[Nek5000-users] Setting up a case from scratch
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Thu Nov 29 03:24:57 CST 2012
Praveen,
You can also merge your rea files using either prex or, if your
boundary conditions are set already, pretex.
Simply read in mesh 1, then IMPORT MESH and read in mesh 2.
Paul
On Thu, 29 Nov 2012, nek5000-users at lists.mcs.anl.gov wrote:
> Thanks. I will be eagerly waiting for this.
>
> praveen
>
> On Thu, Nov 29, 2012 at 4:15 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
>
>> Oh, right, ok. I'd forgotten that those parts of NekCEM and Nek5000 are
>> different.
>>
>> - tim
>>
>> On 11/28/2012 01:35 PM, Misun Min wrote:
>>
>>>
>>> Hi Tim
>>>
>>> MOAB supporting 2D quad meshes have been tested for NekCEM/LBM
>>> codes but not tested with nek5000. I'll check with Aleks to make
>>> sure the updated moab routines not to conflict with nek5000 and
>>> commit soon.
>>>
>>> Thanks
>>> Misun
>>>
>>>
>>> ----- Original Message -----
>>> From: "Tim Tautges" <tautges at mcs.anl.gov>
>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>,
>>> "Misun Min" <mmin at mcs.anl.gov>
>>> Sent: Wednesday, November 28, 2012 1:23:02 PM
>>> Subject: Re: [Nek5000-users] Setting up a case from scratch
>>>
>>> Misun and one of her students had that working recently, but I'm not sure
>>> if all her updates have been committed to the
>>> code. Misun?
>>>
>>> - tim
>>>
>>> On 11/28/2012 11:28 AM, nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>>>
>>>> It looks like Nek does not get the mesh from MOAB...
>>>>
>>>> Also I doubt the currecnt version of Nek/MOAB supports 2D Quad meshes --
>>>> only 3D hexes, right, Tim?
>>>>
>>>> Thanks.
>>>> Aleks
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>
>>>> To: nek5000-users at lists.mcs.anl.**gov <nek5000-users at lists.mcs.anl.gov>
>>>> Sent: Wed, 28 Nov 2012 11:23:04 -0600 (CST)
>>>> Subject: Re: [Nek5000-users] Setting up a case from scratch
>>>>
>>>> Thanks. I am making little progress. Now I can compile. When running on
>>>> h5m
>>>> mesh I get
>>>>
>>>> read .rea file
>>>> ABORT: nelv is invalid in nekmoab_proc_map
>>>> nelv, lelv = 0 1850
>>>>
>>>> But mbsize shows
>>>>
>>>> $ mbsize karman.h5m
>>>> File karman.h5m:
>>>> type count total minimum average rms maximum
>>>> std.dev.
>>>> ------- ----- ------- ----------- ----------- ----------- -----------
>>>> -----------
>>>> Edge 212 5.5 0.0063678 0.026102 0.029283 0.048844
>>>> 0.013273
>>>> Quad 1832 0.89 3.8386e-05 0.0004881 0.00054375 0.0011788
>>>> 0.00023963
>>>> 1D Side 7328 1.8e+02 0.0037915 0.024086 0.027266 0.048844
>>>> 0.012777
>>>> Vertex 7540
>>>>
>>>> praveen
>>>>
>>>> On Wed, Nov 28, 2012 at 10:27 PM, <nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>>
>>>> wrote:
>>>>
>>>> Hi Praven,
>>>>>
>>>>> use examples/moab/SIZE
>>>>>
>>>>> Thanks.
>>>>> Aleks
>>>>>
>>>>>
>>>>>
>>>>> On Wed, 28 Nov 2012, nek5000-users at lists.mcs.anl.****gov<
>>>>> nek5000-users at lists.mcs.**anl.gov <nek5000-users at lists.mcs.anl.gov>
>>>>>> wrote:
>>>>>
>>>>> The gmsh file does have all vertices for the higher order elements.
>>>>>
>>>>>>
>>>>>> I am now trying to compile with moab. I am doing everything in serial
>>>>>> for
>>>>>> now. I compiled moab succesfully and can convert from gmsh to h5m.
>>>>>>
>>>>>> But when compiling nek with moab I get this type of errors. This is the
>>>>>> first one.
>>>>>>
>>>>>> gcc -c -O2 -DMOAB -DPTRSIZE8 -DLONGINT8 -DUNDERSCORE
>>>>>> -DGLOBAL_LONG_LONG
>>>>>> /Users/praveen/Applications/****nek5_svn/trunk/nek/3rd_party/***
>>>>>> *imeshcutil.c
>>>>>> -o
>>>>>> obj/imeshcutil.o
>>>>>> SIZE:5.21:
>>>>>> Included at
>>>>>> /Users/praveen/Applications/****nek5_svn/trunk/nek/3rd_party/***
>>>>>> *MOABCORE:17:
>>>>>> Included at
>>>>>> /Users/praveen/Applications/****nek5_svn/trunk/nek/3rd_party/***
>>>>>> *NEKMOAB:51:
>>>>>> Included at
>>>>>> /Users/praveen/Applications/****nek5_svn/trunk/nek/3rd_party/***
>>>>>> *moab.f:79:
>>>>>>
>>>>>> parameter (ldim=2)
>>>>>> 1
>>>>>> Error: Symbol 'ldim' at (1) has no IMPLICIT type
>>>>>>
>>>>>> My makenek looks like this
>>>>>>
>>>>>> # Fortran compiler
>>>>>> F77="gfortran"
>>>>>>
>>>>>> # C compiler
>>>>>> CC="gcc"
>>>>>>
>>>>>> # pre-processor symbol list
>>>>>> # (set PPLIST=? to get a list of available symbols)
>>>>>> PPLIST="MOAB"
>>>>>>
>>>>>> # plug-in list
>>>>>> PLUGIN_LIST=""
>>>>>>
>>>>>>
>>>>>> # OPTIONAL SETTINGS
>>>>>> # -----------------
>>>>>>
>>>>>> # enable MPI (default true)
>>>>>> IFMPI="false"
>>>>>>
>>>>>> # auxilliary files to compile
>>>>>> # NOTE: source files have to located in the same directory as makenek
>>>>>> # a makefile_usr.inc has to be provided containing the build
>>>>>> rules
>>>>>> #USR="foo.o"
>>>>>>
>>>>>> # linking flags
>>>>>> #USR_LFLAGS="-L/usr/lib -lfoo"
>>>>>>
>>>>>>
>>>>>> # generic compiler flags
>>>>>> #G="-g"
>>>>>>
>>>>>> # optimization flags
>>>>>> #OPT_FLAGS_STD=""
>>>>>> #OPT_FLAGS_MAG=""
>>>>>>
>>>>>> # enable AMG coarse grid solver (default XXT)
>>>>>> #IFAMG="true"
>>>>>> #IFAMG_DUMP="true"
>>>>>>
>>>>>> # CVODE path
>>>>>> #CVODE_DIR=$HOME/cvode/lib
>>>>>>
>>>>>> # MOAB/iMESH path
>>>>>> MOAB_DIR="/opt/moab"
>>>>>>
>>>>>> # For linking to MOAB, the following might be needed:
>>>>>> # NOTE: compiler specific, use the appropriate one depending on your
>>>>>> compiler
>>>>>> # GNU:
>>>>>> USR_LFLAGS="-lmpi_cxx -lstdc++"
>>>>>> # Intel:
>>>>>> # USR_LFLAGS="-cxxlib"
>>>>>> # PGI:
>>>>>> # USR_LFLAGS="-pgcpplibs"
>>>>>> # USR_LFLAGS=" -lmpi_cxx -lstdc++"
>>>>>>
>>>>>> What am I doing wrong ?
>>>>>>
>>>>>> Thanks
>>>>>> praveen
>>>>>>
>>>>>> On Wed, Nov 28, 2012 at 8:46 PM, <nek5000-users at lists.mcs.anl.****gov<
>>>>>> nek5000-users at lists.mcs.**anl.gov <nek5000-users at lists.mcs.anl.gov>>>
>>>>>> wrote:
>>>>>>
>>>>>> Try running 'mbsize' on the gmsh file, and check the number of
>>>>>> vertices
>>>>>>
>>>>>>> to
>>>>>>> make sure it's getting all of them. Or, run mbsize -ll, piping the
>>>>>>> output
>>>>>>> to a file, and check one of the hexes to make sure it's 27-noded. If
>>>>>>> that's the case, we're all set (modulo how to handle the BC's).
>>>>>>>
>>>>>>> - tim
>>>>>>>
>>>>>>>
>>>>>>> ______________________________****_________________
>>>>>>
>>>>> Nek5000-users mailing list
>>>>> Nek5000-users at lists.mcs.anl.****gov <Nek5000-users at lists.mcs.anl.**gov<Nek5000-users at lists.mcs.anl.gov>
>>>>>>
>>>>> https://lists.mcs.anl.gov/****mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users>
>>>>> **<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>> **>
>>>>>
>>>>>
>>>> ______________________________**_________________
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>>>> https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>
>>>>
>>>
>> --
>> ==============================**==============================**====
>> "You will keep in perfect peace him whose mind is
>> steadfast, because he trusts in you." Isaiah 26:3
>>
>> Tim Tautges Argonne National Laboratory
>> (tautges at mcs.anl.gov) (telecommuting from UW-Madison)
>> phone (gvoice): (608) 354-1459 1500 Engineering Dr.
>> fax: (608) 263-4499 Madison, WI 53706
>>
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>>
>
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