[Nek5000-users] turbulent 3d box

Mon Dec 16 11:37:45 CST 2013

Sorry - by "blank" .usr file, I meant one of the zero.usr files from

nek5_svn/trunk/nek

________________________________
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, December 16, 2013 2:31 AM
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] turbulent 3d box

Hi Paul,
It seems that many more things are missing. Here is the compilation errors:

mpicc -c  -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG  -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/xxt.c -o obj/jl_xxt.o
mpicc -c  -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG  -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/fcrs.c -o obj/jl_fcrs.o
mpif77 -c  -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -I/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox -I/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek -I./ /home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox/turbBox.f    -o obj/turbBox.o
mpif77 -o nek5000  obj/turbBox.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o
obj/drive1.o: In function `nek_init_':
drive1.f:(.text+0x48b): undefined reference to `usrdat_'
drive1.f:(.text+0x578): undefined reference to `usrdat3_'
drive1.f:(.text+0x5b5): undefined reference to `userchk_'
obj/drive1.o: In function `nek_solve_':
drive1.f:(.text+0xc7e): undefined reference to `userchk_'
drive1.f:(.text+0xcf7): undefined reference to `userchk_'
obj/bdry.o: In function `faceiv_':
bdry.f:(.text+0x2a5f): undefined reference to `userbc_'
bdry.f:(.text+0x2e74): undefined reference to `userbc_'
bdry.f:(.text+0x2f53): undefined reference to `userbc_'
bdry.f:(.text+0x309f): undefined reference to `userbc_'
bdry.f:(.text+0x31d9): undefined reference to `userbc_'
obj/bdry.o:bdry.f:(.text+0x3352): more undefined references to `userbc_' follow
obj/conduct.o: In function `nekuq_':
conduct.f:(.text+0xdcf): undefined reference to `userq_'
obj/ic.o: In function `nekuic_':
ic.f:(.text+0x6a6): undefined reference to `useric_'
ic.f:(.text+0x980): undefined reference to `useric_'
ic.f:(.text+0xad0): undefined reference to `useric_'
obj/ssolv.o: In function `gostep_':
ssolv.f:(.text+0x1954): undefined reference to `userchk_'
obj/ssolv.o: In function `go1step_':
ssolv.f:(.text+0x2424): undefined reference to `userchk_'
obj/subs1.o: In function `nekuvp_':
subs1.f:(.text+0x90c): undefined reference to `uservp_'
collect2: error: ld returned 1 exit status
make: *** [nek5000] Error 1

Attached the .usr and .box files which I used. What about the turBox.f file ?
All the best,
Barak

Quoting nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>:

Hi Barak,

Just take the box file from turbChannel
and set nelx nely nelz to (say) -8 -8 -8
with periodic BCs  P  ,P  ,P  ,P  ,P  ,

Then, use a blank .usr file and set ffx fry ffz to be the
formulas you have below in userf() in the .usr file.

Finally, add the following to usrdat2()

     a=0
     b=2*pi
     call rescale_x(xm1,a,b)
     call rescale_x(ym1,a,b)
     call rescale_x(zm1,a,b)

which will put your box on [0,2pi]^3.

Paul

----- Original Message -----
From: nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>
To: nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>
Sent: Sunday, December 15, 2013 4:14:22 PM
Subject: [Nek5000-users] turbulent 3d box

Dear nek's,
I would like to run the following problem:
a 3D periodic box, small viscosity and the following forcing:

fx=cos(y)+sin(z)
fy=cos(z)+sin(x)
fz=cos(x)+sin(y)

Do you have a similar example?

Many thanks,
Barak

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