:14:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 16:14:15 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() Message-ID: Hi Neks, I was wondering if there is any maximum number of history points one should put in the case.his file. If someone could help me regarding that topic, I haven't found any information yet. Thank you for your time, Best, Arnold From nek5000-users at lists.mcs.anl.gov Thu Mar 29 09:30:54 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 16:30:54 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: Hi Arnold, You can set it in the SIZE file: param(lhis=100) ! # of pts a proc reads from hpts.in ??????????????????????????? ! Note: lhis*np > npoints in hpts.in best, Pierre On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I was wondering if there is any maximum number of history points one > should put in the case.his file. If someone could help me regarding > that topic, I haven't found any information yet. > > Thank you for your time, > > Best, > > Arnold > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Mar 29 10:06:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 17:06:49 +0200 Subject: [Nek5000-users] genmap for 130k elements Message-ID: I don't think this is related to the number of elements. You can adjust the maximum number of elements in maketools (see MAXNEL variable). Looks like the connectivity is somehow messed up. How do you generate this mesh? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 29th March 2018 6:56 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] genmap for 130k elements > > Hi all, > > Now I am trying to build the mesh with more than 130k elements, so I find out that genmap can not process properly the mesh. I catch the errors like: > > not connected? 1? 4? 5? 0 . > > But when I reduce the number of elements to ~ 129k it works great. > > Is it a bug or I must use some flag ? > > Regards, > Vatslav > _______________________________________________ > 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 Mar 29 10:17:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 17:17:49 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: Hello Pierre, In my case my case.his file contains 39960 points and lhis=39961, however when I increased the first value and the lhis variable accordingly it doesn't work anymore. Is there something I'm missing? Best, Arnold Le 29/03/2018 ? 16:30, nek5000-users at lists.mcs.anl.gov a ?crit : > Hi Arnold, > > You can set it in the SIZE file: > > param(lhis=100) ! # of pts a proc reads from hpts.in > ! Note: lhis*np > npoints in hpts.in > > best, > Pierre > > > > On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Neks, >> >> I was wondering if there is any maximum number of history points one >> should put in the case.his file. If someone could help me regarding >> that topic, I haven't found any information yet. >> >> Thank you for your time, >> >> Best, >> >> Arnold >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: khjkinhdgjfmgfdg.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 29 10:27:08 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 17:27:08 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: What do you mean with doesn't work anymore. How does it manifest itself? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 29th March 2018 17:23 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > > Hello Pierre, > In my case my case.his file contains 39960 points and lhis=39961, > however when I increased the first value and the lhis variable > accordingly it doesn't work anymore. Is there something I'm > missing? > Best, > > Arnold > > > Le 29/03/2018 ? 16:30, > nek5000-users at lists.mcs.anl.gov a ?crit?: > Hi > Arnold, > > > You can set it in the SIZE file: > > > param(lhis=100) ! # of pts a proc reads from hpts.in > > ??????????????????????????? ! Note: lhis*np > npoints in > hpts.in > > > best, > > Pierre > > > > > On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Neks, > > > I was wondering if there is any maximum number of history points > one should put in the case.his file. If someone could help me > regarding that topic, I haven't found any information yet. > > > Thank you for your time, > > > Best, > > > Arnold > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > 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 Mar 29 10:53:55 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 17:53:55 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: I'm executing 9 times nek5000 to call hpts (using different case.his files containing each 39960 points, using a shell script) because I need When I'm using 359640=9*39660 points This works perfectly fine. However when I'm trying to use a single file in order to execute nek5000 once, it gives the following error following error when the number of points is equal to 359640 : dump history points reading history points found 359640 points APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) I guess I'm encountering some memory problems.. Best regards, Arnold Le 29/03/2018 ? 17:27, nek5000-users at lists.mcs.anl.gov a ?crit : > What do you mean with doesn't work anymore. How does it manifest itself? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 29th March 2018 17:23 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Maximum number of history points using hpts() >> >> Hello Pierre, >> In my case my case.his file contains 39960 points and lhis=39961, >> however when I increased the first value and the lhis variable >> accordingly it doesn't work anymore. Is there something I'm >> missing? >> Best, >> >> Arnold >> >> >> Le 29/03/2018 ? 16:30, >> nek5000-users at lists.mcs.anl.gov a ?crit : >> Hi >> Arnold, >> >> >> You can set it in the SIZE file: >> >> >> param(lhis=100) ! # of pts a proc reads from hpts.in >> >> ! Note: lhis*np > npoints in >> hpts.in >> >> >> best, >> >> Pierre >> >> >> >> >> On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Neks, >> >> >> I was wondering if there is any maximum number of history points >> one should put in the case.his file. If someone could help me >> regarding that topic, I haven't found any information yet. >> >> >> Thank you for your time, >> >> >> Best, >> >> >> Arnold >> >> >> _______________________________________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.gov >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> _______________________________________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.gov >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> -- >> Arnold Wakim >> Ph.D. Student >> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >> INST >> T?l: +33 1 46 23 51 83 >> >> ONERA - The French Aerospace Lab - Centre de Meudon >> 8, rue des Vertugadins - 92190 MEUDON >> >> Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook >> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ >> 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 > -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ogdgbmmbekfebfjb.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 29 10:57:34 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 29 Mar 2018 17:57:34 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: What's your lhis? How many MPI ranks are you using? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 29th March 2018 17:54 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > > I'm executing 9 times nek5000 to call hpts (using different > case.his files containing each 39960 points, using a shell script) > because I need When I'm using 359640=9*39660 points > This works perfectly fine. However when I'm trying to use a > single file in order to execute nek5000 once, it gives the > following error following error when the number of points is equal > to 359640 : > > dump history points > ?reading history points > ?found?????? 359640? points > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > (signal 11) > > I guess I'm encountering some memory problems.. > > Best regards, > > Arnold > > Le 29/03/2018 ? 17:27, > nek5000-users at lists.mcs.anl.gov a ?crit?: > What do you mean with doesn't work anymore. How does it manifest itself? > -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Thursday 29th March 2018 17:23 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > Hello Pierre, > In my case my case.his file contains 39960 points and lhis=39961, > however when I increased the first value and the lhis variable > accordingly it doesn't work anymore. Is there something I'm > missing? > Best, > Arnold > Le 29/03/2018 ? 16:30, > nek5000-users at lists.mcs.anl.gov a ?crit?: > Hi > Arnold, > You can set it in the SIZE file: > param(lhis=100) ! # of pts a proc reads from hpts.in > ??????????????????????????? ! Note: lhis*np > npoints in > hpts.in > best, > Pierre > On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > I was wondering if there is any maximum number of history points > one should put in the case.his file. If someone could help me > regarding that topic, I haven't found any information yet. > Thank you for your time, > Best, > Arnold > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > 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 > > -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 02:48:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 09:48:19 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: Hi so lhis is equal to 359641 and I'm using 7 ranks.. However I can try and increase that value (which I will try immediately). Best, Arnold Le 29/03/2018 ? 17:57, nek5000-users at lists.mcs.anl.gov a ?crit : > What's your lhis? How many MPI ranks are you using? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 29th March 2018 17:54 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Maximum number of history points using hpts() >> >> I'm executing 9 times nek5000 to call hpts (using different >> case.his files containing each 39960 points, using a shell script) >> because I need When I'm using 359640=9*39660 points >> This works perfectly fine. However when I'm trying to use a >> single file in order to execute nek5000 once, it gives the >> following error following error when the number of points is equal >> to 359640 : >> >> dump history points >> reading history points >> found 359640 points >> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault >> (signal 11) >> >> I guess I'm encountering some memory problems.. >> >> Best regards, >> >> Arnold >> >> Le 29/03/2018 ? 17:27, >> nek5000-users at lists.mcs.anl.gov a ?crit : >> What do you mean with doesn't work anymore. How does it manifest itself? >> -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Thursday 29th March 2018 17:23 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] Maximum number of history points using hpts() >> Hello Pierre, >> In my case my case.his file contains 39960 points and lhis=39961, >> however when I increased the first value and the lhis variable >> accordingly it doesn't work anymore. Is there something I'm >> missing? >> Best, >> Arnold >> Le 29/03/2018 ? 16:30, >> nek5000-users at lists.mcs.anl.gov a ?crit : >> Hi >> Arnold, >> You can set it in the SIZE file: >> param(lhis=100) ! # of pts a proc reads from hpts.in >> ! Note: lhis*np > npoints in >> hpts.in >> best, >> Pierre >> On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Neks, >> I was wondering if there is any maximum number of history points >> one should put in the case.his file. If someone could help me >> regarding that topic, I haven't found any information yet. >> Thank you for your time, >> Best, >> Arnold >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> -- >> Arnold Wakim >> Ph.D. Student >> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >> INST >> T?l: +33 1 46 23 51 83 >> ONERA - The French Aerospace Lab - Centre de Meudon >> 8, rue des Vertugadins - 92190 MEUDON >> Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook >> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ >> 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 >> >> -- >> Arnold Wakim >> Ph.D. Student >> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >> INST >> T?l: +33 1 46 23 51 83 >> >> ONERA - The French Aerospace Lab - Centre de Meudon >> 8, rue des Vertugadins - 92190 MEUDON >> >> Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook >> Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ >> 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 > -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: kpihedjcpkkieahd.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 30 03:29:57 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 13:59:57 +0530 Subject: [Nek5000-users] logfile Message-ID: Hi Neks, What are the entries in the logfile that is output from running the code. Please let me know where the entries are determined in the code. Thanks Swarandeep From nek5000-users at lists.mcs.anl.gov Fri Mar 30 03:29:57 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 10:29:57 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() In-Reply-To: References: Message-ID: I have increased the number of MPI ranks and it worked just fine. Thank you, Best regards, Arnold Le 30/03/2018 ? 09:48, nek5000-users at lists.mcs.anl.gov a ?crit : > > Hi so lhis is equal to 359641 and I'm using 7 ranks.. However I can > try and increase that value (which I will try immediately). > > Best, > > Arnold > > > Le 29/03/2018 ? 17:57, nek5000-users at lists.mcs.anl.gov a ?crit : >> What's your lhis? How many MPI ranks are you using? >> >> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Thursday 29th March 2018 17:54 >>> To:nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] Maximum number of history points using hpts() >>> >>> I'm executing 9 times nek5000 to call hpts (using different >>> case.his files containing each 39960 points, using a shell script) >>> because I need When I'm using 359640=9*39660 points >>> This works perfectly fine. However when I'm trying to use a >>> single file in order to execute nek5000 once, it gives the >>> following error following error when the number of points is equal >>> to 359640 : >>> >>> dump history points >>> reading history points >>> found 359640 points >>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault >>> (signal 11) >>> >>> I guess I'm encountering some memory problems.. >>> >>> Best regards, >>> >>> Arnold >>> >>> Le 29/03/2018 ? 17:27, >>> nek5000-users at lists.mcs.anl.gov a ?crit : >>> What do you mean with doesn't work anymore. How does it manifest itself? >>> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Thursday 29th March 2018 17:23 >>> To:nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] Maximum number of history points using hpts() >>> Hello Pierre, >>> In my case my case.his file contains 39960 points and lhis=39961, >>> however when I increased the first value and the lhis variable >>> accordingly it doesn't work anymore. Is there something I'm >>> missing? >>> Best, >>> Arnold >>> Le 29/03/2018 ? 16:30, >>> nek5000-users at lists.mcs.anl.gov a ?crit : >>> Hi >>> Arnold, >>> You can set it in the SIZE file: >>> param(lhis=100) ! # of pts a proc reads from hpts.in >>> ! Note: lhis*np > npoints in >>> hpts.in >>> best, >>> Pierre >>> On 2018-03-29 16:14,nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Neks, >>> I was wondering if there is any maximum number of history points >>> one should put in the case.his file. If someone could help me >>> regarding that topic, I haven't found any information yet. >>> Thank you for your time, >>> Best, >>> Arnold >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> -- >>> Arnold Wakim >>> Ph.D. Student >>> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >>> INST >>> T?l: +33 1 46 23 51 83 >>> ONERA - The French Aerospace Lab - Centre de Meudon >>> 8, rue des Vertugadins - 92190 MEUDON >>> Nous suivre sur :www.onera.fr | Twitter | LinkedIn | Facebook >>> Avertissement/disclaimerhttp://www.onera.fr/onera-en/emails-terms _______________________________________________ >>> 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 >>> >>> -- >>> Arnold Wakim >>> Ph.D. Student >>> D?partement A?rodynamique, A?ro?lasticit?, Acoustique >>> INST >>> T?l: +33 1 46 23 51 83 >>> >>> ONERA - The French Aerospace Lab - Centre de Meudon >>> 8, rue des Vertugadins - 92190 MEUDON >>> >>> Nous suivre sur :www.onera.fr | Twitter | LinkedIn | Facebook >>> Avertissement/disclaimerhttp://www.onera.fr/onera-en/emails-terms _______________________________________________ >>> 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 >> > > -- > *Arnold Wakim* > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > > ONERA - The French Aerospace Lab - Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur : www.onera.fr | Twitter > | LinkedIn > | Facebook > > > > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- *Arnold Wakim* Ph.D. Student D?partement A?rodynamique, A?ro?lasticit?, Acoustique INST T?l: +33 1 46 23 51 83 ONERA - The French Aerospace Lab - Centre de Meudon 8, rue des Vertugadins - 92190 MEUDON Nous suivre sur : www.onera.fr | Twitter | LinkedIn | Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: kpihedjcpkkieahd.gif Type: image/gif Size: 1041 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: jenllgglbcegjbfi.gif Type: image/gif Size: 1041 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 30 04:35:18 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 11:35:18 +0200 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: I am not sure what you are talking about? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 10:30 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] logfile > > Hi Neks, > > What are the entries in the logfile that is output from running > the code. Please let me know where the entries are determined in the > code. > > Thanks > Swarandeep > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 04:40:48 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 11:40:48 +0200 Subject: [Nek5000-users] Maximum number of history points using hpts() Message-ID: A Nek5000 run on NP ranks with (in total) 359640 history points requires lhis >= 359640/NP + 1. I don't see why with lhis = 359641 you need more than 1 MPI ranks. At least from a history point memory perspective. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 10:30 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > > I have increased the number of MPI ranks and it worked just fine. > Thank you, > > Best regards, > > Arnold > > > Le 30/03/2018 ? 09:48, > nek5000-users at lists.mcs.anl.gov a ?crit?: > Hi so lhis is equal to 359641 and I'm using 7 ranks.. However I > can try and increase that value (which I will try immediately). > > Best, > Arnold > > Le 29/03/2018 ? 17:57, nek5000-users at lists.mcs.anl.gov a > ?crit?: > What's your lhis? How many MPI ranks are you using? > -----Original message----- > From:nek5000-users at lists.mcs.anl.gov Sent: Thursday 29th March 2018 17:54 > To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > I'm executing 9 times nek5000 to call hpts (using different > case.his files containing each 39960 points, using a shell script) > because I need When I'm using 359640=9*39660 points > This works perfectly fine. However when I'm trying to use a > single file in order to execute nek5000 once, it gives the > following error following error when the number of points is equal > to 359640 : > dump history points > ?reading history points > ?found?????? 359640? points > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > (signal 11) > I guess I'm encountering some memory problems.. > Best regards, > Arnold > Le 29/03/2018 ? 17:27, > nek5000-users at lists.mcs.anl.gov a ?crit?: > What do you mean with doesn't work anymore. How does it manifest itself? > -----Original message----- > From:nek5000-users at lists.mcs.anl.gov Sent: Thursday 29th March 2018 17:23 > To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Maximum number of history points using hpts() > Hello Pierre, > In my case my case.his file contains 39960 points and lhis=39961, > however when I increased the first value and the lhis variable > accordingly it doesn't work anymore. Is there something I'm > missing? > Best, > Arnold > Le 29/03/2018 ? 16:30, > nek5000-users at lists.mcs.anl.gov a ?crit?: > Hi > Arnold, > You can set it in the SIZE file: > param(lhis=100) ! # of pts a proc reads from hpts.in > ??????????????????????????? ! Note: lhis*np > npoints in > hpts.in > best, > Pierre > On 2018-03-29 16:14, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > I was wondering if there is any maximum number of history points > one should put in the case.his file. If someone could help me > regarding that topic, I haven't found any information yet. > Thank you for your time, > Best, > Arnold > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > 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 -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > 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 > -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? > LinkedIn ?|?Facebook > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- > Arnold Wakim > Ph.D. Student > D?partement A?rodynamique, A?ro?lasticit?, Acoustique > INST > T?l: +33 1 46 23 51 83 > > ONERA?-?The French Aerospace Lab?-?Centre de Meudon > 8, rue des Vertugadins - 92190 MEUDON > > Nous suivre sur :?www.onera.fr ?|?Twitter ?|? LinkedIn ?|?Facebook > Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 04:52:26 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 15:22:26 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: The following is my logfile entry (sample lines). The first line is understandable. What do the values in the third and following lines denote? ------------------------------------------------------ Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 Solving for Hmholtz scalars 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 1520 Scalars done 7.6000E-02 8.3823E-02 Solving for fluid 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 1.0000E-10 7.8799E-01 3.0171E+00 1520 Fluid done 7.6000E-02 3.3650E+00 -------------------------------------------------------- On Fri, Mar 30, 2018 at 3:05 PM, wrote: > I am not sure what you are talking about? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 30th March 2018 10:30 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] logfile >> >> Hi Neks, >> >> What are the entries in the logfile that is output from running >> the code. Please let me know where the entries are determined in the >> code. >> >> Thanks >> Swarandeep >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 05:00:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 12:00:35 +0200 Subject: [Nek5000-users] logfile Message-ID: >Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration >1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 timestep, solve type, iteration counter, final residual, initial residual, solver tolerance ... -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 11:52 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > The following is my logfile entry (sample lines). The first line is > understandable. What do the values in the third and following lines > denote? > > > ------------------------------------------------------ > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > 3.5403E+00 > Solving for Hmholtz scalars > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > 1520 Scalars done 7.6000E-02 8.3823E-02 > Solving for fluid > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > 1.0000E-10 7.8799E-01 3.0171E+00 > 1520 Fluid done 7.6000E-02 3.3650E+00 > -------------------------------------------------------- > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: > > I am not sure what you are talking about? > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Friday 30th March 2018 10:30 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: [Nek5000-users] logfile > >> > >> Hi Neks, > >> > >> What are the entries in the logfile that is output from running > >> the code. Please let me know where the entries are determined in the > >> code. > >> > >> Thanks > >> Swarandeep > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 06:21:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 16:51:39 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Thanks for the information. In my calculation, I am using a variable viscosity formulation. The viscosity depends on the temperature. As the run proceeds the initial residual for the TEMP gradually rises from 1E+03 until at around at the value 6E+07, the logfile shows an error for non-positive diffusivity. I have checked the temperature distribution which has no such value so as to make the diffusivity negative (or zero). Please indicate what I may be doing wrong. Thank you Swarandeep On Fri, Mar 30, 2018 at 3:30 PM, wrote: > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > > ... > > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 30th March 2018 11:52 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] logfile >> >> The following is my logfile entry (sample lines). The first line is >> understandable. What do the values in the third and following lines >> denote? >> >> >> ------------------------------------------------------ >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >> 3.5403E+00 >> Solving for Hmholtz scalars >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >> 1520 Scalars done 7.6000E-02 8.3823E-02 >> Solving for fluid >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >> 1.0000E-10 7.8799E-01 3.0171E+00 >> 1520 Fluid done 7.6000E-02 3.3650E+00 >> -------------------------------------------------------- >> >> On Fri, Mar 30, 2018 at 3:05 PM, wrote: >> > I am not sure what you are talking about? >> > >> > -----Original message----- >> >> From:nek5000-users at lists.mcs.anl.gov >> >> Sent: Friday 30th March 2018 10:30 >> >> To: nek5000-users at lists.mcs.anl.gov >> >> Subject: [Nek5000-users] logfile >> >> >> >> Hi Neks, >> >> >> >> What are the entries in the logfile that is output from running >> >> the code. Please let me know where the entries are determined in the >> >> code. >> >> >> >> Thanks >> >> Swarandeep >> >> _______________________________________________ >> >> Nek5000-users mailing list >> >> Nek5000-users at lists.mcs.anl.gov >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 06:29:29 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 13:29:29 +0200 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Can you please attach your logfile? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 13:21 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks for the information. > > In my calculation, I am using a variable viscosity formulation. The > viscosity depends on the temperature. As the run proceeds the initial > residual for the TEMP gradually rises from 1E+03 until at around at > the value 6E+07, the logfile shows an error for non-positive > diffusivity. I have checked the temperature distribution which has no > such value so as to make the diffusivity negative (or zero). Please > indicate what I may be doing wrong. > > Thank you > Swarandeep > > On Fri, Mar 30, 2018 at 3:30 PM, wrote: > > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > > > > ... > > > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Friday 30th March 2018 11:52 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] logfile > >> > >> The following is my logfile entry (sample lines). The first line is > >> understandable. What do the values in the third and following lines > >> denote? > >> > >> > >> ------------------------------------------------------ > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > >> 3.5403E+00 > >> Solving for Hmholtz scalars > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > >> 1520 Scalars done 7.6000E-02 8.3823E-02 > >> Solving for fluid > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > >> 1.0000E-10 7.8799E-01 3.0171E+00 > >> 1520 Fluid done 7.6000E-02 3.3650E+00 > >> -------------------------------------------------------- > >> > >> On Fri, Mar 30, 2018 at 3:05 PM, wrote: > >> > I am not sure what you are talking about? > >> > > >> > -----Original message----- > >> >> From:nek5000-users at lists.mcs.anl.gov > >> >> Sent: Friday 30th March 2018 10:30 > >> >> To: nek5000-users at lists.mcs.anl.gov > >> >> Subject: [Nek5000-users] logfile > >> >> > >> >> Hi Neks, > >> >> > >> >> What are the entries in the logfile that is output from running > >> >> the code. Please let me know where the entries are determined in the > >> >> code. > >> >> > >> >> Thanks > >> >> Swarandeep > >> >> _______________________________________________ > >> >> Nek5000-users mailing list > >> >> Nek5000-users at lists.mcs.anl.gov > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> >> > >> > _______________________________________________ > >> > Nek5000-users mailing list > >> > Nek5000-users at lists.mcs.anl.gov > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 06:42:12 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 17:12:12 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Please find the link for the logfile? logfile ? On Fri, Mar 30, 2018 at 4:59 PM, wrote: > Can you please attach your logfile? > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 30th March 2018 13:21 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Thanks for the information. > > > > In my calculation, I am using a variable viscosity formulation. The > > viscosity depends on the temperature. As the run proceeds the initial > > residual for the TEMP gradually rises from 1E+03 until at around at > > the value 6E+07, the logfile shows an error for non-positive > > diffusivity. I have checked the temperature distribution which has no > > such value so as to make the diffusivity negative (or zero). Please > > indicate what I may be doing wrong. > > > > Thank you > > Swarandeep > > > > On Fri, Mar 30, 2018 at 3:30 PM, > wrote: > > > > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > 3.5403E+00 > > > timestep, time, dt, Courant Number, elapsed solver time, solver time > of last time iteration > > > > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > timestep, solve type, iteration counter, final residual, initial > residual, solver tolerance > > > > > > ... > > > > > > > > > -----Original message----- > > >> From:nek5000-users at lists.mcs.anl.gov > > > >> Sent: Friday 30th March 2018 11:52 > > >> To: nek5000-users at lists.mcs.anl.gov > > >> Subject: Re: [Nek5000-users] logfile > > >> > > >> The following is my logfile entry (sample lines). The first line is > > >> understandable. What do the values in the third and following lines > > >> denote? > > >> > > >> > > >> ------------------------------------------------------ > > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > >> 3.5403E+00 > > >> Solving for Hmholtz scalars > > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 > 1.0000E-10 > > >> 1520 Scalars done 7.6000E-02 8.3823E-02 > > >> Solving for fluid > > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 > 1.0000E-10 > > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > >> 1.0000E-10 7.8799E-01 3.0171E+00 > > >> 1520 Fluid done 7.6000E-02 3.3650E+00 > > >> -------------------------------------------------------- > > >> > > >> On Fri, Mar 30, 2018 at 3:05 PM, > wrote: > > >> > I am not sure what you are talking about? > > >> > > > >> > -----Original message----- > > >> >> From:nek5000-users at lists.mcs.anl.gov gov> > > >> >> Sent: Friday 30th March 2018 10:30 > > >> >> To: nek5000-users at lists.mcs.anl.gov > > >> >> Subject: [Nek5000-users] logfile > > >> >> > > >> >> Hi Neks, > > >> >> > > >> >> What are the entries in the logfile that is output from > running > > >> >> the code. Please let me know where the entries are determined in > the > > >> >> code. > > >> >> > > >> >> Thanks > > >> >> Swarandeep > > >> >> _______________________________________________ > > >> >> Nek5000-users mailing list > > >> >> Nek5000-users at lists.mcs.anl.gov > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> >> > > >> > _______________________________________________ > > >> > Nek5000-users mailing list > > >> > Nek5000-users at lists.mcs.anl.gov > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> _______________________________________________ > > >> Nek5000-users mailing list > > >> Nek5000-users at lists.mcs.anl.gov > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 30 07:05:29 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 12:05:29 +0000 Subject: [Nek5000-users] logfile In-Reply-To: References: , Message-ID: 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting with a residual of 4.5e7, with target residual 1.e-10. [ This is actually too tight of a tolerance, since you are asking for 17 orders of magnitude reduction in residual and are working only with 16 significant digits. It seems like you might need to change your .rea file in the following way: set p21 and p22 to 0 set p24, tolrel , to 1.e-3 set p25, tolabs, to 1.e-3 The only time you'll need tolrel/abs tighter than this is if you're doing an analytic convergence study where you know the answer to an infinite number of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The residual tolerances are set conservatively based on these input values. 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 1.0000E-10 7.8799E-01 3.0171E+00 You have 17 iterations for the moment equations. You have 120 iterations for pressure. Again, your tolerances are too tight for engineering calculations -- you do not need 1.e-10 for divergence (i.e., for the pressure residual tolerance). hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, March 30, 2018 4:52:26 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] logfile The following is my logfile entry (sample lines). The first line is understandable. What do the values in the third and following lines denote? ------------------------------------------------------ Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 Solving for Hmholtz scalars 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 1520 Scalars done 7.6000E-02 8.3823E-02 Solving for fluid 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 1.0000E-10 7.8799E-01 3.0171E+00 1520 Fluid done 7.6000E-02 3.3650E+00 -------------------------------------------------------- On Fri, Mar 30, 2018 at 3:05 PM, wrote: > I am not sure what you are talking about? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 30th March 2018 10:30 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] logfile >> >> Hi Neks, >> >> What are the entries in the logfile that is output from running >> the code. Please let me know where the entries are determined in the >> code. >> >> Thanks >> Swarandeep >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 30 07:18:51 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 17:48:51 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Thanks, Paul, Could you please tell me the parameters in terms of ###.par file. I am using the latest version. Thank you On Fri, Mar 30, 2018 at 5:35 PM, wrote: > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > with a residual of 4.5e7, with target residual 1.e-10. > > > [ This is actually too tight of a tolerance, since you are asking for 17 > orders of magnitude reduction in residual and are working only with 16 > significant digits. It seems like you might need to change your .rea file in > the following way: > > > set p21 and p22 to 0 > > > set p24, tolrel , to 1.e-3 > > set p25, tolabs, to 1.e-3 > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > analytic convergence study where you know the answer to an infinite number > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > residual tolerances are set conservatively based on these input values. > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > 1.0000E-10 7.8799E-01 3.0171E+00 > > > You have 17 iterations for the moment equations. > > > You have 120 iterations for pressure. Again, your tolerances are too tight > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > for the pressure residual tolerance). > > > hth, > > Paul > > > ________________________________ > From: Nek5000-users on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Friday, March 30, 2018 4:52:26 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > The following is my logfile entry (sample lines). The first line is > understandable. What do the values in the third and following lines > denote? > > > ------------------------------------------------------ > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > 3.5403E+00 > Solving for Hmholtz scalars > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > 1520 Scalars done 7.6000E-02 8.3823E-02 > Solving for fluid > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > 1.0000E-10 7.8799E-01 3.0171E+00 > 1520 Fluid done 7.6000E-02 3.3650E+00 > -------------------------------------------------------- > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: >> I am not sure what you are talking about? >> >> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Friday 30th March 2018 10:30 >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: [Nek5000-users] logfile >>> >>> Hi Neks, >>> >>> What are the entries in the logfile that is output from running >>> the code. Please let me know where the entries are determined in the >>> code. >>> >>> Thanks >>> Swarandeep >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 08:24:53 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 15:24:53 +0200 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Can you please change the permissions such that everyone with the link can read it. Thanks! -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 13:42 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Please find the link for the logfile? > ?logfile ? > > On Fri, Mar 30, 2018 at 4:59 PM, > wrote: > Can you please attach your logfile? > > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > > Sent: Friday 30th March 2018 13:21 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Thanks for the information. > > > > In my calculation, I am using a variable viscosity formulation. The > > viscosity depends on the temperature. As the run proceeds the initial > > residual for the TEMP gradually rises from 1E+03 until at around at > > the value 6E+07, the logfile shows an error for non-positive > > diffusivity. I have checked the temperature distribution which has no > > such value so as to make the diffusivity negative (or zero). Please > > indicate what I may be doing wrong. > > > > Thank you > > Swarandeep > > > > On Fri, Mar 30, 2018 at 3:30 PM,? > wrote: > > > > > >>Step? ?1520, t= 7.6000000E-02, DT= 5.0000000E-05, C=? 0.072 5.3831E+03 3.5403E+00 > > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > > > > > >>1520? Hmholtz TEMP? ? ? 12? ?3.8789E-11? ?4.5120E+07? ?1.0000E-10 > > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > > > > > > ... > > > > > > > > > -----Original message----- > > >> From:nek5000-users at lists.mcs.anl.gov > > > >> Sent: Friday 30th March 2018 11:52 > > >> To: nek5000-users at lists.mcs.anl.gov > > >> Subject: Re: [Nek5000-users] logfile > > >> > > >> The following is my logfile entry (sample lines). The first line is > > >> understandable. What do the values in the third and following lines > > >> denote? > > >> > > >> > > >> ------------------------------------------------------ > > >> Step? ?1520, t= 7.6000000E-02, DT= 5.0000000E-05, C=? 0.072 5.3831E+03 > > >> 3.5403E+00 > > >>? ? ? ? ? ? ? Solving for Hmholtz scalars > > >>? ? ? ? 1520? Hmholtz TEMP? ? ? 12? ?3.8789E-11? ?4.5120E+07? ?1.0000E-10 > > >>? ? ? ? 1520? Scalars done? 7.6000E-02? 8.3823E-02 > > >>? ? ? ? ? ? ? Solving for fluid > > >>? ? ? ? 1520? Helmh3 fluid? ? ? 17? ?3.6594E-11? ?4.7524E-01? ?1.0000E-10 > > >>? ? ? ? 1520? U-PRES gmres? ? ?120? ?1.3494E-08? ?4.5675E-06 > > >> 1.0000E-10? ?7.8799E-01? ?3.0171E+00 > > >>? ? ? ? 1520? Fluid done? 7.6000E-02? 3.3650E+00 > > >> -------------------------------------------------------- > > >> > > >> On Fri, Mar 30, 2018 at 3:05 PM,? > wrote: > > >> > I am not sure what you are talking about? > > >> > > > >> > -----Original message----- > > >> >> From:nek5000-users at lists.mcs.anl.gov > > > >> >> Sent: Friday 30th March 2018 10:30 > > >> >> To: nek5000-users at lists.mcs.anl.gov > > >> >> Subject: [Nek5000-users] logfile > > >> >> > > >> >> Hi Neks, > > >> >> > > >> >>? ? ? What are the entries in the logfile that is output from running > > >> >> the code.? Please let me know where the entries are determined in the > > >> >> code. > > >> >> > > >> >> Thanks > > >> >> Swarandeep > > >> >> _______________________________________________ > > >> >> Nek5000-users mailing list > > >> >> Nek5000-users at lists.mcs.anl.gov > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> >> > > >> > _______________________________________________ > > >> > Nek5000-users mailing list > > >> > Nek5000-users at lists.mcs.anl.gov > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> _______________________________________________ > > >> Nek5000-users mailing list > > >> Nek5000-users at lists.mcs.anl.gov > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 08:32:17 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 19:02:17 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: Please find the attached link with permissions enabled logfile or try the link: https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=sharing On Fri, Mar 30, 2018 at 6:54 PM, wrote: > Can you please change the permissions such that everyone with the link can > read it. Thanks! > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 30th March 2018 13:42 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Please find the link for the logfile? > > logfile h5Uy2QWtKGnQUYVBEiG5wC/view?usp=drive_web>? > > > > On Fri, Mar 30, 2018 at 4:59 PM, > wrote: > > Can you please attach your logfile? > > > > > > -----Original message----- > > > From:nek5000-users at lists.mcs.anl.gov lists.mcs.anl.gov> nek5000-users at lists.mcs.anl.gov>> > > > Sent: Friday 30th March 2018 13:21 > > > To: nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > Subject: Re: [Nek5000-users] logfile > > > > > > Thanks for the information. > > > > > > In my calculation, I am using a variable viscosity formulation. The > > > viscosity depends on the temperature. As the run proceeds the initial > > > residual for the TEMP gradually rises from 1E+03 until at around at > > > the value 6E+07, the logfile shows an error for non-positive > > > diffusivity. I have checked the temperature distribution which has no > > > such value so as to make the diffusivity negative (or zero). Please > > > indicate what I may be doing wrong. > > > > > > Thank you > > > Swarandeep > > > > > > On Fri, Mar 30, 2018 at 3:30 PM, > wrote: > > > > > > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 > 5.3831E+03 3.5403E+00 > > > > timestep, time, dt, Courant Number, elapsed solver time, solver time > of last time iteration > > > > > > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > timestep, solve type, iteration counter, final residual, initial > residual, solver tolerance > > > > > > > > ... > > > > > > > > > > > > -----Original message----- > > > >> From:nek5000-users at lists.mcs.anl.gov lists.mcs.anl.gov> nek5000-users at lists.mcs.anl.gov>> > > > >> Sent: Friday 30th March 2018 11:52 > > > >> To: nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > >> Subject: Re: [Nek5000-users] logfile > > > >> > > > >> The following is my logfile entry (sample lines). The first line is > > > >> understandable. What do the values in the third and following lines > > > >> denote? > > > >> > > > >> > > > >> ------------------------------------------------------ > > > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 > 5.3831E+03 > > > >> 3.5403E+00 > > > >> Solving for Hmholtz scalars > > > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 > 1.0000E-10 > > > >> 1520 Scalars done 7.6000E-02 8.3823E-02 > > > >> Solving for fluid > > > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 > 1.0000E-10 > > > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > >> 1.0000E-10 7.8799E-01 3.0171E+00 > > > >> 1520 Fluid done 7.6000E-02 3.3650E+00 > > > >> -------------------------------------------------------- > > > >> > > > >> On Fri, Mar 30, 2018 at 3:05 PM, > wrote: > > > >> > I am not sure what you are talking about? > > > >> > > > > >> > -----Original message----- > > > >> >> From:nek5000-users at lists.mcs.anl.gov From%3Anek5000-users at lists.mcs.anl.gov> > > > > >> >> Sent: Friday 30th March 2018 10:30 > > > >> >> To: nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > >> >> Subject: [Nek5000-users] logfile > > > >> >> > > > >> >> Hi Neks, > > > >> >> > > > >> >> What are the entries in the logfile that is output from > running > > > >> >> the code. Please let me know where the entries are determined > in the > > > >> >> code. > > > >> >> > > > >> >> Thanks > > > >> >> Swarandeep > > > >> >> _______________________________________________ > > > >> >> Nek5000-users mailing list > > > >> >> Nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > >> >> > > > >> > _______________________________________________ > > > >> > Nek5000-users mailing list > > > >> > Nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > >> _______________________________________________ > > > >> Nek5000-users mailing list > > > >> Nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > >> > > > > _______________________________________________ > > > > Nek5000-users mailing list > > > > Nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov mcs.anl.gov> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users < > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 30 08:34:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 15:34:49 +0200 Subject: [Nek5000-users] logfile Message-ID: That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 14:19 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users on behalf of > > nek5000-users at lists.mcs.anl.gov > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:nek5000-users at lists.mcs.anl.gov > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users at lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 08:45:30 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 15:45:30 +0200 Subject: [Nek5000-users] logfile Message-ID: Some random observations/comments from the logfile: - Please use the latest offical replease (available as a tarball) instead of the master branch on GitHub - Your're using a dimensional setup with (unreasonably) tight tolerances (as discussed) - Is your flow incompressible? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 15:33 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Please find the attached link with permissions enabled > ?logfile or try the?link: > > https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=sharing > > On Fri, Mar 30, 2018 at 6:54 PM, > wrote: > Can you please change the permissions such that everyone with the link can read it. Thanks! > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > > Sent: Friday 30th March 2018 13:42 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Please find the link for the logfile? > > ?logfile >? > > > > On Fri, Mar 30, 2018 at 4:59 PM,? >> wrote: > > Can you please attach your logfile? > > > > > > -----Original message----- > > > From:nek5000-users at lists.mcs.anl.gov > >> > > > Sent: Friday 30th March 2018 13:21 > > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: Re: [Nek5000-users] logfile > > > > > > Thanks for the information. > > > > > > In my calculation, I am using a variable viscosity formulation. The > > > viscosity depends on the temperature. As the run proceeds the initial > > > residual for the TEMP gradually rises from 1E+03 until at around at > > > the value 6E+07, the logfile shows an error for non-positive > > > diffusivity. I have checked the temperature distribution which has no > > > such value so as to make the diffusivity negative (or zero). Please > > > indicate what I may be doing wrong. > > > > > > Thank you > > > Swarandeep > > > > > > On Fri, Mar 30, 2018 at 3:30 PM,? >> wrote: > > > > > > > >>Step? ?1520, t= 7.6000000E-02, DT= 5.0000000E-05, C=? 0.072 5.3831E+03 3.5403E+00 > > > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > > > > > > > >>1520? Hmholtz TEMP? ? ? 12? ?3.8789E-11? ?4.5120E+07? ?1.0000E-10 > > > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > > > > > > > > ... > > > > > > > > > > > > -----Original message----- > > > >> From:nek5000-users at lists.mcs.anl.gov > >> > > > >> Sent: Friday 30th March 2018 11:52 > > > >> To: nek5000-users at lists.mcs.anl.gov > > > > >> Subject: Re: [Nek5000-users] logfile > > > >> > > > >> The following is my logfile entry (sample lines). The first line is > > > >> understandable. What do the values in the third and following lines > > > >> denote? > > > >> > > > >> > > > >> ------------------------------------------------------ > > > >> Step? ?1520, t= 7.6000000E-02, DT= 5.0000000E-05, C=? 0.072 5.3831E+03 > > > >> 3.5403E+00 > > > >>? ? ? ? ? ? ? Solving for Hmholtz scalars > > > >>? ? ? ? 1520? Hmholtz TEMP? ? ? 12? ?3.8789E-11? ?4.5120E+07? ?1.0000E-10 > > > >>? ? ? ? 1520? Scalars done? 7.6000E-02? 8.3823E-02 > > > >>? ? ? ? ? ? ? Solving for fluid > > > >>? ? ? ? 1520? Helmh3 fluid? ? ? 17? ?3.6594E-11? ?4.7524E-01? ?1.0000E-10 > > > >>? ? ? ? 1520? U-PRES gmres? ? ?120? ?1.3494E-08? ?4.5675E-06 > > > >> 1.0000E-10? ?7.8799E-01? ?3.0171E+00 > > > >>? ? ? ? 1520? Fluid done? 7.6000E-02? 3.3650E+00 > > > >> -------------------------------------------------------- > > > >> > > > >> On Fri, Mar 30, 2018 at 3:05 PM,? >> wrote: > > > >> > I am not sure what you are talking about? > > > >> > > > > >> > -----Original message----- > > > >> >> From:nek5000-users at lists.mcs.anl.gov > >> > > > >> >> Sent: Friday 30th March 2018 10:30 > > > >> >> To: nek5000-users at lists.mcs.anl.gov > > > > >> >> Subject: [Nek5000-users] logfile > > > >> >> > > > >> >> Hi Neks, > > > >> >> > > > >> >>? ? ? What are the entries in the logfile that is output from running > > > >> >> the code.? Please let me know where the entries are determined in the > > > >> >> code. > > > >> >> > > > >> >> Thanks > > > >> >> Swarandeep > > > >> >> _______________________________________________ > > > >> >> Nek5000-users mailing list > > > >> >> Nek5000-users at lists.mcs.anl.gov > > > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > >> >> > > > >> > _______________________________________________ > > > >> > Nek5000-users mailing list > > > >> > Nek5000-users at lists.mcs.anl.gov > > > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > >> _______________________________________________ > > > >> Nek5000-users mailing list > > > >> Nek5000-users at lists.mcs.anl.gov > > > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > >> > > > > _______________________________________________ > > > > Nek5000-users mailing list > > > > Nek5000-users at lists.mcs.anl.gov > > > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 09:54:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 20:24:42 +0530 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: I am using the latest release. The flow is incompressible. I will check with the non-dimensional formulation On Fri, Mar 30, 2018 at 7:15 PM, wrote: > Some random observations/comments from the logfile: > > - Please use the latest offical replease (available as a tarball) instead of the master branch on GitHub > - Your're using a dimensional setup with (unreasonably) tight tolerances (as discussed) > - Is your flow incompressible? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 30th March 2018 15:33 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] logfile >> >> Please find the attached link with permissions enabled >> logfile or try the link: >> >> https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=sharing >> >> On Fri, Mar 30, 2018 at 6:54 PM, > wrote: >> Can you please change the permissions such that everyone with the link can read it. Thanks! >> >> -----Original message----- >> > From:nek5000-users at lists.mcs.anl.gov > >> > Sent: Friday 30th March 2018 13:42 >> > To: nek5000-users at lists.mcs.anl.gov >> > Subject: Re: [Nek5000-users] logfile >> > >> > Please find the link for the logfile >> > logfile > >> > >> > On Fri, Mar 30, 2018 at 4:59 PM, >> wrote: >> > Can you please attach your logfile? >> > >> > >> > -----Original message----- >> > > From:nek5000-users at lists.mcs.anl.gov > >> >> > > Sent: Friday 30th March 2018 13:21 >> > > To: nek5000-users at lists.mcs.anl.gov > >> > > Subject: Re: [Nek5000-users] logfile >> > > >> > > Thanks for the information. >> > > >> > > In my calculation, I am using a variable viscosity formulation. The >> > > viscosity depends on the temperature. As the run proceeds the initial >> > > residual for the TEMP gradually rises from 1E+03 until at around at >> > > the value 6E+07, the logfile shows an error for non-positive >> > > diffusivity. I have checked the temperature distribution which has no >> > > such value so as to make the diffusivity negative (or zero). Please >> > > indicate what I may be doing wrong. >> > > >> > > Thank you >> > > Swarandeep >> > > >> > > On Fri, Mar 30, 2018 at 3:30 PM, >> wrote: >> > > > >> > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 >> > > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration >> > > > >> > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >> > > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance >> > > > >> > > > ... >> > > > >> > > > >> > > > -----Original message----- >> > > >> From:nek5000-users at lists.mcs.anl.gov > >> >> > > >> Sent: Friday 30th March 2018 11:52 >> > > >> To: nek5000-users at lists.mcs.anl.gov > >> > > >> Subject: Re: [Nek5000-users] logfile >> > > >> >> > > >> The following is my logfile entry (sample lines). The first line is >> > > >> understandable. What do the values in the third and following lines >> > > >> denote? >> > > >> >> > > >> >> > > >> ------------------------------------------------------ >> > > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >> > > >> 3.5403E+00 >> > > >> Solving for Hmholtz scalars >> > > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >> > > >> 1520 Scalars done 7.6000E-02 8.3823E-02 >> > > >> Solving for fluid >> > > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >> > > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >> > > >> 1.0000E-10 7.8799E-01 3.0171E+00 >> > > >> 1520 Fluid done 7.6000E-02 3.3650E+00 >> > > >> -------------------------------------------------------- >> > > >> >> > > >> On Fri, Mar 30, 2018 at 3:05 PM, >> wrote: >> > > >> > I am not sure what you are talking about? >> > > >> > >> > > >> > -----Original message----- >> > > >> >> From:nek5000-users at lists.mcs.anl.gov > >> >> > > >> >> Sent: Friday 30th March 2018 10:30 >> > > >> >> To: nek5000-users at lists.mcs.anl.gov > >> > > >> >> Subject: [Nek5000-users] logfile >> > > >> >> >> > > >> >> Hi Neks, >> > > >> >> >> > > >> >> What are the entries in the logfile that is output from running >> > > >> >> the code. Please let me know where the entries are determined in the >> > > >> >> code. >> > > >> >> >> > > >> >> Thanks >> > > >> >> Swarandeep >> > > >> >> _______________________________________________ >> > > >> >> Nek5000-users mailing list >> > > >> >> Nek5000-users at lists.mcs.anl.gov > >> > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > >> >> >> > > >> > _______________________________________________ >> > > >> > Nek5000-users mailing list >> > > >> > Nek5000-users at lists.mcs.anl.gov > >> > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > >> _______________________________________________ >> > > >> Nek5000-users mailing list >> > > >> Nek5000-users at lists.mcs.anl.gov > >> > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > >> >> > > > _______________________________________________ >> > > > Nek5000-users mailing list >> > > > Nek5000-users at lists.mcs.anl.gov > >> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > _______________________________________________ >> > > Nek5000-users mailing list >> > > Nek5000-users at lists.mcs.anl.gov > >> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Mar 30 10:01:38 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 17:01:38 +0200 Subject: [Nek5000-users] logfile In-Reply-To: References: Message-ID: The logfile says v17.0-rc1 where the latest release prints v17.0 -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 16:55 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > I am using the latest release. The flow is incompressible. I will > check with the non-dimensional formulation > > On Fri, Mar 30, 2018 at 7:15 PM, wrote: > > Some random observations/comments from the logfile: > > > > - Please use the latest offical replease (available as a tarball) instead of the master branch on GitHub > > - Your're using a dimensional setup with (unreasonably) tight tolerances (as discussed) > > - Is your flow incompressible? > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Friday 30th March 2018 15:33 > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] logfile > >> > >> Please find the attached link with permissions enabled > >> logfile or try the link: > >> > >> https://drive.google.com/file/d/1co21p9SNAq_Vs0YQgSp9Y_PeAWvOfem3/view?usp=sharing > >> > >> On Fri, Mar 30, 2018 at 6:54 PM, > wrote: > >> Can you please change the permissions such that everyone with the link can read it. Thanks! > >> > >> -----Original message----- > >> > From:nek5000-users at lists.mcs.anl.gov > > >> > Sent: Friday 30th March 2018 13:42 > >> > To: nek5000-users at lists.mcs.anl.gov > >> > Subject: Re: [Nek5000-users] logfile > >> > > >> > Please find the link for the logfile > >> > logfile > > >> > > >> > On Fri, Mar 30, 2018 at 4:59 PM, >> wrote: > >> > Can you please attach your logfile? > >> > > >> > > >> > -----Original message----- > >> > > From:nek5000-users at lists.mcs.anl.gov > >> > >> > > Sent: Friday 30th March 2018 13:21 > >> > > To: nek5000-users at lists.mcs.anl.gov > > >> > > Subject: Re: [Nek5000-users] logfile > >> > > > >> > > Thanks for the information. > >> > > > >> > > In my calculation, I am using a variable viscosity formulation. The > >> > > viscosity depends on the temperature. As the run proceeds the initial > >> > > residual for the TEMP gradually rises from 1E+03 until at around at > >> > > the value 6E+07, the logfile shows an error for non-positive > >> > > diffusivity. I have checked the temperature distribution which has no > >> > > such value so as to make the diffusivity negative (or zero). Please > >> > > indicate what I may be doing wrong. > >> > > > >> > > Thank you > >> > > Swarandeep > >> > > > >> > > On Fri, Mar 30, 2018 at 3:30 PM, >> wrote: > >> > > > > >> > > >>Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 3.5403E+00 > >> > > > timestep, time, dt, Courant Number, elapsed solver time, solver time of last time iteration > >> > > > > >> > > >>1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > >> > > > timestep, solve type, iteration counter, final residual, initial residual, solver tolerance > >> > > > > >> > > > ... > >> > > > > >> > > > > >> > > > -----Original message----- > >> > > >> From:nek5000-users at lists.mcs.anl.gov > >> > >> > > >> Sent: Friday 30th March 2018 11:52 > >> > > >> To: nek5000-users at lists.mcs.anl.gov > > >> > > >> Subject: Re: [Nek5000-users] logfile > >> > > >> > >> > > >> The following is my logfile entry (sample lines). The first line is > >> > > >> understandable. What do the values in the third and following lines > >> > > >> denote? > >> > > >> > >> > > >> > >> > > >> ------------------------------------------------------ > >> > > >> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > >> > > >> 3.5403E+00 > >> > > >> Solving for Hmholtz scalars > >> > > >> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > >> > > >> 1520 Scalars done 7.6000E-02 8.3823E-02 > >> > > >> Solving for fluid > >> > > >> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > >> > > >> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > >> > > >> 1.0000E-10 7.8799E-01 3.0171E+00 > >> > > >> 1520 Fluid done 7.6000E-02 3.3650E+00 > >> > > >> -------------------------------------------------------- > >> > > >> > >> > > >> On Fri, Mar 30, 2018 at 3:05 PM, >> wrote: > >> > > >> > I am not sure what you are talking about? > >> > > >> > > >> > > >> > -----Original message----- > >> > > >> >> From:nek5000-users at lists.mcs.anl.gov > >> > >> > > >> >> Sent: Friday 30th March 2018 10:30 > >> > > >> >> To: nek5000-users at lists.mcs.anl.gov > > >> > > >> >> Subject: [Nek5000-users] logfile > >> > > >> >> > >> > > >> >> Hi Neks, > >> > > >> >> > >> > > >> >> What are the entries in the logfile that is output from running > >> > > >> >> the code. Please let me know where the entries are determined in the > >> > > >> >> code. > >> > > >> >> > >> > > >> >> Thanks > >> > > >> >> Swarandeep > >> > > >> >> _______________________________________________ > >> > > >> >> Nek5000-users mailing list > >> > > >> >> Nek5000-users at lists.mcs.anl.gov > > >> > > >> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > >> >> > >> > > >> > _______________________________________________ > >> > > >> > Nek5000-users mailing list > >> > > >> > Nek5000-users at lists.mcs.anl.gov > > >> > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > >> _______________________________________________ > >> > > >> Nek5000-users mailing list > >> > > >> Nek5000-users at lists.mcs.anl.gov > > >> > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > >> > >> > > > _______________________________________________ > >> > > > Nek5000-users mailing list > >> > > > Nek5000-users at lists.mcs.anl.gov > > >> > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > _______________________________________________ > >> > > Nek5000-users mailing list > >> > > Nek5000-users at lists.mcs.anl.gov > > >> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > > >> > _______________________________________________ > >> > Nek5000-users mailing list > >> > Nek5000-users at lists.mcs.anl.gov > > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >> > > >> > _______________________________________________ > >> > Nek5000-users mailing list > >> > Nek5000-users at lists.mcs.anl.gov > >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Mar 30 10:49:55 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Mar 2018 15:49:55 +0000 Subject: [Nek5000-users] pretex error when reading BC from file with no velocity field and passive scalars Message-ID: Dear Neks, I am constructing a mesh for conjugate heat transfer simulations. My temperature is a passive scalar and I want to add more passive scalars. However, when I am combining fluid-solid rea files with pretex (choosing option 3), I get the following error while reading boundary conditions of solids (only the relevant part is pasted here, I can upload the whole output if necessary): > Showing only 90 elements of 142912 > input name of new .rea file > walls_gen > Found 0 curve sides. > IFLD: 2 3 F T > ***** THERMAL BOUNDARY CONDITIONS ***** > ***** THERMAL BOUNDARY CONDITIONS *****$ > I 11 0.00000 0.00000 0.00000 0.00000 0.00000 > I 11 0.00000 0.00000 0.00000 0.00000 0.00000$ > made it to: 10640 6 > nelin,ifld: 10640 3 > Error reading boundary conditions. Returning. > start locglob_lexico: 8 142912 1143296 2.00000009E-03 > locglob: 1 1 1143296 > locglob: 2 137 1143296 > locglob: 3 5287 1143296 > locglob: 1 153323 1143296 > locglob: 2 153323 1143296 > locglob: 3 153323 1143296 > locglob: 1 153323 1143296 > locglob: 2 153323 1143296 > locglob: 3 153323 1143296 > Performing unique_vertex2 self_chk 1143296 > done locglob_lexico: 153323 153323 1143296 8 > Performing makecell self_chk 1143296 > > *** MIDWAY BREAK MENU *** Note the two lines that end with $, which I think are the indication of the problem. My solid walls have exactly 10640 elements. I think the issue is in the file build.f at line https://github.com/Nek5000/Nek5000/blob/f0a6dd029cd2116fbfdbb1f6e7bfbfdd1808d86a/tools/prenek/build.f#L1282 which IMHO should be executed outside of the do loop that starts a line before. The header for no fluid BCs should not be read in the do loop, because this field is not processed. The header of currently processed field is read inside imp_bc function at line https://github.com/Nek5000/Nek5000/blob/f0a6dd029cd2116fbfdbb1f6e7bfbfdd1808d86a/tools/prenek/build.f#L1545 and printed after that. In the output above, these are the four lines with two of them ending with $. The third and fourth of those lines should be 'PASSIVE SCALAR 1 BOUNDARY CONDITIONS', not the boundary condition for the first element itself. After rotating lines 1282 and 1283 my mesh gets properly constructed. However, I am not aware of other use cases that would require dummy reading inside the loop if the velocity field is not present. Should I open an issue about this in the github repository or maybe provide a simplified example? Best regards, Jure Oder From nek5000-users at lists.mcs.anl.gov Sat Mar 31 03:45:05 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 08:45:05 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 109, Issue 32 In-Reply-To: References: Message-ID: Dear Nek experts, I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. ________________________________________ Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov Gesendet: Freitag, 30. M?rz 2018 17:02 An: nek5000-users at lists.mcs.anl.gov Betreff: Nek5000-users Digest, Vol 109, Issue 32 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: logfile (nek5000-users at lists.mcs.anl.gov) 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 30 Mar 2018 15:34:49 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] logfile Message-ID: Content-Type: text/plain; charset=utf-8 That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 14:19 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users on behalf of > > nek5000-users at lists.mcs.anl.gov > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:nek5000-users at lists.mcs.anl.gov > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users at lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 31 04:06:58 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 09:06:58 +0000 Subject: [Nek5000-users] Guidelines for Tolerances In-Reply-To: <1522485904680.73801@kit.edu> References: , <1522485904680.73801@kit.edu> Message-ID: Dear Nek experts, sorry, my first mail was incomplete. I will start again. I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. The log for one timestep is given below (sorry about the formatting). As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? Best regards, Steffen Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 Solving for Hmholtz scalars 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 99999 Scalars done 8.5000E+02 1.7601E-01 Solving for fluid 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 99999 Fluid done 8.5000E+02 1.2875E-01 ________________________________________ Von: Straub, Steffen (ISTM) Gesendet: Samstag, 31. M?rz 2018 10:45 An: nek5000-users at lists.mcs.anl.gov Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 Dear Nek experts, I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. ________________________________________ Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov Gesendet: Freitag, 30. M?rz 2018 17:02 An: nek5000-users at lists.mcs.anl.gov Betreff: Nek5000-users Digest, Vol 109, Issue 32 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: logfile (nek5000-users at lists.mcs.anl.gov) 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 30 Mar 2018 15:34:49 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] logfile Message-ID: Content-Type: text/plain; charset=utf-8 That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: * Specify the parameters below in usrdat3 of your usr file. * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure -- Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 30th March 2018 14:19 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > > Thanks, Paul, > Could you please tell me the parameters in terms of ###.par file. > I am using the latest version. > > Thank you > > On Fri, Mar 30, 2018 at 5:35 PM, wrote: > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > orders of magnitude reduction in residual and are working only with 16 > > significant digits. It seems like you might need to change your .rea file in > > the following way: > > > > > > set p21 and p22 to 0 > > > > > > set p24, tolrel , to 1.e-3 > > > > set p25, tolabs, to 1.e-3 > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > analytic convergence study where you know the answer to an infinite number > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > residual tolerances are set conservatively based on these input values. > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > You have 17 iterations for the moment equations. > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > for the pressure residual tolerance). > > > > > > hth, > > > > Paul > > > > > > ________________________________ > > From: Nek5000-users on behalf of > > nek5000-users at lists.mcs.anl.gov > > Sent: Friday, March 30, 2018 4:52:26 AM > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > The following is my logfile entry (sample lines). The first line is > > understandable. What do the values in the third and following lines > > denote? > > > > > > ------------------------------------------------------ > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > 3.5403E+00 > > Solving for Hmholtz scalars > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > Solving for fluid > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > 1.0000E-10 7.8799E-01 3.0171E+00 > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > -------------------------------------------------------- > > > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: > >> I am not sure what you are talking about? > >> > >> -----Original message----- > >>> From:nek5000-users at lists.mcs.anl.gov > >>> Sent: Friday 30th March 2018 10:30 > >>> To: nek5000-users at lists.mcs.anl.gov > >>> Subject: [Nek5000-users] logfile > >>> > >>> Hi Neks, > >>> > >>> What are the entries in the logfile that is output from running > >>> the code. Please let me know where the entries are determined in the > >>> code. > >>> > >>> Thanks > >>> Swarandeep > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >>> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 31 04:20:06 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 11:20:06 +0200 Subject: [Nek5000-users] Guidelines for Tolerances Message-ID: Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. -- Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Saturday 31st March 2018 11:07 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Guidelines for Tolerances > > Dear Nek experts, > > sorry, my first mail was incomplete. I will start again. > > I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. > The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. > > In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. > > The log for one timestep is given below (sorry about the formatting). > As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. > Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? > > Best regards, > Steffen > > > Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 > Solving for Hmholtz scalars > 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 > 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 > 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 > 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 > 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 > 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 > 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 > 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 > 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 > 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 > 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 > 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 > 99999 Scalars done 8.5000E+02 1.7601E-01 > Solving for fluid > 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 > 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 > 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 > 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 > 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 > 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 > 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 > 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 > 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 > 99999 Fluid done 8.5000E+02 1.2875E-01 > ________________________________________ > Von: Straub, Steffen (ISTM) > Gesendet: Samstag, 31. M?rz 2018 10:45 > An: nek5000-users at lists.mcs.anl.gov > Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 > > Dear Nek experts, > > I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. > The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. > > > ________________________________________ > Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov > Gesendet: Freitag, 30. M?rz 2018 17:02 > An: nek5000-users at lists.mcs.anl.gov > Betreff: Nek5000-users Digest, Vol 109, Issue 32 > > 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: logfile (nek5000-users at lists.mcs.anl.gov) > 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) > 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) > 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2018 15:34:49 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] logfile > Message-ID: > > Content-Type: text/plain; charset=utf-8 > > That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: > > * Specify the parameters below in usrdat3 of your usr file. > * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure > > -- > Stefan > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 30th March 2018 14:19 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] logfile > > > > Thanks, Paul, > > Could you please tell me the parameters in terms of ###.par file. > > I am using the latest version. > > > > Thank you > > > > On Fri, Mar 30, 2018 at 5:35 PM, wrote: > > > > > > > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > > > > > > > On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting > > > with a residual of 4.5e7, with target residual 1.e-10. > > > > > > > > > [ This is actually too tight of a tolerance, since you are asking for 17 > > > orders of magnitude reduction in residual and are working only with 16 > > > significant digits. It seems like you might need to change your .rea file in > > > the following way: > > > > > > > > > set p21 and p22 to 0 > > > > > > > > > set p24, tolrel , to 1.e-3 > > > > > > set p25, tolabs, to 1.e-3 > > > > > > > > > The only time you'll need tolrel/abs tighter than this is if you're doing an > > > analytic convergence study where you know the answer to an infinite number > > > of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The > > > residual tolerances are set conservatively based on these input values. > > > > > > > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > > > > > > > You have 17 iterations for the moment equations. > > > > > > > > > You have 120 iterations for pressure. Again, your tolerances are too tight > > > for engineering calculations -- you do not need 1.e-10 for divergence (i.e., > > > for the pressure residual tolerance). > > > > > > > > > hth, > > > > > > Paul > > > > > > > > > ________________________________ > > > From: Nek5000-users on behalf of > > > nek5000-users at lists.mcs.anl.gov > > > Sent: Friday, March 30, 2018 4:52:26 AM > > > To: nek5000-users at lists.mcs.anl.gov > > > Subject: Re: [Nek5000-users] logfile > > > > > > The following is my logfile entry (sample lines). The first line is > > > understandable. What do the values in the third and following lines > > > denote? > > > > > > > > > ------------------------------------------------------ > > > Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 > > > 3.5403E+00 > > > Solving for Hmholtz scalars > > > 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 > > > 1520 Scalars done 7.6000E-02 8.3823E-02 > > > Solving for fluid > > > 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 > > > 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 > > > 1.0000E-10 7.8799E-01 3.0171E+00 > > > 1520 Fluid done 7.6000E-02 3.3650E+00 > > > -------------------------------------------------------- > > > > > > On Fri, Mar 30, 2018 at 3:05 PM, wrote: > > >> I am not sure what you are talking about? > > >> > > >> -----Original message----- > > >>> From:nek5000-users at lists.mcs.anl.gov > > >>> Sent: Friday 30th March 2018 10:30 > > >>> To: nek5000-users at lists.mcs.anl.gov > > >>> Subject: [Nek5000-users] logfile > > >>> > > >>> Hi Neks, > > >>> > > >>> What are the entries in the logfile that is output from running > > >>> the code. Please let me know where the entries are determined in the > > >>> code. > > >>> > > >>> Thanks > > >>> Swarandeep > > >>> _______________________________________________ > > >>> Nek5000-users mailing list > > >>> Nek5000-users at lists.mcs.anl.gov > > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > >>> > > >> _______________________________________________ > > >> Nek5000-users mailing list > > >> Nek5000-users at lists.mcs.anl.gov > > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 31 12:09:31 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 19:09:31 +0200 Subject: [Nek5000-users] Guidelines for Tolerances In-Reply-To: References: Message-ID: I guess in the end the chosen/requested tolerances depend on what one is interested in, and how sensitive a specific flow case is. Also, the spatial distribution of the divergence error might be an interesting quantity to look at. However, I have a question to Stefan: I am not sure I fully understand your comment regarding spatial resolution. Do you mean that the spatial errors are so large that a specific divergence tolerance cannot be fulfilled? Philipp On 2018-03-31 11:20, nek5000-users at lists.mcs.anl.gov wrote: > Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. > > -- > Stefan > > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Saturday 31st March 2018 11:07 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Guidelines for Tolerances >> >> Dear Nek experts, >> >> sorry, my first mail was incomplete. I will start again. >> >> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >> >> In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. >> >> The log for one timestep is given below (sorry about the formatting). >> As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. >> Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? >> >> Best regards, >> Steffen >> >> >> Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 >> Solving for Hmholtz scalars >> 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 >> 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 >> 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 >> 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 >> 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 >> 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 >> 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 >> 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 >> 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 >> 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 >> 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 >> 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 >> 99999 Scalars done 8.5000E+02 1.7601E-01 >> Solving for fluid >> 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 >> 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 >> 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 >> 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 >> 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 >> 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 >> 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 >> 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 >> 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 >> 99999 Fluid done 8.5000E+02 1.2875E-01 >> ________________________________________ >> Von: Straub, Steffen (ISTM) >> Gesendet: Samstag, 31. M?rz 2018 10:45 >> An: nek5000-users at lists.mcs.anl.gov >> Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 >> >> Dear Nek experts, >> >> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >> >> >> ________________________________________ >> Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov >> Gesendet: Freitag, 30. M?rz 2018 17:02 >> An: nek5000-users at lists.mcs.anl.gov >> Betreff: Nek5000-users Digest, Vol 109, Issue 32 >> >> 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: logfile (nek5000-users at lists.mcs.anl.gov) >> 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) >> 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) >> 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 30 Mar 2018 15:34:49 +0200 >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] logfile >> Message-ID: >> >> Content-Type: text/plain; charset=utf-8 >> >> That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: >> >> * Specify the parameters below in usrdat3 of your usr file. >> * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure >> >> -- >> Stefan >> >> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Friday 30th March 2018 14:19 >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] logfile >>> >>> Thanks, Paul, >>> Could you please tell me the parameters in terms of ###.par file. >>> I am using the latest version. >>> >>> Thank you >>> >>> On Fri, Mar 30, 2018 at 5:35 PM, wrote: >>>> >>>> >>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>> >>>> >>>> On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting >>>> with a residual of 4.5e7, with target residual 1.e-10. >>>> >>>> >>>> [ This is actually too tight of a tolerance, since you are asking for 17 >>>> orders of magnitude reduction in residual and are working only with 16 >>>> significant digits. It seems like you might need to change your .rea file in >>>> the following way: >>>> >>>> >>>> set p21 and p22 to 0 >>>> >>>> >>>> set p24, tolrel , to 1.e-3 >>>> >>>> set p25, tolabs, to 1.e-3 >>>> >>>> >>>> The only time you'll need tolrel/abs tighter than this is if you're doing an >>>> analytic convergence study where you know the answer to an infinite number >>>> of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The >>>> residual tolerances are set conservatively based on these input values. >>>> >>>> >>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>> >>>> >>>> You have 17 iterations for the moment equations. >>>> >>>> >>>> You have 120 iterations for pressure. Again, your tolerances are too tight >>>> for engineering calculations -- you do not need 1.e-10 for divergence (i.e., >>>> for the pressure residual tolerance). >>>> >>>> >>>> hth, >>>> >>>> Paul >>>> >>>> >>>> ________________________________ >>>> From: Nek5000-users on behalf of >>>> nek5000-users at lists.mcs.anl.gov >>>> Sent: Friday, March 30, 2018 4:52:26 AM >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] logfile >>>> >>>> The following is my logfile entry (sample lines). The first line is >>>> understandable. What do the values in the third and following lines >>>> denote? >>>> >>>> >>>> ------------------------------------------------------ >>>> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >>>> 3.5403E+00 >>>> Solving for Hmholtz scalars >>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>> 1520 Scalars done 7.6000E-02 8.3823E-02 >>>> Solving for fluid >>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>> 1520 Fluid done 7.6000E-02 3.3650E+00 >>>> -------------------------------------------------------- >>>> >>>> On Fri, Mar 30, 2018 at 3:05 PM, wrote: >>>>> I am not sure what you are talking about? >>>>> >>>>> -----Original message----- >>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Friday 30th March 2018 10:30 >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: [Nek5000-users] logfile >>>>>> >>>>>> Hi Neks, >>>>>> >>>>>> What are the entries in the logfile that is output from running >>>>>> the code. Please let me know where the entries are determined in the >>>>>> code. >>>>>> >>>>>> Thanks >>>>>> Swarandeep >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 31 13:44:49 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 20:44:49 +0200 Subject: [Nek5000-users] Guidelines for Tolerances In-Reply-To: References: Message-ID: In the PnPn formulation you don?t project into a divergence free space so you don?t prescribe the divergence. It?s a simulation result. > On 31 Mar 2018, at 19:09, "nek5000-users at lists.mcs.anl.gov" wrote: > > I guess in the end the chosen/requested tolerances depend on what one is > interested in, and how sensitive a specific flow case is. Also, the > spatial distribution of the divergence error might be an interesting > quantity to look at. > > However, I have a question to Stefan: I am not sure I fully understand > your comment regarding spatial resolution. Do you mean that the spatial > errors are so large that a specific divergence tolerance cannot be > fulfilled? > > Philipp > >> On 2018-03-31 11:20, nek5000-users at lists.mcs.anl.gov wrote: >> Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. >> >> -- >> Stefan >> >> >> -----Original message----- >>> From:nek5000-users at lists.mcs.anl.gov >>> Sent: Saturday 31st March 2018 11:07 >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: [Nek5000-users] Guidelines for Tolerances >>> >>> Dear Nek experts, >>> >>> sorry, my first mail was incomplete. I will start again. >>> >>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>> >>> In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. >>> >>> The log for one timestep is given below (sorry about the formatting). >>> As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. >>> Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? >>> >>> Best regards, >>> Steffen >>> >>> >>> Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 >>> Solving for Hmholtz scalars >>> 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 >>> 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 >>> 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 >>> 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 >>> 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 >>> 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 >>> 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 >>> 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 >>> 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 >>> 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 >>> 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 >>> 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 >>> 99999 Scalars done 8.5000E+02 1.7601E-01 >>> Solving for fluid >>> 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 >>> 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 >>> 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 >>> 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 >>> 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 >>> 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 >>> 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 >>> 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 >>> 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 >>> 99999 Fluid done 8.5000E+02 1.2875E-01 >>> ________________________________________ >>> Von: Straub, Steffen (ISTM) >>> Gesendet: Samstag, 31. M?rz 2018 10:45 >>> An: nek5000-users at lists.mcs.anl.gov >>> Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 >>> >>> Dear Nek experts, >>> >>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>> >>> >>> ________________________________________ >>> Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov >>> Gesendet: Freitag, 30. M?rz 2018 17:02 >>> An: nek5000-users at lists.mcs.anl.gov >>> Betreff: Nek5000-users Digest, Vol 109, Issue 32 >>> >>> 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: logfile (nek5000-users at lists.mcs.anl.gov) >>> 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>> 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>> 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Fri, 30 Mar 2018 15:34:49 +0200 >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] logfile >>> Message-ID: >>> >>> Content-Type: text/plain; charset=utf-8 >>> >>> That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: >>> >>> * Specify the parameters below in usrdat3 of your usr file. >>> * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure >>> >>> -- >>> Stefan >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Friday 30th March 2018 14:19 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] logfile >>>> >>>> Thanks, Paul, >>>> Could you please tell me the parameters in terms of ###.par file. >>>> I am using the latest version. >>>> >>>> Thank you >>>> >>>>> On Fri, Mar 30, 2018 at 5:35 PM, wrote: >>>>> >>>>> >>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>> >>>>> >>>>> On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting >>>>> with a residual of 4.5e7, with target residual 1.e-10. >>>>> >>>>> >>>>> [ This is actually too tight of a tolerance, since you are asking for 17 >>>>> orders of magnitude reduction in residual and are working only with 16 >>>>> significant digits. It seems like you might need to change your .rea file in >>>>> the following way: >>>>> >>>>> >>>>> set p21 and p22 to 0 >>>>> >>>>> >>>>> set p24, tolrel , to 1.e-3 >>>>> >>>>> set p25, tolabs, to 1.e-3 >>>>> >>>>> >>>>> The only time you'll need tolrel/abs tighter than this is if you're doing an >>>>> analytic convergence study where you know the answer to an infinite number >>>>> of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The >>>>> residual tolerances are set conservatively based on these input values. >>>>> >>>>> >>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>> >>>>> >>>>> You have 17 iterations for the moment equations. >>>>> >>>>> >>>>> You have 120 iterations for pressure. Again, your tolerances are too tight >>>>> for engineering calculations -- you do not need 1.e-10 for divergence (i.e., >>>>> for the pressure residual tolerance). >>>>> >>>>> >>>>> hth, >>>>> >>>>> Paul >>>>> >>>>> >>>>> ________________________________ >>>>> From: Nek5000-users on behalf of >>>>> nek5000-users at lists.mcs.anl.gov >>>>> Sent: Friday, March 30, 2018 4:52:26 AM >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: Re: [Nek5000-users] logfile >>>>> >>>>> The following is my logfile entry (sample lines). The first line is >>>>> understandable. What do the values in the third and following lines >>>>> denote? >>>>> >>>>> >>>>> ------------------------------------------------------ >>>>> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >>>>> 3.5403E+00 >>>>> Solving for Hmholtz scalars >>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>> 1520 Scalars done 7.6000E-02 8.3823E-02 >>>>> Solving for fluid >>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>> 1520 Fluid done 7.6000E-02 3.3650E+00 >>>>> -------------------------------------------------------- >>>>> >>>>>> On Fri, Mar 30, 2018 at 3:05 PM, wrote: >>>>>> I am not sure what you are talking about? >>>>>> >>>>>> -----Original message----- >>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>> Sent: Friday 30th March 2018 10:30 >>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>> Subject: [Nek5000-users] logfile >>>>>>> >>>>>>> Hi Neks, >>>>>>> >>>>>>> What are the entries in the logfile that is output from running >>>>>>> the code. Please let me know where the entries are determined in the >>>>>>> code. >>>>>>> >>>>>>> Thanks >>>>>>> Swarandeep >>>>>>> _______________________________________________ >>>>>>> Nek5000-users mailing list >>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>> >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sat Mar 31 13:48:41 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 20:48:41 +0200 Subject: [Nek5000-users] Guidelines for Tolerances In-Reply-To: References: Message-ID: ah ok, that comment was related to PnPn? On 2018-03-31 20:44, nek5000-users at lists.mcs.anl.gov wrote: > In the PnPn formulation you don?t project into a divergence free space so you don?t prescribe the divergence. It?s a simulation result. > >> On 31 Mar 2018, at 19:09, "nek5000-users at lists.mcs.anl.gov" wrote: >> >> I guess in the end the chosen/requested tolerances depend on what one is >> interested in, and how sensitive a specific flow case is. Also, the >> spatial distribution of the divergence error might be an interesting >> quantity to look at. >> >> However, I have a question to Stefan: I am not sure I fully understand >> your comment regarding spatial resolution. Do you mean that the spatial >> errors are so large that a specific divergence tolerance cannot be >> fulfilled? >> >> Philipp >> >>> On 2018-03-31 11:20, nek5000-users at lists.mcs.anl.gov wrote: >>> Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. >>> >>> -- >>> Stefan >>> >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Saturday 31st March 2018 11:07 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: [Nek5000-users] Guidelines for Tolerances >>>> >>>> Dear Nek experts, >>>> >>>> sorry, my first mail was incomplete. I will start again. >>>> >>>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>>> >>>> In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. >>>> >>>> The log for one timestep is given below (sorry about the formatting). >>>> As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. >>>> Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? >>>> >>>> Best regards, >>>> Steffen >>>> >>>> >>>> Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 >>>> Solving for Hmholtz scalars >>>> 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 >>>> 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 >>>> 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 >>>> 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 >>>> 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 >>>> 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 >>>> 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 >>>> 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 >>>> 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 >>>> 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 >>>> 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 >>>> 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 >>>> 99999 Scalars done 8.5000E+02 1.7601E-01 >>>> Solving for fluid >>>> 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 >>>> 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 >>>> 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 >>>> 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 >>>> 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 >>>> 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 >>>> 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 >>>> 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 >>>> 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 >>>> 99999 Fluid done 8.5000E+02 1.2875E-01 >>>> ________________________________________ >>>> Von: Straub, Steffen (ISTM) >>>> Gesendet: Samstag, 31. M?rz 2018 10:45 >>>> An: nek5000-users at lists.mcs.anl.gov >>>> Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 >>>> >>>> Dear Nek experts, >>>> >>>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>>> >>>> >>>> ________________________________________ >>>> Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov >>>> Gesendet: Freitag, 30. M?rz 2018 17:02 >>>> An: nek5000-users at lists.mcs.anl.gov >>>> Betreff: Nek5000-users Digest, Vol 109, Issue 32 >>>> >>>> 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: logfile (nek5000-users at lists.mcs.anl.gov) >>>> 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>> 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>> 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Fri, 30 Mar 2018 15:34:49 +0200 >>>> From: nek5000-users at lists.mcs.anl.gov >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Subject: Re: [Nek5000-users] logfile >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset=utf-8 >>>> >>>> That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: >>>> >>>> * Specify the parameters below in usrdat3 of your usr file. >>>> * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure >>>> >>>> -- >>>> Stefan >>>> >>>> -----Original message----- >>>>> From:nek5000-users at lists.mcs.anl.gov >>>>> Sent: Friday 30th March 2018 14:19 >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: Re: [Nek5000-users] logfile >>>>> >>>>> Thanks, Paul, >>>>> Could you please tell me the parameters in terms of ###.par file. >>>>> I am using the latest version. >>>>> >>>>> Thank you >>>>> >>>>>> On Fri, Mar 30, 2018 at 5:35 PM, wrote: >>>>>> >>>>>> >>>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>>> >>>>>> >>>>>> On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting >>>>>> with a residual of 4.5e7, with target residual 1.e-10. >>>>>> >>>>>> >>>>>> [ This is actually too tight of a tolerance, since you are asking for 17 >>>>>> orders of magnitude reduction in residual and are working only with 16 >>>>>> significant digits. It seems like you might need to change your .rea file in >>>>>> the following way: >>>>>> >>>>>> >>>>>> set p21 and p22 to 0 >>>>>> >>>>>> >>>>>> set p24, tolrel , to 1.e-3 >>>>>> >>>>>> set p25, tolabs, to 1.e-3 >>>>>> >>>>>> >>>>>> The only time you'll need tolrel/abs tighter than this is if you're doing an >>>>>> analytic convergence study where you know the answer to an infinite number >>>>>> of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The >>>>>> residual tolerances are set conservatively based on these input values. >>>>>> >>>>>> >>>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>>> >>>>>> >>>>>> You have 17 iterations for the moment equations. >>>>>> >>>>>> >>>>>> You have 120 iterations for pressure. Again, your tolerances are too tight >>>>>> for engineering calculations -- you do not need 1.e-10 for divergence (i.e., >>>>>> for the pressure residual tolerance). >>>>>> >>>>>> >>>>>> hth, >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> ________________________________ >>>>>> From: Nek5000-users on behalf of >>>>>> nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Friday, March 30, 2018 4:52:26 AM >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: Re: [Nek5000-users] logfile >>>>>> >>>>>> The following is my logfile entry (sample lines). The first line is >>>>>> understandable. What do the values in the third and following lines >>>>>> denote? >>>>>> >>>>>> >>>>>> ------------------------------------------------------ >>>>>> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >>>>>> 3.5403E+00 >>>>>> Solving for Hmholtz scalars >>>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>>> 1520 Scalars done 7.6000E-02 8.3823E-02 >>>>>> Solving for fluid >>>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>>> 1520 Fluid done 7.6000E-02 3.3650E+00 >>>>>> -------------------------------------------------------- >>>>>> >>>>>>> On Fri, Mar 30, 2018 at 3:05 PM, wrote: >>>>>>> I am not sure what you are talking about? >>>>>>> >>>>>>> -----Original message----- >>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>> Sent: Friday 30th March 2018 10:30 >>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>> Subject: [Nek5000-users] logfile >>>>>>>> >>>>>>>> Hi Neks, >>>>>>>> >>>>>>>> What are the entries in the logfile that is output from running >>>>>>>> the code. Please let me know where the entries are determined in the >>>>>>>> code. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Swarandeep >>>>>>>> _______________________________________________ >>>>>>>> Nek5000-users mailing list >>>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Nek5000-users mailing list >>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Mar 31 13:50:42 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 20:50:42 +0200 Subject: [Nek5000-users] Guidelines for Tolerances In-Reply-To: References: Message-ID: Yes this is for PnPn only. Sorry for the confusion. > On 31 Mar 2018, at 20:49, "nek5000-users at lists.mcs.anl.gov" wrote: > > ah ok, that comment was related to PnPn? > >> On 2018-03-31 20:44, nek5000-users at lists.mcs.anl.gov wrote: >> In the PnPn formulation you don?t project into a divergence free space so you don?t prescribe the divergence. It?s a simulation result. >> >>> On 31 Mar 2018, at 19:09, "nek5000-users at lists.mcs.anl.gov" wrote: >>> >>> I guess in the end the chosen/requested tolerances depend on what one is >>> interested in, and how sensitive a specific flow case is. Also, the >>> spatial distribution of the divergence error might be an interesting >>> quantity to look at. >>> >>> However, I have a question to Stefan: I am not sure I fully understand >>> your comment regarding spatial resolution. Do you mean that the spatial >>> errors are so large that a specific divergence tolerance cannot be >>> fulfilled? >>> >>> Philipp >>> >>>> On 2018-03-31 11:20, nek5000-users at lists.mcs.anl.gov wrote: >>>> Your tolerances look good to me. Typically 1e-5 for pressure is accurate enough. Note, in the Pn/Pn-2 formulation the tolerance is equivalent to the desired divergence error. This is in contract to Pn/Pn where such a relation does not exists. In most cases the divergence error is dominated by the spatial resolution. That's something you can try - just lower the tol to say 1e-5. If you'll get a similiar divergence error (compared to 1e-8) try to lower it even further. >>>> >>>> -- >>>> Stefan >>>> >>>> >>>> -----Original message----- >>>>> From:nek5000-users at lists.mcs.anl.gov >>>>> Sent: Saturday 31st March 2018 11:07 >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: [Nek5000-users] Guidelines for Tolerances >>>>> >>>>> Dear Nek experts, >>>>> >>>>> sorry, my first mail was incomplete. I will start again. >>>>> >>>>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>>>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>>>> >>>>> In the par file, I set residualTol = 1e-08 for pressure velocity and all thermal fields. Having read the recent discussion about another logfile, I was wondering whether these settings might be too tight. >>>>> >>>>> The log for one timestep is given below (sorry about the formatting). >>>>> As you can see, I need 16 - 21 iterations for the scalar fields of Pr=0.025. >>>>> Do you think I could reduce the residualTol for the low Pr fields to speedup the simulation? >>>>> >>>>> Best regards, >>>>> Steffen >>>>> >>>>> >>>>> Step 99999, t= 8.4999900E+02, DT= 1.0000000E-03, C= 0.291 3.3389E+04 3.2523E-01 >>>>> Solving for Hmholtz scalars >>>>> 99999 Project TEMP 9.7160E-08 5.5444E+00 5.7064E+07 8 8 >>>>> 99999 Hmholtz TEMP 6 8.0673E-09 3.1410E-05 1.0000E-08 >>>>> 99999 Project PS 1 1.9038E-07 6.6127E+00 3.4734E+07 8 8 >>>>> 99999 Hmholtz PS 1 7 6.2818E-09 6.1081E-05 1.0000E-08 >>>>> 99999 Project PS 2 5.7194E-06 1.1100E+01 1.9408E+06 7 8 >>>>> 99999 Hmholtz PS 2 8 4.7345E-09 1.5839E-03 1.0000E-08 >>>>> 99999 Project PS 3 1.6110E-09 2.0874E-01 1.2958E+08 8 8 >>>>> 99999 Hmholtz PS 3 16 8.1941E-09 6.8549E-07 1.0000E-08 >>>>> 99999 Project PS 4 1.8743E-09 2.5528E-01 1.3620E+08 8 8 >>>>> 99999 Hmholtz PS 4 16 9.3461E-09 7.7774E-07 1.0000E-08 >>>>> 99999 Project PS 5 4.9138E-08 4.4469E-01 9.0499E+06 7 8 >>>>> 99999 Hmholtz PS 5 21 8.2110E-09 1.3142E-05 1.0000E-08 >>>>> 99999 Scalars done 8.5000E+02 1.7601E-01 >>>>> Solving for fluid >>>>> 99999 Project VELX 5.5774E-09 6.9874E-03 1.2528E+06 8 8 >>>>> 99999 Hmholtz VELX 4 2.7784E-09 1.7303E-06 1.0000E-08 >>>>> 99999 Project VELY 5.4643E-09 6.9118E-03 1.2649E+06 8 8 >>>>> 99999 Hmholtz VELY 4 2.7477E-09 1.6969E-06 1.0000E-08 >>>>> 99999 Project VELZ 5.0326E-09 6.9213E-03 1.3753E+06 8 8 >>>>> 99999 Hmholtz VELZ 4 6.0439E-09 2.0347E-06 1.0000E-08 >>>>> 99999 Project PRES 1.5397E-04 9.8607E-02 6.4043E+02 14 20 >>>>> 99999 U-PRES gmres 13 9.9860E-09 8.3983E-08 1.0000E-08 4.3257E-02 7.0065E-02 >>>>> 99999 volflow Z 1.8796E-02 8.0416E-06 7.8539E-01 7.8540E-01 >>>>> 99999 Fluid done 8.5000E+02 1.2875E-01 >>>>> ________________________________________ >>>>> Von: Straub, Steffen (ISTM) >>>>> Gesendet: Samstag, 31. M?rz 2018 10:45 >>>>> An: nek5000-users at lists.mcs.anl.gov >>>>> Betreff: AW: Nek5000-users Digest, Vol 109, Issue 32 >>>>> >>>>> Dear Nek experts, >>>>> >>>>> I am simulating turbulent pipe flow with 6 thermal fields treated as passive scalars. >>>>> The first three thermal fields use Pr=0.71 and the remaining three use Pr=0.025. >>>>> >>>>> >>>>> ________________________________________ >>>>> Von: Nek5000-users im Auftrag von nek5000-users-request at lists.mcs.anl.gov >>>>> Gesendet: Freitag, 30. M?rz 2018 17:02 >>>>> An: nek5000-users at lists.mcs.anl.gov >>>>> Betreff: Nek5000-users Digest, Vol 109, Issue 32 >>>>> >>>>> 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: logfile (nek5000-users at lists.mcs.anl.gov) >>>>> 2. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>>> 3. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>>> 4. Re: logfile (nek5000-users at lists.mcs.anl.gov) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Fri, 30 Mar 2018 15:34:49 +0200 >>>>> From: nek5000-users at lists.mcs.anl.gov >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> Subject: Re: [Nek5000-users] logfile >>>>> Message-ID: >>>>> >>>>> Content-Type: text/plain; charset=utf-8 >>>>> >>>>> That par file doesn't currently support a relative and absolute tolerance for the Helmholtz solver. I think there are two options to tackle your tolerance problem: >>>>> >>>>> * Specify the parameters below in usrdat3 of your usr file. >>>>> * Solve a non-dimensional problem and use a residual tolerance of e.g. 1e-8 (for velocity and temp) and 1e-5 for pressure >>>>> >>>>> -- >>>>> Stefan >>>>> >>>>> -----Original message----- >>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>> Sent: Friday 30th March 2018 14:19 >>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>> Subject: Re: [Nek5000-users] logfile >>>>>> >>>>>> Thanks, Paul, >>>>>> Could you please tell me the parameters in terms of ###.par file. >>>>>> I am using the latest version. >>>>>> >>>>>> Thank you >>>>>> >>>>>>> On Fri, Mar 30, 2018 at 5:35 PM, wrote: >>>>>>> >>>>>>> >>>>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>>>> >>>>>>> >>>>>>> On Step 1520, it took 12 iterations to reach a residual of 3.8e-11, starting >>>>>>> with a residual of 4.5e7, with target residual 1.e-10. >>>>>>> >>>>>>> >>>>>>> [ This is actually too tight of a tolerance, since you are asking for 17 >>>>>>> orders of magnitude reduction in residual and are working only with 16 >>>>>>> significant digits. It seems like you might need to change your .rea file in >>>>>>> the following way: >>>>>>> >>>>>>> >>>>>>> set p21 and p22 to 0 >>>>>>> >>>>>>> >>>>>>> set p24, tolrel , to 1.e-3 >>>>>>> >>>>>>> set p25, tolabs, to 1.e-3 >>>>>>> >>>>>>> >>>>>>> The only time you'll need tolrel/abs tighter than this is if you're doing an >>>>>>> analytic convergence study where you know the answer to an infinite number >>>>>>> of digits. For engineering calculations, 1.e-2 to 1.e-3 is fine. The >>>>>>> residual tolerances are set conservatively based on these input values. >>>>>>> >>>>>>> >>>>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>>>> >>>>>>> >>>>>>> You have 17 iterations for the moment equations. >>>>>>> >>>>>>> >>>>>>> You have 120 iterations for pressure. Again, your tolerances are too tight >>>>>>> for engineering calculations -- you do not need 1.e-10 for divergence (i.e., >>>>>>> for the pressure residual tolerance). >>>>>>> >>>>>>> >>>>>>> hth, >>>>>>> >>>>>>> Paul >>>>>>> >>>>>>> >>>>>>> ________________________________ >>>>>>> From: Nek5000-users on behalf of >>>>>>> nek5000-users at lists.mcs.anl.gov >>>>>>> Sent: Friday, March 30, 2018 4:52:26 AM >>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>> Subject: Re: [Nek5000-users] logfile >>>>>>> >>>>>>> The following is my logfile entry (sample lines). The first line is >>>>>>> understandable. What do the values in the third and following lines >>>>>>> denote? >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------ >>>>>>> Step 1520, t= 7.6000000E-02, DT= 5.0000000E-05, C= 0.072 5.3831E+03 >>>>>>> 3.5403E+00 >>>>>>> Solving for Hmholtz scalars >>>>>>> 1520 Hmholtz TEMP 12 3.8789E-11 4.5120E+07 1.0000E-10 >>>>>>> 1520 Scalars done 7.6000E-02 8.3823E-02 >>>>>>> Solving for fluid >>>>>>> 1520 Helmh3 fluid 17 3.6594E-11 4.7524E-01 1.0000E-10 >>>>>>> 1520 U-PRES gmres 120 1.3494E-08 4.5675E-06 >>>>>>> 1.0000E-10 7.8799E-01 3.0171E+00 >>>>>>> 1520 Fluid done 7.6000E-02 3.3650E+00 >>>>>>> -------------------------------------------------------- >>>>>>> >>>>>>>> On Fri, Mar 30, 2018 at 3:05 PM, wrote: >>>>>>>> I am not sure what you are talking about? >>>>>>>> >>>>>>>> -----Original message----- >>>>>>>>> From:nek5000-users at lists.mcs.anl.gov >>>>>>>>> Sent: Friday 30th March 2018 10:30 >>>>>>>>> To: nek5000-users at lists.mcs.anl.gov >>>>>>>>> Subject: [Nek5000-users] logfile >>>>>>>>> >>>>>>>>> Hi Neks, >>>>>>>>> >>>>>>>>> What are the entries in the logfile that is output from running >>>>>>>>> the code. Please let me know where the entries are determined in the >>>>>>>>> code. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Swarandeep >>>>>>>>> _______________________________________________ >>>>>>>>> Nek5000-users mailing list >>>>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Nek5000-users mailing list >>>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>> _______________________________________________ >>>>>>> Nek5000-users mailing list >>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Nek5000-users mailing list >>>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>>> >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sat Mar 31 19:41:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 31 Mar 2018 20:41:15 -0400 Subject: [Nek5000-users] Coefficient multiplying the advection term Message-ID: Hey Neks, I have a general question. I want to multiply my advection term, that is u.\grad u with a small constant co-efficient in the momentum equation. I would like to know how to make this change. 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: