From nek5000-users at lists.mcs.anl.gov Tue Jul 1 05:08:53 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 01 Jul 2014 12:08:53 +0200 Subject: [Nek5000-users] SFD error message from p66 In-Reply-To: References: Message-ID: Hi Adam, thank you very much. I have solved the problem that I posted here about the SFD code and now it seems to work. However, I'm still doing some tests to validate the code. It will take me some more time. If you agree, I think it would be nice to discuss in private about these two versions of the SFD code. I will let you know how this code works and we could compare this version with your code. Regarding the error that I posted, the problem was not related with param 66, but with the dimension of the variables. In the correct version of the code: ntot=nx1*ny1*nz1*nelv call rzero(vx,ntot) However, in the wrong version I was defining ntot as: ntot=nx1*ny1*nz1*nz1*nelv The wrong definition of the dimensions of the velocity vector was leading to the error that I posted. Regards SL El 30-06-2014 09:51, nek5000-users at lists.mcs.anl.gov escribi?: > Hi SL > > We have implemented SFD some time ago and we can share the code if you > wish. It is probably good to have single tested version of the code > than develop number of variations. We've already shared the code with > Elia. > Regards > Adam > > > On 27/06/14 17:28, nek5000-users at lists.mcs.anl.gov wrote: >> Dear Nek's, >> >> I'm trying to program a Selective Frequency Damping following the >> article of Akervik et. al (Physics of Fluids, 2006) and some Nek5000 >> posts. >> >> I'm able to compile the code, however, when I try to run my >> simulation, I find the following error message: >> >> 0 0.0000E+00 Write checkpoint: >> >> 0 0.0000E+00 OPEN: >> At line 335 of file User/nek5_svn/trunk/nek/prepost.f (unit = 24, file >> = '') >> Fortran runtime error: File '' does not exist >> >> It seems to be something related to param 66. I've tried with p66=6, >> 0, 1, -1, but I always get the same error. >> >> Do you know what happens? >> >> Thanks >> SL >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/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 Tue Jul 1 06:56:44 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 01 Jul 2014 13:56:44 +0200 Subject: [Nek5000-users] Error in generalev with MHD In-Reply-To: References: Message-ID: Hello Neks, I' trying to solve the MHD equations and encounter the same error reported here: http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-June/001365.html. For testing, I have set up a small grid (384 elements) with B=0 at the boundaries and B=0 as initial conditions, and the error appears before the first timestep. As mentioned in the documentation, I have used the same BC-types for the B Field as for the velocity, so in the .rea file it reads: 5909 ***** PASSIVE SCALAR 1 BOUNDARY CONDITIONS ***** 5910 E 1 1 0.00000 0.00000 0.00000 0.00000 0.00000 5911 E 1 2 0.00000 0.00000 0.00000 0.00000 0.00000 5912 V 1 3 0.00000 0.00000 0.00000 0.00000 0.00000 5913 E 1 4 0.00000 0.00000 0.00000 0.00000 0.00000 5914 E 1 5 0.00000 0.00000 0.00000 0.00000 0.00000 5915 E 1 6 0.00000 0.00000 0.00000 0.00000 0.00000 5916 E 2 1 0.00000 0.00000 0.00000 0.00000 0.00000 5917 E 2 2 0.00000 0.00000 0.00000 0.00000 0.00000 5918 E 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 5919 E 2 4 0.00000 0.00000 0.00000 0.00000 0.00000 5920 E 2 5 0.00000 0.00000 0.00000 0.00000 0.00000 5921 E 2 6 0.00000 0.00000 0.00000 0.00000 0.00000 5922 E 3 1 0.00000 0.00000 0.00000 0.00000 0.00000 5923 E 3 2 0.00000 0.00000 0.00000 0.00000 0.00000 5924 E 3 3 0.00000 0.00000 0.00000 0.00000 0.00000 5925 E 3 4 0.00000 0.00000 0.00000 0.00000 0.00000 5926 E 3 5 0.00000 0.00000 0.00000 0.00000 0.00000 5927 E 3 6 0.00000 0.00000 0.00000 0.00000 0.00000 5928 v 4 1 0.00000 0.00000 0.00000 0.00000 0.00000 5929 E 4 2 0.00000 0.00000 0.00000 0.00000 0.00000 5930 E 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 etc. The thread above mentioned that it was due to incorrect BCs, but unfortunately no more details were given. Cheers, Jan From nek5000-users at lists.mcs.anl.gov Tue Jul 1 07:51:02 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 01 Jul 2014 14:51:02 +0200 Subject: [Nek5000-users] Error in generalev with MHD In-Reply-To: References: Message-ID: Hi Jan, On line 5912, velocity BC is written with capital letter V instead of small letter v (as in 5928). If you write velocity with small letter, it'll read the BC in the .usr file (userbc subroutine), otherwise you have to specify the values of velocity in the .rea file. In addition, in the elements (E) BC you have to specify E n1 n2 n3 n4 0 0 0 n1: Number of element n2: side of element n3: element connected n4: side of the element connected. However, you've set n3 and n4 to 0. I hope it helps you. Regards, SL El 01-07-2014 13:56, nek5000-users at lists.mcs.anl.gov escribi?: > Hello Neks, > I' trying to solve the MHD equations and encounter the same error > reported here: > http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-June/001365.html. > For testing, I have set up a small grid (384 elements) with B=0 at the > boundaries and B=0 as initial conditions, and the error appears before > the first timestep. As mentioned in the documentation, I have used the > same BC-types for the B Field as for the velocity, so in the .rea file > it reads: > > 5909 ***** PASSIVE SCALAR 1 BOUNDARY CONDITIONS ***** > 5910 E 1 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5911 E 1 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5912 V 1 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5913 E 1 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5914 E 1 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5915 E 1 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5916 E 2 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5917 E 2 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5918 E 2 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5919 E 2 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5920 E 2 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5921 E 2 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5922 E 3 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5923 E 3 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5924 E 3 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5925 E 3 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5926 E 3 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5927 E 3 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5928 v 4 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5929 E 4 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5930 E 4 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > etc. > > The thread above mentioned that it was due to incorrect BCs, but > unfortunately no more details were given. > > Cheers, > Jan > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Jul 1 08:02:34 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 01 Jul 2014 15:02:34 +0200 Subject: [Nek5000-users] Error in generalev with MHD In-Reply-To: References: Message-ID: Hey, thanks for the suggestions. I want to change some of the boundarie values to values =!0 for the actual simulations, that's why there is a mix of small and capital V's. However, userbc sets the bc to zero. I will try to use only one of the two, in case there is a problem with mixing v and V. As far as I know, the specification for the Element-Element-Boundary (E) you mentioned is outdated and handled by the solver. I have run several hydrodynamic simulations with 0 for the options and never encountered any problems. Am 01.07.14 14:51, schrieb nek5000-users at lists.mcs.anl.gov: > Hi Jan, > > On line 5912, velocity BC is written with capital letter V instead of > small letter v (as in 5928). > > If you write velocity with small letter, it'll read the BC in the .usr > file (userbc subroutine), otherwise you have to specify the values of > velocity in the .rea file. > > In addition, in the elements (E) BC you have to specify > > E n1 n2 n3 n4 0 0 0 > n1: Number of element > n2: side of element > n3: element connected > n4: side of the element connected. > > However, you've set n3 and n4 to 0. > > I hope it helps you. > > Regards, > SL > > > > El 01-07-2014 13:56, nek5000-users at lists.mcs.anl.gov escribi?: >> Hello Neks, >> I' trying to solve the MHD equations and encounter the same error >> reported here: >> http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-June/001365.html. >> For testing, I have set up a small grid (384 elements) with B=0 at the >> boundaries and B=0 as initial conditions, and the error appears before >> the first timestep. As mentioned in the documentation, I have used the >> same BC-types for the B Field as for the velocity, so in the .rea file >> it reads: >> >> 5909 ***** PASSIVE SCALAR 1 BOUNDARY CONDITIONS ***** >> 5910 E 1 1 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5911 E 1 2 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5912 V 1 3 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5913 E 1 4 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5914 E 1 5 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5915 E 1 6 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5916 E 2 1 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5917 E 2 2 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5918 E 2 3 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5919 E 2 4 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5920 E 2 5 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5921 E 2 6 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5922 E 3 1 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5923 E 3 2 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5924 E 3 3 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5925 E 3 4 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5926 E 3 5 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5927 E 3 6 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5928 v 4 1 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5929 E 4 2 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> 5930 E 4 3 0.00000 0.00000 0.00000 0.00000 >> 0.00000 >> etc. >> >> The thread above mentioned that it was due to incorrect BCs, but >> unfortunately no more details were given. >> >> Cheers, >> Jan >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/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 Tue Jul 1 08:06:52 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Jul 2014 13:06:52 +0000 Subject: [Nek5000-users] Error in generalev with MHD In-Reply-To: References: , Message-ID: Hi Jan and SL, Good point, SL, about the line 5912 but I suspect the problem lies in the fact that in our MHD implementation we only focused on 'v ' type boundary condition and hot on 'V ' so, Jan, I suggest to modify 'V ' to 'v ' and use userbc() to set zero BC for ifield=ifldmhd Let me know if you have any questions. Aleks ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, July 01, 2014 7:51 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Error in generalev with MHD Hi Jan, On line 5912, velocity BC is written with capital letter V instead of small letter v (as in 5928). If you write velocity with small letter, it'll read the BC in the .usr file (userbc subroutine), otherwise you have to specify the values of velocity in the .rea file. In addition, in the elements (E) BC you have to specify E n1 n2 n3 n4 0 0 0 n1: Number of element n2: side of element n3: element connected n4: side of the element connected. However, you've set n3 and n4 to 0. I hope it helps you. Regards, SL El 01-07-2014 13:56, nek5000-users at lists.mcs.anl.gov escribi?: > Hello Neks, > I' trying to solve the MHD equations and encounter the same error > reported here: > http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-June/001365.html. > For testing, I have set up a small grid (384 elements) with B=0 at the > boundaries and B=0 as initial conditions, and the error appears before > the first timestep. As mentioned in the documentation, I have used the > same BC-types for the B Field as for the velocity, so in the .rea file > it reads: > > 5909 ***** PASSIVE SCALAR 1 BOUNDARY CONDITIONS ***** > 5910 E 1 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5911 E 1 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5912 V 1 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5913 E 1 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5914 E 1 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5915 E 1 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5916 E 2 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5917 E 2 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5918 E 2 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5919 E 2 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5920 E 2 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5921 E 2 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5922 E 3 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5923 E 3 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5924 E 3 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5925 E 3 4 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5926 E 3 5 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5927 E 3 6 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5928 v 4 1 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5929 E 4 2 0.00000 0.00000 0.00000 0.00000 > 0.00000 > 5930 E 4 3 0.00000 0.00000 0.00000 0.00000 > 0.00000 > etc. > > The thread above mentioned that it was due to incorrect BCs, but > unfortunately no more details were given. > > Cheers, > Jan > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Jul 2 07:49:14 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 02 Jul 2014 14:49:14 +0200 Subject: [Nek5000-users] Error in generalev with MHD In-Reply-To: References: Message-ID: Hello again, I changed all BC's for the magnetic field to 'v' and used userbc to set the value to zero, but the error popped up again. The output reads: 216 Matrix: 0 aa 6 6 6 217 0 aa 7.80579E+01 -6.39449E+01 1.81958E+01 -7.90484E+00 2.16525E+00 0.00000E+00 218 0 aa -6.39449E+01 8.67803E+01 -4.74885E+01 1.84117E+01 -1.07792E+01 5.66872E+00 219 0 aa 1.81958E+01 -4.74885E+01 5.96643E+01 -4.03684E+01 3.02051E+01 -2.06952E+01 220 0 aa -7.90484E+00 1.84117E+01 -4.03684E+01 6.64609E+01 -7.64969E+01 4.76373E+01 221 0 aa 2.16525E+00 -1.07792E+01 3.02051E+01 -7.64969E+01 1.90127E+02 -1.67410E+02 222 0 aa 0.00000E+00 5.66872E+00 -2.06952E+01 4.76373E+01 -1.67410E+02 Infinity 223 224 Matrix: 0 bb 6 6 6 225 0 bb 7.19606E-02 9.84283E-03 -2.07087E-03 -1.02002E-03 7.34397E-04 0.00000E+00 226 0 bb 9.84283E-03 4.07143E-02 -4.22288E-03 7.31377E-03 -3.21920E-03 0.00000E+00 227 0 bb -2.07087E-03 -4.22288E-03 1.05630E-01 -1.61560E-02 6.44826E-03 0.00000E+00 228 0 bb -1.02002E-03 7.31377E-03 -1.61560E-02 1.05960E-01 -6.21764E-03 0.00000E+00 229 0 bb 7.34397E-04 -3.21920E-03 6.44826E-03 -6.21764E-03 5.05023E-02 0.00000E+00 230 0 bb 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 NaN 231 232 Matrix: 0 Aeig 6 6 6 233 0 Aeig NaN NaN NaN NaN NaN NaN 234 0 Aeig NaN NaN NaN NaN NaN NaN 235 0 Aeig NaN NaN NaN NaN NaN NaN 236 0 Aeig NaN NaN NaN NaN NaN NaN 237 0 Aeig NaN NaN NaN NaN NaN NaN 238 0 Aeig NaN NaN NaN NaN NaN NaN 239 240 Matrix: 0 Deig 1 6 6 241 0 Deig NaN NaN NaN NaN NaN NaN 242 Error in generalev, info= 5 6 1 243 244 call exitt: dying ... So the problem is probably the NaN and Inf entries. As a next step, I took the gpf example as a starting point, copy pasted my own grid and bc descriptions, set the bc's to zero in the usr-file and removed the Temperaturefield. This produced the same error. Can this be linked to the absence of the temperature field? If I leave out the B-Field the case is running just fine, altough the BC's are the same in the *.rea file. Jan From nek5000-users at lists.mcs.anl.gov Wed Jul 2 11:36:04 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Jul 2014 18:36:04 +0200 Subject: [Nek5000-users] n2to3 for axisymmetry mesh In-Reply-To: References: Message-ID: Hi Nekers, Do you have any experience on generating an axisymmetry mesh via "n2to3"? Now I want to extrude a 2D mesh into a 3D axisymmetry mesh. I found that the rotating axis is y-axis, does anyone know to define the rotating axis into x-directiong? when I keep the default rotating axis (y-direction) , n2to3 only works when there is no edge coincide with the y-axis. in this situation, there is a hole in the center, which is obvious wrong. For example, this is the 2D genbox file. 1 base.rea 2 2 spatial dimension (if negative dump binary re2 and .rea file) 3 1 number of fields 4 # 5 #======================================================================= 6 # 7 box_1 any string with 1st character .ne. "c" or "C" 8 -8 -4 1 nelx,nely,nelz (if <0, length to be equally divided) 9 -0.0 2.0 1. x_0 x_Nelx ratio 10 -0.5 0.5 1. 11 v ,O ,W ,W bc's ! west,east,south,north,bottom,top (fixed 3CHAR format) I want make an axisymmetry tube with the center line is y=0. I know the genbox can extrude a circle face into a tube. but here I want first try to this simple case. Since the mesh is axisymmetric, I choose the boundary type of Z(5) and Z(6) as "E". It can generated the 3D.rea. but after I run genmap, it failed, even I try the much smaller tolerance. NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.1 reading .rea file data ... start locglob_lexico: 8 640 5120 0.10000000000000001 locglob: 1 1 5120 locglob: 2 55 5120 locglob: 3 161 5120 locglob: 1 805 5120 locglob: 2 805 5120 locglob: 3 805 5120 locglob: 1 805 5120 locglob: 2 805 5120 locglob: 3 805 5120 1 2 4 Matrix: SELF!! 1 SELF!! 401 402 401 402 2 SELF!! 506 507 491 492 cont: SELF!! 1 ?? ABORT: SELF-CHK 1 5 1 0 Try to tighten the mesh tolerance! 0 quit ========================================== so does anyone know how to solve it or use some third party tools? thanks Alberto. From nek5000-users at lists.mcs.anl.gov Mon Jul 7 09:37:51 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 7 Jul 2014 14:37:51 +0000 Subject: [Nek5000-users] T-junction with two outlets Message-ID: Hi Neks, I?m working on a simulation involving ducted flow of a t-jucntion with an inlet and two outlets. I want to be able to control the mass flow through one of the outlets. Has anyone every dealt with this issue, or are there any suggestion of how to write a subroutine to do this? Thanks, Ravon From nek5000-users at lists.mcs.anl.gov Mon Jul 7 09:55:56 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 7 Jul 2014 14:55:56 +0000 Subject: [Nek5000-users] T-junction with two outlets In-Reply-To: References: Message-ID: Ravon, See the paper with Loth & Bassiouny on my webpage: www.mcs.anl.gov/~fischer/pubhtml/high_re.pdf I'll see if I can find the routines that allow you to control the flow split. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, July 07, 2014 9:37 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] T-junction with two outlets Hi Neks, I?m working on a simulation involving ducted flow of a t-jucntion with an inlet and two outlets. I want to be able to control the mass flow through one of the outlets. Has anyone every dealt with this issue, or are there any suggestion of how to write a subroutine to do this? Thanks, Ravon _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Jul 7 12:27:52 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 7 Jul 2014 17:27:52 +0000 Subject: [Nek5000-users] T-junction with two outlets In-Reply-To: References: Message-ID: Hi Paul, Thank you for the paper, very helpful. If you can find the routines that will be great, but in the meantime I?ll try to write the subroutines using the method discussed in the paper Thanks again, Ravon On Jul 7, 2014, at 10:55 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Ravon, > > See the paper with Loth & Bassiouny on my webpage: > > www.mcs.anl.gov/~fischer/pubhtml/high_re.pdf > > I'll see if I can find the routines that allow you to control the flow split. > > Paul > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Monday, July 07, 2014 9:37 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] T-junction with two outlets > > Hi Neks, > I?m working on a simulation involving ducted flow of a t-jucntion with an inlet and two outlets. > I want to be able to control the mass flow through one of the outlets. > Has anyone every dealt with this issue, or are there any suggestion > of how to write a subroutine to do this? > > Thanks, > Ravon > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/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 Tue Jul 8 10:13:22 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 08 Jul 2014 11:13:22 -0400 Subject: [Nek5000-users] Governing equations Message-ID: Hi, I want to know the equations solved by the code; for example time stepping.. How can I find them? Where are they in the files? Thanks Arash From nek5000-users at lists.mcs.anl.gov Wed Jul 9 05:57:50 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Jul 2014 10:57:50 +0000 Subject: [Nek5000-users] Error when creating own mesh Message-ID: Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 9 08:29:36 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Jul 2014 13:29:36 +0000 Subject: [Nek5000-users] Error when creating own mesh In-Reply-To: References: Message-ID: Dear Friedrich, I recommend running "diff" on the example file and your file. Assuming that the example file works you should then be close to understanding the source of difficulty. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Wednesday, July 09, 2014 5:57 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Error when creating own mesh Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 10 13:05:07 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Jul 2014 20:05:07 +0200 Subject: [Nek5000-users] failed to write derivatives in one file In-Reply-To: References: Message-ID: Dear all, I tried to write all the velocity derivatives into one file, so I added some lines of code into the prepost.f, like subroutine outpost3(v1,v2,v3 $,v4,v5,v6 $,v7,v8,v9 $,vp,vt,name3) include 'SIZE' include 'INPUT' real v1(1),v2(1),v3(1),vp(1),vt(1) real v4(1),v5(1),v6(1) real v7(1),v8(1),v9(1) character*3 name3 itmp=0 if (ifto) itmp=1 call outpost4(v1,v2,v3 $,v4,v5,v6 $,v7,v8,v9 $,vp,vt,itmp,name3) return end c------------------------------------------ subroutine outpost4(v1,v2,v3 $,v4,v5,v6 $,v7,v8,v9 $,vp,vt,nfldt,name3) character*3 name3 logical if_save(ldimt) c ntot1 = nx1*ny1*nz1*nelv ntot1t = nx1*ny1*nz1*nelt ntot2 = nx2*ny2*nz2*nelv if(nfldt.gt.ldimt) then write(6,*) 'ABORT: outpost data too large (nfldt>ldimt)!' call exitt endif c store solution call copy(w1,vxx,ntot1) call copy(w2,vxy,ntot1) call copy(w3,vxz,ntot1) call copy(w4,vyx,ntot1) call copy(w5,vyy,ntot1) call copy(w6,vyz,ntot1) call copy(w7,vzx,ntot1) call copy(w8,vzy,ntot1) call copy(w9,vzz,ntot1) call copy(wp,pr,ntot2) do i = 1,nfldt call copy(wt(1,i),t(1,1,1,1,i),ntot1t) enddo c swap with data to dump call copy(vxx,v1,ntot1) call copy(vxy,v2,ntot1) call copy(vxz,v3,ntot1) call copy(vyx,v4,ntot1) call copy(vyy,v6,ntot1) call copy(vyz,v6,ntot1) call copy(vzx,v7,ntot1) call copy(vzy,v8,ntot1) call copy(vzz,v9,ntot1) call copy(pr,vp,ntot2) do i = 1,nfldt call copy(t(1,1,1,1,i),vt(1,i),ntot1t) enddo c dump data if_save(1) = ifto ifto = .false. if(nfldt.gt.0) ifto = .true. do i = 1,ldimt-1 if_save(i+1) = ifpsco(i) ifpsco(i) = .false. if(i+1.le.nfldt) ifpsco(i) = .true. enddo call prepost(.true.,name3) ifto = if_save(1) do i = 1,ldimt-1 ifpsco(i) = if_save(i+1) enddo c restore solution data call copy(vxx,w1,ntot1) call copy(vxy,w2,ntot1) call copy(vxz,w3,ntot1) call copy(vyx,w4,ntot1) call copy(vyy,w5,ntot1) call copy(vyz,w6,ntot1) call copy(vzx,w7,ntot1) call copy(vzy,w8,ntot1) call copy(vzz,w9,ntot1) call copy(pr,wp,ntot2) do i = 1,nfldt call copy(t(1,1,1,1,i),wt(1,i),ntot1t) enddo return end c--------------------------- in the userchk file, .................. call gradm1(vxx,vxy,vxz,vx) ..................... call outpost3(vxx,vxy,vxz $,vyx,vyy,vyz $,vzx,vzy,vzz $,pr,t,'derivate') ................... there are errors, like this: /Users/wei/nek5_svn/trunk/nek/prepost.f:1998.34: subroutine outpost3(v1,v2,v3 1 Error: Unexpected junk in formal argument list at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:1999.8: $,v4,v5,v6 1 Error: Invalid character in name at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:2001.8: $,vp,vt,name3) 1 Error: Invalid character in name at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:2017.72: $,v7,v8,v9 1 Error: Syntax error in argument list at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:2018.8: $,vp,vt,itmp,name3) 1 Error: Invalid character in name at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:2025.15: $,v7,v8,v9 1 Error: Unexpected junk in formal argument list at (1) /Users/wei/nek5_svn/trunk/nek/prepost.f:2026.8: $,vp,vt,nfldt,name3) 1 Error: Invalid character in name at (1) SIZE:5.72: Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2003: parameter (ldim=3) 1 SIZE:5.72: Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2028: parameter (ldim=3) 2 Error: Two main PROGRAMs at (1) and (2) make: *** [obj/prepost.o] Error 1 so what should I do? Thanks, Wei From nek5000-users at lists.mcs.anl.gov Thu Jul 10 13:22:12 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Jul 2014 13:22:12 -0500 (CDT) Subject: [Nek5000-users] failed to write derivatives in one file In-Reply-To: References: Message-ID: Dear Wei, I would just user outpost and control the fields that are written via ifto, ifxyo, ifvo, ifpo, etc. parameter (l=lx1*ly1*lz1*lelt) common /mystuff/ u1(l),u2(l),u3(l) call gradm1(u1,u2,u3,vx) call outpost(u1,u2,u3,pr,t,'vxd') call gradm1(u1,u2,u3,vy) call outpost(u1,u2,u3,pr,t,'vyd') call gradm1(u1,u2,u3,vz) call outpost(u1,u2,u3,pr,t,'vzd') would do the job. Paul On Thu, 10 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > Dear all, > > I tried to write all the velocity derivatives into one file, so I added some lines of code into the prepost.f, like > > subroutine outpost3(v1,v2,v3 > $,v4,v5,v6 > $,v7,v8,v9 > $,vp,vt,name3) > > include 'SIZE' > include 'INPUT' > > real v1(1),v2(1),v3(1),vp(1),vt(1) > real v4(1),v5(1),v6(1) > real v7(1),v8(1),v9(1) > character*3 name3 > > > itmp=0 > if (ifto) itmp=1 > call outpost4(v1,v2,v3 > $,v4,v5,v6 > $,v7,v8,v9 > $,vp,vt,itmp,name3) > > return > end > c------------------------------------------ > subroutine outpost4(v1,v2,v3 > $,v4,v5,v6 > $,v7,v8,v9 > $,vp,vt,nfldt,name3) > character*3 name3 > logical if_save(ldimt) > c > ntot1 = nx1*ny1*nz1*nelv > ntot1t = nx1*ny1*nz1*nelt > ntot2 = nx2*ny2*nz2*nelv > > if(nfldt.gt.ldimt) then > write(6,*) 'ABORT: outpost data too large (nfldt>ldimt)!' > call exitt > endif > > c store solution > call copy(w1,vxx,ntot1) > call copy(w2,vxy,ntot1) > call copy(w3,vxz,ntot1) > call copy(w4,vyx,ntot1) > call copy(w5,vyy,ntot1) > call copy(w6,vyz,ntot1) > call copy(w7,vzx,ntot1) > call copy(w8,vzy,ntot1) > call copy(w9,vzz,ntot1) > call copy(wp,pr,ntot2) > do i = 1,nfldt > call copy(wt(1,i),t(1,1,1,1,i),ntot1t) > enddo > c swap with data to dump > call copy(vxx,v1,ntot1) > call copy(vxy,v2,ntot1) > call copy(vxz,v3,ntot1) > call copy(vyx,v4,ntot1) > call copy(vyy,v6,ntot1) > call copy(vyz,v6,ntot1) > call copy(vzx,v7,ntot1) > call copy(vzy,v8,ntot1) > call copy(vzz,v9,ntot1) > call copy(pr,vp,ntot2) > do i = 1,nfldt > call copy(t(1,1,1,1,i),vt(1,i),ntot1t) > enddo > > c dump data > if_save(1) = ifto > ifto = .false. > if(nfldt.gt.0) ifto = .true. > do i = 1,ldimt-1 > if_save(i+1) = ifpsco(i) > ifpsco(i) = .false. > if(i+1.le.nfldt) ifpsco(i) = .true. > enddo > > call prepost(.true.,name3) > > ifto = if_save(1) > do i = 1,ldimt-1 > ifpsco(i) = if_save(i+1) > enddo > > c restore solution data > call copy(vxx,w1,ntot1) > call copy(vxy,w2,ntot1) > call copy(vxz,w3,ntot1) > call copy(vyx,w4,ntot1) > call copy(vyy,w5,ntot1) > call copy(vyz,w6,ntot1) > call copy(vzx,w7,ntot1) > call copy(vzy,w8,ntot1) > call copy(vzz,w9,ntot1) > call copy(pr,wp,ntot2) > do i = 1,nfldt > call copy(t(1,1,1,1,i),wt(1,i),ntot1t) > enddo > > return > end > c--------------------------- > > in the userchk file, > .................. > call gradm1(vxx,vxy,vxz,vx) > ..................... > call outpost3(vxx,vxy,vxz > $,vyx,vyy,vyz > $,vzx,vzy,vzz > $,pr,t,'derivate') > ................... > > there are errors, like this: > > > > /Users/wei/nek5_svn/trunk/nek/prepost.f:1998.34: > > subroutine outpost3(v1,v2,v3 > 1 > Error: Unexpected junk in formal argument list at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:1999.8: > > $,v4,v5,v6 > 1 > Error: Invalid character in name at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:2001.8: > > $,vp,vt,name3) > 1 > Error: Invalid character in name at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:2017.72: > > $,v7,v8,v9 > 1 > Error: Syntax error in argument list at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:2018.8: > > $,vp,vt,itmp,name3) > 1 > Error: Invalid character in name at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:2025.15: > > $,v7,v8,v9 > 1 > Error: Unexpected junk in formal argument list at (1) > /Users/wei/nek5_svn/trunk/nek/prepost.f:2026.8: > > $,vp,vt,nfldt,name3) > 1 > Error: Invalid character in name at (1) > SIZE:5.72: > Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2003: > > parameter (ldim=3) > 1 > SIZE:5.72: > Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2028: > > parameter (ldim=3) > 2 > Error: Two main PROGRAMs at (1) and (2) > make: *** [obj/prepost.o] Error 1 > > so what should I do? > Thanks, > Wei > _______________________________________________ > 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 Jul 10 13:52:40 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Jul 2014 20:52:40 +0200 Subject: [Nek5000-users] failed to write derivatives in one file In-Reply-To: References: Message-ID: Thank you Paul, I tried this way. It works. the 9 derivatives have been written in 3 independent files. I checked the data format, e.g. "vxd*****", it looks like x y z dux duy duz is it possible to put vyd and vzd together with vxd? like x y z dux duy duz dvx dvy dyz dwx dwy dwz then it will be much convenient to visualize the du in visit. Thank you very much again! Wei On Jul 10, 2014, at 8:22 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Dear Wei, > > I would just user outpost and control the fields that > are written via ifto, ifxyo, ifvo, ifpo, etc. > > parameter (l=lx1*ly1*lz1*lelt) > common /mystuff/ u1(l),u2(l),u3(l) > call gradm1(u1,u2,u3,vx) > call outpost(u1,u2,u3,pr,t,'vxd') > > call gradm1(u1,u2,u3,vy) > call outpost(u1,u2,u3,pr,t,'vyd') > > call gradm1(u1,u2,u3,vz) > call outpost(u1,u2,u3,pr,t,'vzd') > > would do the job. > > Paul > > > On Thu, 10 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear all, >> >> I tried to write all the velocity derivatives into one file, so I added some lines of code into the prepost.f, like >> >> subroutine outpost3(v1,v2,v3 >> $,v4,v5,v6 >> $,v7,v8,v9 >> $,vp,vt,name3) >> >> include 'SIZE' >> include 'INPUT' >> >> real v1(1),v2(1),v3(1),vp(1),vt(1) >> real v4(1),v5(1),v6(1) >> real v7(1),v8(1),v9(1) >> character*3 name3 >> >> >> itmp=0 >> if (ifto) itmp=1 >> call outpost4(v1,v2,v3 >> $,v4,v5,v6 >> $,v7,v8,v9 >> $,vp,vt,itmp,name3) >> >> return >> end >> c------------------------------------------ >> subroutine outpost4(v1,v2,v3 >> $,v4,v5,v6 >> $,v7,v8,v9 >> $,vp,vt,nfldt,name3) >> character*3 name3 >> logical if_save(ldimt) >> c >> ntot1 = nx1*ny1*nz1*nelv >> ntot1t = nx1*ny1*nz1*nelt >> ntot2 = nx2*ny2*nz2*nelv >> >> if(nfldt.gt.ldimt) then >> write(6,*) 'ABORT: outpost data too large (nfldt>ldimt)!' >> call exitt >> endif >> >> c store solution >> call copy(w1,vxx,ntot1) >> call copy(w2,vxy,ntot1) >> call copy(w3,vxz,ntot1) >> call copy(w4,vyx,ntot1) >> call copy(w5,vyy,ntot1) >> call copy(w6,vyz,ntot1) >> call copy(w7,vzx,ntot1) >> call copy(w8,vzy,ntot1) >> call copy(w9,vzz,ntot1) >> call copy(wp,pr,ntot2) >> do i = 1,nfldt >> call copy(wt(1,i),t(1,1,1,1,i),ntot1t) >> enddo >> c swap with data to dump >> call copy(vxx,v1,ntot1) >> call copy(vxy,v2,ntot1) >> call copy(vxz,v3,ntot1) >> call copy(vyx,v4,ntot1) >> call copy(vyy,v6,ntot1) >> call copy(vyz,v6,ntot1) >> call copy(vzx,v7,ntot1) >> call copy(vzy,v8,ntot1) >> call copy(vzz,v9,ntot1) >> call copy(pr,vp,ntot2) >> do i = 1,nfldt >> call copy(t(1,1,1,1,i),vt(1,i),ntot1t) >> enddo >> >> c dump data >> if_save(1) = ifto >> ifto = .false. >> if(nfldt.gt.0) ifto = .true. >> do i = 1,ldimt-1 >> if_save(i+1) = ifpsco(i) >> ifpsco(i) = .false. >> if(i+1.le.nfldt) ifpsco(i) = .true. >> enddo >> >> call prepost(.true.,name3) >> >> ifto = if_save(1) >> do i = 1,ldimt-1 >> ifpsco(i) = if_save(i+1) >> enddo >> >> c restore solution data >> call copy(vxx,w1,ntot1) >> call copy(vxy,w2,ntot1) >> call copy(vxz,w3,ntot1) >> call copy(vyx,w4,ntot1) >> call copy(vyy,w5,ntot1) >> call copy(vyz,w6,ntot1) >> call copy(vzx,w7,ntot1) >> call copy(vzy,w8,ntot1) >> call copy(vzz,w9,ntot1) >> call copy(pr,wp,ntot2) >> do i = 1,nfldt >> call copy(t(1,1,1,1,i),wt(1,i),ntot1t) >> enddo >> >> return >> end >> c--------------------------- >> >> in the userchk file, >> .................. >> call gradm1(vxx,vxy,vxz,vx) >> ..................... >> call outpost3(vxx,vxy,vxz >> $,vyx,vyy,vyz >> $,vzx,vzy,vzz >> $,pr,t,'derivate') >> ................... >> >> there are errors, like this: >> >> >> >> /Users/wei/nek5_svn/trunk/nek/prepost.f:1998.34: >> >> subroutine outpost3(v1,v2,v3 >> 1 >> Error: Unexpected junk in formal argument list at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:1999.8: >> >> $,v4,v5,v6 >> 1 >> Error: Invalid character in name at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:2001.8: >> >> $,vp,vt,name3) >> 1 >> Error: Invalid character in name at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:2017.72: >> >> $,v7,v8,v9 >> 1 >> Error: Syntax error in argument list at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:2018.8: >> >> $,vp,vt,itmp,name3) >> 1 >> Error: Invalid character in name at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:2025.15: >> >> $,v7,v8,v9 >> 1 >> Error: Unexpected junk in formal argument list at (1) >> /Users/wei/nek5_svn/trunk/nek/prepost.f:2026.8: >> >> $,vp,vt,nfldt,name3) >> 1 >> Error: Invalid character in name at (1) >> SIZE:5.72: >> Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2003: >> >> parameter (ldim=3) >> 1 >> SIZE:5.72: >> Included at /Users/wei/nek5_svn/trunk/nek/prepost.f:2028: >> >> parameter (ldim=3) >> 2 >> Error: Two main PROGRAMs at (1) and (2) >> make: *** [obj/prepost.o] Error 1 >> >> so what should I do? >> Thanks, >> Wei >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/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 Jul 10 16:10:37 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Jul 2014 16:10:37 -0500 (CDT) Subject: [Nek5000-users] 2014 Users Meeting, Aug. 21-22 Message-ID: Dear Nek5000 Users, We will soon finalize the schedule for upcoming Nek5000 User-Developer Meeting, August 21-22 in Thessaloniki, Greece. Last count indicates 22 registered participants. Based on the 2010 and 2014 meetings, we're expecting about 30 total. We are aware of several users who have indicated interest in attending the meeting but are not yet registered. We will hold registration open until 12 noon, Chicago time, Friday, July 18. At that point we will draw up the schedule. Note, if you intend to make a presentation (15 min.) please send a Title and a 2-3 sentence Abstract. While we had planned organized trips to the archeological site and to the beach it appears that there will not be sufficient participants in these activities to warrant a bus. We could organize something more informal once we have the final registration count and demonstrated interest. The conference dinner will take place on August 21 with details to be provided soon. We will collect a fee to cover the dinner on the morning of the first day (Thursday). The exact figure is yet to be determined but is estimated to be about 50 euro. We remind all participants to make travel plans and book their hotel rooms through the conference website: http://nek5000meeting.web.uowm.gr/index.html We look forward to seeing you in August! Sincerely, The Nek5000 Development Group From nek5000-users at lists.mcs.anl.gov Mon Jul 14 05:06:55 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 14 Jul 2014 10:06:55 +0000 Subject: [Nek5000-users] Introducing Turbulence Message-ID: Dear all, I am currently running my own 3D channel flow simulation, it runs very nicely, however I wish to introduce some random white noise in to the simulation to initiate turbulence. Thus I would like to ask your opinion on the method before ploughing into a dead end! When creating the initial mesh using prex or pretex there is an option to switch on turbulence modelling, however when I click it nothing happens, is this a bug or is there some other thing I should be doing to enable this? Secondly to introduce white noise I am thinking I create a subfunction which generates a random number and then feed this into userf or useric to start turbulence, is this an appropriate method or is there another way which I have missed? Thank you for the swift response to my previous question and thanks for any help with this issue in advance, Friedrich. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 15 05:44:07 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Jul 2014 15:14:07 +0430 Subject: [Nek5000-users] Request to Dr. Fischer Message-ID: Dear Dr. Fischer We already sent you an email (to fischer at mcs.anl.gov) regarding a request on Jul 9th, but we did not get any answer from you. We apologized for sending this email to "Nek5000-users forum". We would be so pleased if you could consider our request. Sincerely Yours, Bijan Zarif, Omid Atlaschian. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 15 13:36:20 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Jul 2014 11:36:20 -0700 Subject: [Nek5000-users] Midside Node Support for Nek5000 Message-ID: Neks, I am working on a script for translating 3rd-Party grids to Nek5000 and mid-side node support would greatly improve the quality of the grids. I am wondering inf Nek5000 supports midside nodes? I was looking through the archived user lists and saw a thread from 2010 about a matlab script for translating Gambit grids to Nekton that supported midside nodes, but I wasn't sure if Nek5000 supports this feature. If so, could some please provide an example of how this is structured in the *rea file? Or additionally, if someone could share the 2010 matlab script with me that would be greatly appreciated. Thanks, -- Phil Sakievich psakievi at asu.edu PhD Student - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 15 15:27:35 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Jul 2014 20:27:35 +0000 Subject: [Nek5000-users] Midside Node Support for Nek5000 In-Reply-To: References: Message-ID: Hi Phil, Yes - nek5000 supports midside nodes (20-noded bricks). The nodes are entered as curve side info with the "m" character discriminator. I don't see any examples illustrating usage, but it is similar to the "C" curved side, save that you place "m" instead of C, and that there can be 12 edges. The first 3 reals in the indicator are the x,y,z coords of the midside. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, July 15, 2014 1:36 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Midside Node Support for Nek5000 Neks, I am working on a script for translating 3rd-Party grids to Nek5000 and mid-side node support would greatly improve the quality of the grids. I am wondering inf Nek5000 supports midside nodes? I was looking through the archived user lists and saw a thread from 2010 about a matlab script for translating Gambit grids to Nekton that supported midside nodes, but I wasn't sure if Nek5000 supports this feature. If so, could some please provide an example of how this is structured in the *rea file? Or additionally, if someone could share the 2010 matlab script with me that would be greatly appreciated. Thanks, -- Phil Sakievich psakievi at asu.edu PhD Student - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 15 16:28:49 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Jul 2014 17:28:49 -0400 Subject: [Nek5000-users] issue w/ insulated wall? Message-ID: Hello all, Following the issue that I have had with temperature field in my problem (see https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/ 2014-June/002883.html), I have been performing several test cases and trying to solve the issue. I just wanted to share two of these tests, and wondered if anyone have any comments/thoughts on them. I have a 3D cylindrical domain with several embedded horizontal holes in it and an inflow (at the top) and an outflow (at the bottom). I solved both momentum and heat equations for this problem, but no heat source was added to the domain. In the first test, the problem was initialized with a temperature (equal to the inflow temperature) and all walls were set as no-slip insulated boundary condition. For this setup, one expects temperature to remain unchanged forever. However, after around t=200 (of convective time scales), the temperature starts to grow gradually leading to NAN value. This usually occurs for elements attached to the wall and inflow opening. In the second test, everything is identical to the first test, except that I changed the walls temperature boundary condition to a constant value equal to initial temperature. Temperature remains constant so far (after t = 1000). Although, these two examples are physically different (in terms of boundary conditions), but it might raise the question whether there is any issue with insulated (i.e., 'I ' flag in .rea) boundary condition. It, however, certainly shows that the issue begins from walls. I should note that the walls are curved surfaces (i.e., not parallel to coordinate planes). I searched the users archive and apparently, similar issue with insulated wall was reported: https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2012-February/ 001688.html Regards, Mohsen From nek5000-users at lists.mcs.anl.gov Tue Jul 15 17:36:13 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Jul 2014 15:36:13 -0700 Subject: [Nek5000-users] Transitional Turbulence convergence/ solution time Message-ID: Hello All, I have a basic question, what is the best way to calculate the solution time for transitional turbulence? I am running Transitional Turbulence, but I have some problem on finding the point to stop simulation, one idea would be to get the velocity norm behaviour repeatable in time; is that a good way?!! Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 16 02:40:02 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Jul 2014 09:40:02 +0200 Subject: [Nek5000-users] periodic boundary conditions Message-ID: Hi Neks, I'm trying to simulate the flow past a flat plate. I've generated the mesh with Gambit and later I've used the code from Michael Meador to convert the Gambit file to Nek5000. Everything works fine, however I have a problem with the periodic boundary conditions. I've imposed periodic BC in 2 sides of the domain. The output of the code to Nek5000 for the periodic BC is (e.g.): P 1 3 0.00000 0.00000 0.00000 0.00000 0.00000 So, I cannot link the two sides of the domain. Do you know if there is any way to link these sides? Thanks SL From nek5000-users at lists.mcs.anl.gov Wed Jul 16 04:02:15 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Jul 2014 11:02:15 +0200 Subject: [Nek5000-users] Midside Node Support for Nek5000 In-Reply-To: References: Message-ID: Hello I have a naca0012 example using midside nodes. The 8-node quad mesh is generated using gmsh and converted to rea file using a python converter. See here https://bitbucket.org/cpraveen/nek5000/src/master/naca0012/ This works only for 2d at present. Mesh converter is here https://bitbucket.org/cpraveen/nek5000/src/master/gmsh2nek/ Best praveen On Tue, Jul 15, 2014 at 8:36 PM, wrote: > Neks, > > I am working on a script for translating 3rd-Party grids to Nek5000 and > mid-side node support would greatly improve the quality of the grids. > > I am wondering inf Nek5000 supports midside nodes? I was looking through > the archived user lists and saw a thread from 2010 about a matlab script > for translating Gambit grids to Nekton that supported midside nodes, but I > wasn't sure if Nek5000 supports this feature. If so, could some please > provide an example of how this is structured in the *rea file? Or > additionally, if someone could share the 2010 matlab script with me that > would be greatly appreciated. > > Thanks, > -- > Phil Sakievich > > psakievi at asu.edu > PhD Student - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of Matter > Transport and Energy > Tempe, Arizona > > _______________________________________________ > 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 Jul 16 10:05:23 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Jul 2014 17:05:23 +0200 Subject: [Nek5000-users] periodic boundary conditions In-Reply-To: References: Message-ID: Hi Neks, related to the latter post. Is it possible to establish the connectivity between two faces in the usr file? I mean, if I set in the rea file p 1 3 0 0 0 0 0 p 2 4 0 0 0 0 0 What should I write in the usr file to connect these two faces? Is it possible to do what I want? Thanks in advance. SL El 16-07-2014 09:40, nek5000-users at lists.mcs.anl.gov escribi?: > Hi Neks, > > I'm trying to simulate the flow past a flat plate. I've generated the > mesh with Gambit and later I've used the code from Michael Meador to > convert the Gambit file to Nek5000. Everything works fine, however I > have a problem with the periodic boundary conditions. > > I've imposed periodic BC in 2 sides of the domain. The output of the > code to Nek5000 for the periodic BC is (e.g.): > > P 1 3 0.00000 0.00000 0.00000 > 0.00000 0.00000 > > So, I cannot link the two sides of the domain. > > Do you know if there is any way to link these sides? > > Thanks > SL > _______________________________________________ > 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 Jul 16 19:37:07 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Jul 2014 10:37:07 +1000 Subject: [Nek5000-users] Specifying boundary condition from external text file Message-ID: Hi All, I'm using NEK5000 for a university project. I've found it to be blissfully fast and relatively easy to use. The problem I'm doing is a blasius boundary layer case with perturbations (simulating Tollmien?Schlichting waves), initially in 2D as per the blasius example, then eventually moving to 3D. I've so far been successful in running the blasius example case, and modifying the mesh, polynomial order and other input parameters. Now however, I want to change the way the boundary conditions are defined. I have input files that are unique for each time step specifying velocity and pressures along a line (the inlet) in text format. It would be possible to re-format these as .csv or another file if necessary. *How can I get NEK to read these files as boundary conditions on the inlet for each time step?* I understand it will be a specification in the user userbc subroutine in blasius.usr however I'm not sure how to actually implement this. Doing it in 2D will be a precursor to a 3D simulation with the file specifying the inlet *plane *in a text file, rather than just a *line*. Looking forward to a response. Warm Regards, Tom. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 17 04:30:39 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Jul 2014 11:30:39 +0200 Subject: [Nek5000-users] Error reading parameter data Message-ID: Howdy Nek's, It has been a while since I last posted a question. Here is my problem. I try to simulate the flow within a stenotic pipe. The code compiles fine, however when I want to run it here is the output I get in the logfile. I have no idea where does the error comes from since this case was running fine a few months ago. Any idea? Thanks a lots, JC Number of processors: 24 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /home/loiseau/STENOSIS/CASE_0/BASEFLOW/RE40/stenosis.rea timer accuracy: 0.0000000E+00 sec read .rea file ERROR READING PARAMETER DATA ABORTING IN ROUTINE RDPARAM. -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 17 05:15:27 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Jul 2014 12:15:27 +0200 Subject: [Nek5000-users] Error reading parameter data In-Reply-To: References: Message-ID: Hi again, I found my error. I had a parameter reading 0..000 Thanks anyway 2014-07-17 11:30 GMT+02:00 : > Howdy Nek's, > > It has been a while since I last posted a question. Here is my problem. I > try to simulate the flow within a stenotic pipe. The code compiles fine, > however when I want to run it here is the output I get in the logfile. I > have no idea where does the error comes from since this case was running > fine a few months ago. > > Any idea? > > Thanks a lots, > JC > > Number of processors: 24 > REAL wdsize : 8 > INTEGER wdsize : 4 > > > Beginning session: > > /home/loiseau/STENOSIS/CASE_0/BASEFLOW/RE40/stenosis.rea > > > > timer accuracy: 0.0000000E+00 sec > > read .rea file > ERROR READING PARAMETER DATA > ABORTING IN ROUTINE RDPARAM. > > -- > Jean-Christophe Loiseau > Homepage > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 17 05:40:19 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Jul 2014 12:40:19 +0200 Subject: [Nek5000-users] Initialise with random noise Message-ID: Hi again Nek's, I am working on the simple pipe flow as well, and I have a question regarding the initialisation of the perturbation mode. I initialise my perturbation with call random_number(vxp) call random_number(vyp) and call random_number(vzp) and run the calculation on 4 processors for validation and tests purposes. The domain is divided in four partitions in the streamwise direction. Unfortunately, the call random_number repoduces four times the same random field and as a consequence prescribes a streamwise wavenumber which I'd like to get rid of. Any ideas on how to do that? Regards, JC -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 17 15:07:08 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Jul 2014 22:07:08 +0200 Subject: [Nek5000-users] Initialise with random noise In-Reply-To: References: Message-ID: Hi, We had the same issue a while back; I guess the simple solution is to use different seeds for the pseudo random number generator depending on the processor you are on; in this way each processor will generate an independent series of random numbers. Depending on which generator you use, and what requirements you have (always the same sequence of numbers or completely random, etc.), maybe it is enough to just call random_seed() on each process before you pull out the numbers. Philipp On 2014-07-17 12:40, nek5000-users at lists.mcs.anl.gov wrote: > Hi again Nek's, > > I am working on the simple pipe flow as well, and I have a question > regarding the initialisation of the perturbation mode. I initialise my > perturbation with call random_number(vxp) call random_number(vyp) and > call random_number(vzp) and run the calculation on 4 processors for > validation and tests purposes. The domain is divided in four partitions > in the streamwise direction. Unfortunately, the call random_number > repoduces four times the same random field and as a consequence > prescribes a streamwise wavenumber which I'd like to get rid of. Any > ideas on how to do that? > > Regards, > JC > > -- > Jean-Christophe Loiseau > Homepage > > > _______________________________________________ > 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 Jul 18 04:36:53 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Jul 2014 11:36:53 +0200 Subject: [Nek5000-users] gambit to nek 2D Message-ID: Neks, do you know how can I convert a 2D mesh generated with Gambit to Nek5000 format? I've seen that the code of Michael Meador only converts 3D geometries. Thanks SL From nek5000-users at lists.mcs.anl.gov Fri Jul 18 15:35:45 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Jul 2014 15:35:45 -0500 (CDT) Subject: [Nek5000-users] Initialise with random noise In-Reply-To: References: Message-ID: JC, There are several questions raised by your situation. Personally, I find that I prefer to have the same "random" number distribution, independent of the number of cores, so that my initial conditions are repeatable if I run today on two cores and tomorrow on 4. So, I usually generate some type of deterministic function that depends on the input argumets to useric(). A favorite: subroutine useric(i,j,k,eg) include 'SIZE' integer eg big = 1.e7*eg + 1.e8*i + 1.e9*j + 1.e10*k rand1 = sin(big) rand2 = sin(rand1*big) rand3 = sin(rand2*big) ux = amp*rand1 uy = amp*rand2 uz = amp*rand3 ...etc. This result is deterministic (and arguably not very random), but should provide enough noise. Paul On Thu, 17 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > Hi again Nek's, > > I am working on the simple pipe flow as well, and I have a question > regarding the initialisation of the perturbation mode. I initialise my > perturbation with call random_number(vxp) call random_number(vyp) and call > random_number(vzp) and run the calculation on 4 processors for validation > and tests purposes. The domain is divided in four partitions in the > streamwise direction. Unfortunately, the call random_number repoduces four > times the same random field and as a consequence prescribes a streamwise > wavenumber which I'd like to get rid of. Any ideas on how to do that? > > Regards, > JC > > -- > Jean-Christophe Loiseau > Homepage > From nek5000-users at lists.mcs.anl.gov Mon Jul 21 12:08:13 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Jul 2014 19:08:13 +0200 Subject: [Nek5000-users] Extruding 2D .fld file to 3D References: <4244B646-21AB-4BA9-922D-C92DDCA9147A@torroja.dmt.upm.es> Message-ID: Hi Neks, I followed what Fisher posted in the below link and tried to extrude a 2D flow into 3D. http://lists.mcs.anl.gov/pipermail/nek5000-users/2013-October/002333.html 85 c----------------------------------------------------------------------- 86 subroutine usrdat2 87 include 'SIZE' 88 include 'TOTAL' 89 90 91 nelx=lelx,nely=lely,nelz=lelz 92 parameter (l2d=lx1*ly1*lelx) 93 common /mystuff/ u2d(l2d),v2d(l2d) 94 95 if (nid.eq.0) then 96 open(33,file='2D.dat') 97 do i=1,l2d 98 read(33,*) u2d(i),v2d(i) 99 enddo 100 close(33) 101 endif 102 nbytes = 8*l2d 103 call bcast(u2d,nbytes) 104 call bcast(v2d,nbytes) 105 106 call z_average_transpose(vx,u2d) 107 call z_average_transpose(vy,v2d) 108 109 call outpost(vx,vy,vz,pr,t,'3d.dat') 110 call exitti('Quit in usrdat2.$',nelgt) 111 112 return 113 end 114 c----------------------------------------------------------------------- 115 subroutine usrdat3 when I compiling the simulation ( with a 2D.rea and new SIZE) it displays errors, nek5000/test/test3dimposed/3d/box.f:91.8: nelx=lelx,nely=lely,nelz=lelz 1 Error: Unclassifiable statement at (1) make: *** [nek5000] Error 1 Is there something I misunderstand ? Thanks! Wei -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 21 17:53:10 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Jul 2014 18:53:10 -0400 Subject: [Nek5000-users] About governing equations Message-ID: Hi, I read in website that NEK5000 can't solve fully compressible flows. How it changes density in low mach number flows (in which we have thermal dilatation effects)? Thanks From nek5000-users at lists.mcs.anl.gov Tue Jul 22 05:02:01 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 Jul 2014 15:32:01 +0530 Subject: [Nek5000-users] nek installation and running errors Message-ID: Hi all, I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 No file SESSION.NAME; using defaults of PATH=. and SESSION=NEK. Beginning session: ./NEK.rea timer accuracy: 0.0000000E+00 sec read .rea file At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') Fortran runtime error: File './NEK.rea' does not exist I have put a copy of the scripts under the /bin directory as well. I dont understand what I am missing and where im going wrong! Thanks. Thangam. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 22 10:10:12 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 22 Jul 2014 10:10:12 -0500 (CDT) Subject: [Nek5000-users] nek installation and running errors In-Reply-To: References: Message-ID: You should use one of the scripts in trunk/tools/scripts The usual command would be nek blah where blah is the name of your .rea file. To run in background (strongly recommended), nekb blah For mpi there are nekmpi and nekbmpi nekmpi blah 4 would run on 4 ranks, etc. There is some description of this in the manual. Paul On Tue, 22 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > Hi all, > > > I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. > > Number of processors: 1 > REAL wdsize : 8 > INTEGER wdsize : 4 > No file SESSION.NAME; using defaults of > PATH=. and SESSION=NEK. > > > Beginning session: > ./NEK.rea > > > timer accuracy: 0.0000000E+00 sec > > read .rea file > At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') > Fortran runtime error: File './NEK.rea' does not exist > > > > > I have put a copy of the scripts under the /bin directory as well. > > I dont understand what I am missing and where im going wrong! > > Thanks. > Thangam. > From nek5000-users at lists.mcs.anl.gov Tue Jul 22 22:47:07 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Jul 2014 09:17:07 +0530 Subject: [Nek5000-users] nek installation and running errors In-Reply-To: References: Message-ID: Thanks Paul. The issue is my system doesnt recognize the commands 'nek' and 'nekb' etc. Do I have to set the environment variables by sourcing the bash file? Thanks. Thangam. From: nek5000-users-request at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 65, Issue 13 To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 12:00:08 -0500 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..." --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Mon, 21 Jul 2014 19:08:13 +0200 Subject: [Nek5000-users] Extruding 2D .fld file to 3D Hi Neks, I followed what Fisher posted in the below link and tried to extrude a 2D flow into 3D. http://lists.mcs.anl.gov/pipermail/nek5000-users/2013-October/002333.html 85 c----------------------------------------------------------------------- 86 subroutine usrdat2 87 include 'SIZE' 88 include 'TOTAL' 89 90 91 nelx=lelx,nely=lely,nelz=lelz 92 parameter (l2d=lx1*ly1*lelx) 93 common /mystuff/ u2d(l2d),v2d(l2d) 94 95 if (nid.eq.0) then 96 open(33,file='2D.dat') 97 do i=1,l2d 98 read(33,*) u2d(i),v2d(i) 99 enddo 100 close(33) 101 endif 102 nbytes = 8*l2d 103 call bcast(u2d,nbytes) 104 call bcast(v2d,nbytes) 105 106 call z_average_transpose(vx,u2d) 107 call z_average_transpose(vy,v2d) 108 109 call outpost(vx,vy,vz,pr,t,'3d.dat') 110 call exitti('Quit in usrdat2.$',nelgt) 111 112 return 113 end 114 c----------------------------------------------------------------------- 115 subroutine usrdat3 when I compiling the simulation ( with a 2D.rea and new SIZE) it displays errors, nek5000/test/test3dimposed/3d/box.f:91.8: nelx=lelx,nely=lely,nelz=lelz 1 Error: Unclassifiable statement at (1) make: *** [nek5000] Error 1 Is there something I misunderstand ? Thanks! Wei --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Mon, 21 Jul 2014 18:53:10 -0400 Subject: [Nek5000-users] About governing equations Hi, I read in website that NEK5000 can't solve fully compressible flows. How it changes density in low mach number flows (in which we have thermal dilatation effects)? Thanks --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 15:32:01 +0530 Subject: [Nek5000-users] nek installation and running errors Hi all, I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 No file SESSION.NAME; using defaults of PATH=. and SESSION=NEK. Beginning session: ./NEK.rea timer accuracy: 0.0000000E+00 sec read .rea file At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') Fortran runtime error: File './NEK.rea' does not exist I have put a copy of the scripts under the /bin directory as well. I dont understand what I am missing and where im going wrong! Thanks. Thangam. --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 10:10:12 -0500 Subject: Re: [Nek5000-users] nek installation and running errors You should use one of the scripts in trunk/tools/scripts The usual command would be nek blah where blah is the name of your .rea file. To run in background (strongly recommended), nekb blah For mpi there are nekmpi and nekbmpi nekmpi blah 4 would run on 4 ranks, etc. There is some description of this in the manual. Paul On Tue, 22 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > Hi all, > > > I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. > > Number of processors: 1 > REAL wdsize : 8 > INTEGER wdsize : 4 > No file SESSION.NAME; using defaults of > PATH=. and SESSION=NEK. > > > Beginning session: > ./NEK.rea > > > timer accuracy: 0.0000000E+00 sec > > read .rea file > At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') > Fortran runtime error: File './NEK.rea' does not exist > > > > > I have put a copy of the scripts under the /bin directory as well. > > I dont understand what I am missing and where im going wrong! > > Thanks. > Thangam. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 23 06:21:20 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Jul 2014 16:51:20 +0530 Subject: [Nek5000-users] nek installation and running errors In-Reply-To: References: , Message-ID: Apparently I did not place the /bin in the executable path. now it works fine! PATH=$PATH:~/.bin export PATH Thanks. Thangam. From: thy_horizon at hotmail.com To: nek5000-users at lists.mcs.anl.gov Subject: nek installation and running errors Date: Wed, 23 Jul 2014 09:17:07 +0530 Thanks Paul. The issue is my system doesnt recognize the commands 'nek' and 'nekb' etc. Do I have to set the environment variables by sourcing the bash file? Thanks. Thangam. From: nek5000-users-request at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 65, Issue 13 To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 12:00:08 -0500 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..." --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Mon, 21 Jul 2014 19:08:13 +0200 Subject: [Nek5000-users] Extruding 2D .fld file to 3D Hi Neks, I followed what Fisher posted in the below link and tried to extrude a 2D flow into 3D. http://lists.mcs.anl.gov/pipermail/nek5000-users/2013-October/002333.html 85 c----------------------------------------------------------------------- 86 subroutine usrdat2 87 include 'SIZE' 88 include 'TOTAL' 89 90 91 nelx=lelx,nely=lely,nelz=lelz 92 parameter (l2d=lx1*ly1*lelx) 93 common /mystuff/ u2d(l2d),v2d(l2d) 94 95 if (nid.eq.0) then 96 open(33,file='2D.dat') 97 do i=1,l2d 98 read(33,*) u2d(i),v2d(i) 99 enddo 100 close(33) 101 endif 102 nbytes = 8*l2d 103 call bcast(u2d,nbytes) 104 call bcast(v2d,nbytes) 105 106 call z_average_transpose(vx,u2d) 107 call z_average_transpose(vy,v2d) 108 109 call outpost(vx,vy,vz,pr,t,'3d.dat') 110 call exitti('Quit in usrdat2.$',nelgt) 111 112 return 113 end 114 c----------------------------------------------------------------------- 115 subroutine usrdat3 when I compiling the simulation ( with a 2D.rea and new SIZE) it displays errors, nek5000/test/test3dimposed/3d/box.f:91.8: nelx=lelx,nely=lely,nelz=lelz 1 Error: Unclassifiable statement at (1) make: *** [nek5000] Error 1 Is there something I misunderstand ? Thanks! Wei --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Mon, 21 Jul 2014 18:53:10 -0400 Subject: [Nek5000-users] About governing equations Hi, I read in website that NEK5000 can't solve fully compressible flows. How it changes density in low mach number flows (in which we have thermal dilatation effects)? Thanks --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 15:32:01 +0530 Subject: [Nek5000-users] nek installation and running errors Hi all, I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 No file SESSION.NAME; using defaults of PATH=. and SESSION=NEK. Beginning session: ./NEK.rea timer accuracy: 0.0000000E+00 sec read .rea file At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') Fortran runtime error: File './NEK.rea' does not exist I have put a copy of the scripts under the /bin directory as well. I dont understand what I am missing and where im going wrong! Thanks. Thangam. --Forwarded Message Attachment-- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Date: Tue, 22 Jul 2014 10:10:12 -0500 Subject: Re: [Nek5000-users] nek installation and running errors You should use one of the scripts in trunk/tools/scripts The usual command would be nek blah where blah is the name of your .rea file. To run in background (strongly recommended), nekb blah For mpi there are nekmpi and nekbmpi nekmpi blah 4 would run on 4 ranks, etc. There is some description of this in the manual. Paul On Tue, 22 Jul 2014, nek5000-users at lists.mcs.anl.gov wrote: > Hi all, > > > I am trying to download and install NEK5000 and trying to get a hang of it. I have downloaded and tried to the first example from the 'quick start' page. The compilation is successful after the makenek command. However, it does not realize further nek commands such as nek, nekb etc. (command not found error)I went on to issue the command ./nek5000 eddy_uv and following was the output. > > Number of processors: 1 > REAL wdsize : 8 > INTEGER wdsize : 4 > No file SESSION.NAME; using defaults of > PATH=. and SESSION=NEK. > > > Beginning session: > ./NEK.rea > > > timer accuracy: 0.0000000E+00 sec > > read .rea file > At line 32 of file /home/thangam/nek5_svn/trunk/nek/connect2.f (unit = 9, file = '') > Fortran runtime error: File './NEK.rea' does not exist > > > > > I have put a copy of the scripts under the /bin directory as well. > > I dont understand what I am missing and where im going wrong! > > Thanks. > Thangam. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 24 04:44:06 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 24 Jul 2014 15:14:06 +0530 Subject: [Nek5000-users] makenek file Message-ID: hi all, Just beginning with nek. Is it mandatory to have the makenek script in every case folder or is there a way to source this script and place it in the executable path?(along with nek5_svn/trunk/tools/scripts ?) Thanks. Thangam. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 24 13:39:50 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 24 Jul 2014 11:39:50 -0700 Subject: [Nek5000-users] makenek file In-Reply-To: References: Message-ID: Have it in your folder which contains your script ./makenek will compile your script. Thanks, Tanmoy On Thu, Jul 24, 2014 at 2:44 AM, wrote: > hi all, > > Just beginning with nek. Is it mandatory to have the makenek script in > every case folder or is there a way to source this script and place it in > the executable path?(along with nek5_svn/trunk/tools/scripts ?) > > Thanks. > > Thangam. > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Jul 27 01:01:28 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 27 Jul 2014 16:01:28 +1000 Subject: [Nek5000-users] Specifying boundary condition from external text file In-Reply-To: References: Message-ID: Hello again, I want to provide more information, and more detail of my exact case to hopefully make it easier to get assistance. Using the 2D blasius example as a base, I have created a mesh file "box.box" that allow me to modify the domain. After renaming the necessary files (program is now called 'box') this works fine with the an unmodified blasius.usr (now 'box.usr') code. The next step I took was to change the boundary conditions in userbc() [and useric()] in box.usr. As I understand, the nodes on the inlet plane are called sequentially from bottom to top, by element number ('e') and then by node number ('iy'). The elements are not numbered sequentially from bottom to top, but rather left-to-right, then back to the start, then up, then left-to-right again. Therefore for a domain of 410 elements in the streamwise (x) direction, the element numbers along the inlet are, from bottom to top: 1, 411, 821, etc. There are 12 elements in the wall normal (y) direction. I have an array ('ArrangedInlet') in the subroutine containing the horizontal velocity component, ux, value for each of the nodes along the inlet according to their y coordinate The original data lives in the file called 'InletArranged.out'. This is output by a process in MATLAB so there is freedom in what is included and how it is arranged and formatted. The data points are currently entered manually. This is initially to test, but it is intended that this is read automatically from the external file. However in order to assign the correct velocity value to the correct position along the inlet, I arranged the data in the array such that the rows counted iy from 1 to 8 (lx1) and each is addressing a node: Row 1=Node 1; Row 2 = Node 2, etc. where the nodes go bottom-to-top (y=0 to y=10), The columns contained the data for each element along the inlet - ordered from bottom to top. At the moment each row . Using the same domain as described above (NELX, NELY)=(410, 12): column 1 contains data at each node ('iy') for element 1, column 2 contains data at each node ('iy') for element 411, column 3 contains data at each node ('iy') for element 821, and so on. I got around this by using the following transformation: COL=((e-1)/NELX)+1 where: COL is the column number of the array (1 to 12); e = gllel(eg) is the element number; NELX = 410 is the number of elements in the streamwise (x) direction. This is then read by the program by: ux = ArrangedInlet(iy,COL) And it works! ... but only for a serial case. Also, it currently only works for the single set of data. As soon as I run the case in parallel the addressing changes and this method does not work. The element addressing no longer appears to have a discernible pattern. *So my questions are primarily:* *1) How can I get the values onto the inlet and make it work in parallel? * and *2) Is there a more elegant/efficient method of doing this? IE. a way of calling the inlet nodes only?* I have attached my case "box_2D_Inlet.tar.gz". I have tested it and it does work, however currently it bombs out after 9 iterations, but I'm really only testing the inlet parameters. Looking forward to any assistance. Thanks, Tom. On 17 July 2014 10:37, Thomas Yankos wrote: > Hi All, > > I'm using NEK5000 for a university project. I've found it to be blissfully > fast and relatively easy to use. > > The problem I'm doing is a blasius boundary layer case with perturbations > (simulating Tollmien?Schlichting waves), initially in 2D as per the blasius > example, then eventually moving to 3D. > I've so far been successful in running the blasius example case, and > modifying the mesh, polynomial order and other input parameters. > > Now however, I want to change the way the boundary conditions are defined. > I have input files that are unique for each time step specifying velocity > and pressures along a line (the inlet) in text format. It would be possible > to re-format these as .csv or another file if necessary. > > *How can I get NEK to read these files as boundary conditions on the inlet > for each time step?* > > I understand it will be a specification in the user userbc subroutine in > blasius.usr however I'm not sure how to actually implement this. > Doing it in 2D will be a precursor to a 3D simulation with the file > specifying the inlet *plane *in a text file, rather than just a *line*. > > Looking forward to a response. > > Warm Regards, > Tom. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: box_2D_Inlet.tar.gz Type: application/x-gzip Size: 39098 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 28 17:05:34 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 28 Jul 2014 17:05:34 -0500 Subject: [Nek5000-users] Specifying boundary condition from external text file In-Reply-To: References: Message-ID: Hi Tom, The problem in parallel is that e=gllel(eg) is giving you the local element count for a global element. Thus, this value is relative to the processor. (I.E. on a 4 element domain with 4 processors running, the global numbers will be 1,2,3,4 whereas the local are 1,1,1,1 because each element is the first element on that processor.) In order to know what element goes to what data point, you will need to use the global number which is probably eg, depending on your setup. Of course, this is all dependant on the fact that your elements are in a nice box that is numbered as you described. There could be a more elegant solution to address the inlet elements, but you would still need to calculate which data point goes to which nodal point since in parallel, you will not necessarily be accessing the array sequentially. hth, Katherine On Sun, Jul 27, 2014 at 1:01 AM, wrote: > Hello again, > > I want to provide more information, and more detail of my exact case to > hopefully make it easier to get assistance. > > Using the 2D blasius example as a base, I have created a mesh file > "box.box" that allow me to modify the domain. > After renaming the necessary files (program is now called 'box') this > works fine with the an unmodified blasius.usr (now 'box.usr') code. > > The next step I took was to change the boundary conditions in userbc() [ > and useric()] in box.usr. > As I understand, the nodes on the inlet plane are called sequentially from > bottom to top, by element number ('e') and then by node number ('iy'). > The elements are not numbered sequentially from bottom to top, but rather > left-to-right, then back to the start, then up, then left-to-right again. > Therefore for a domain of 410 elements in the streamwise (x) direction, > the element numbers along the inlet are, from bottom to top: 1, 411, 821, > etc. > There are 12 elements in the wall normal (y) direction. > > I have an array ('ArrangedInlet') in the subroutine containing the > horizontal velocity component, ux, value for each of the nodes along the > inlet according to their y coordinate The original data lives in the file > called 'InletArranged.out'. This is output by a process in MATLAB so there > is freedom in what is included and how it is arranged and formatted. > The data points are currently entered manually. This is initially to test, > but it is intended that this is read automatically from the external file. > However in order to assign the correct velocity value to the correct > position along the inlet, I arranged the data in the array such that the > rows counted iy from 1 to 8 (lx1) and each is addressing a node: Row > 1=Node 1; Row 2 = Node 2, etc. where the nodes go bottom-to-top (y=0 to > y=10), > The columns contained the data for each element along the inlet - ordered > from bottom to top. At the moment each row . > > Using the same domain as described above (NELX, NELY)=(410, 12): > column 1 contains data at each node ('iy') for element 1, > column 2 contains data at each node ('iy') for element 411, > column 3 contains data at each node ('iy') for element 821, > and so on. > > I got around this by using the following transformation: > COL=((e-1)/NELX)+1 > where: > COL is the column number of the array (1 to 12); > e = gllel(eg) is the element number; > NELX = 410 is the number of elements in the streamwise (x) direction. > > This is then read by the program by: > ux = ArrangedInlet(iy,COL) > > And it works! ... but only for a serial case. Also, it currently only > works for the single set of data. > > As soon as I run the case in parallel the addressing changes and this > method does not work. > The element addressing no longer appears to have a discernible pattern. > > *So my questions are primarily:* > *1) How can I get the values onto the inlet and make it work in parallel? * > and > *2) Is there a more elegant/efficient method of doing this? IE. a way of > calling the inlet nodes only?* > > I have attached my case "box_2D_Inlet.tar.gz". > I have tested it and it does work, however currently it bombs out after 9 > iterations, but I'm really only testing the inlet parameters. > > Looking forward to any assistance. > > Thanks, > > Tom. > > > > On 17 July 2014 10:37, Thomas Yankos wrote: > >> Hi All, >> >> I'm using NEK5000 for a university project. I've found it to be >> blissfully fast and relatively easy to use. >> >> The problem I'm doing is a blasius boundary layer case with perturbations >> (simulating Tollmien?Schlichting waves), initially in 2D as per the blasius >> example, then eventually moving to 3D. >> I've so far been successful in running the blasius example case, and >> modifying the mesh, polynomial order and other input parameters. >> >> Now however, I want to change the way the boundary conditions are defined. >> I have input files that are unique for each time step specifying velocity >> and pressures along a line (the inlet) in text format. It would be possible >> to re-format these as .csv or another file if necessary. >> >> *How can I get NEK to read these files as boundary conditions on the >> inlet for each time step?* >> >> I understand it will be a specification in the user userbc subroutine in >> blasius.usr however I'm not sure how to actually implement this. >> Doing it in 2D will be a precursor to a 3D simulation with the file >> specifying the inlet *plane *in a text file, rather than just a *line*. >> >> Looking forward to a response. >> >> Warm Regards, >> Tom. >> > > > _______________________________________________ > 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: