Dear Professor Sherwin, Thank you for you reply! Apologize for not giving clear explanation to my 'chk file'. Actually, " cylinder1_Spherigon_5.chk" is a folder. It contains several fld files as shown below: [image: Screen Shot 2019-06-06 at 1.59.59 AM.png] I get it due to using mpirun command to do simulation. May I know how can I deal with such .chk file? Thank you a lot again! Best, Shan On Thu, Jun 6, 2019 at 1:49 AM Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:

Hi Shan,

I presume you were running a command like:

FieldConvert -m extract:bnd=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk

The ‘bnd’ here is just shorthand for the boundary region defined in the condition setup of your run.

I wonder if you have included the <CONDITION> section in your cylinder1_Spherigon.xml file? Or is there another file with the information about boundary conditions that you would normally use when running the simulation. I think this error may reflect that it is trying to find the boundary 1 (i.e. bnd=1) but it is not defined since this information is not included in the xml file you have provided?

It should be fine to use the ending chk it is treated just the same as fld

Cheers, Spencer.

On 5 Jun 2019, at 21:14, Shanshan Luo <luoss@sas.upenn.edu> wrote:

Dear all,

When I run the command: FieldConvert -m extract:fldtoboundary=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk

It gives out errors: Fatal : Level 0 assertion violation Variable index out of range. libc++abi.dylib: terminating with uncaught exception of type ErrorUtil::NekError: Level 0 assertion violation Variable index out of range. Abort trap: 6

I want to know can this command run with .chk file? Since we use the parallel computing, our cylinder1_Spherigon_5.chk file contains several .fld files and one info.xml.

Also I want to know for the command in Page 84 of user-guide-4.4.1, what does "bnd" really mean?

Could you help me figure this out? Thank you very much!

Best, Shan _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@imperial.ac.uk South Kensington Campus, Phone: +44 (0)20 7594 5052 Imperial College London, Fax: +44 (0)20 7594 1974 London, SW7 2AZ, UK http://www.imperial.ac.uk/people/s.sherwin/

Dear professor Chun, Thank for your reply very much! I can do it now. The problem is solved. Best, Shan On Thu, Jun 6, 2019 at 2:19 AM Sehun Chun <sehun.chun@yonsei.ac.kr> wrote:

Dear Shan,

I had the same problem, but now I can plot it. You can run FieldConvert as if the chk folder is a file according to Chris.

- Sehun

Sehun Chun, Ph.D. Assistant Professor of Applied Mathematics, Director of the Heart Modeling Center (HMC), ISED, UIC, Yonsei University, #413 Veritas Hall B, Incheon, 21983, South Korea Phone: +82 (0)32 749 3607 Mobile: +82 (0)10 9484 1467 Email: sehun.chun@yonsei.ac.kr <sehun.chun@yonsei.ac.kr> Web: sites.google.com/site/uicschun/

On 6 Jun 2019, at 3:03 PM, Shanshan Luo <luoss@sas.upenn.edu> wrote:

Dear Professor Sherwin,

Thank you for you reply! Apologize for not giving clear explanation to my 'chk file'. Actually, " cylinder1_Spherigon_5.chk" is a folder. It contains several fld files as shown below: <Screen Shot 2019-06-06 at 1.59.59 AM.png> I get it due to using mpirun command to do simulation. May I know how can I deal with such .chk file?

Thank you a lot again!

Best, Shan

On Thu, Jun 6, 2019 at 1:49 AM Sherwin, Spencer J < s.sherwin@imperial.ac.uk> wrote:

...

Hi Shan,

I presume you were running a command like:

FieldConvert -m extract:bnd=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk

The ‘bnd’ here is just shorthand for the boundary region defined in the condition setup of your run.

I wonder if you have included the <CONDITION> section in your cylinder1_Spherigon.xml file? Or is there another file with the information about boundary conditions that you would normally use when running the simulation. I think this error may reflect that it is trying to find the boundary 1 (i.e. bnd=1) but it is not defined since this information is not included in the xml file you have provided?

It should be fine to use the ending chk it is treated just the same as fld

Cheers, Spencer.

On 5 Jun 2019, at 21:14, Shanshan Luo <luoss@sas.upenn.edu> wrote:

Dear all,

When I run the command: FieldConvert -m extract:fldtoboundary=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk

It gives out errors: Fatal : Level 0 assertion violation Variable index out of range. libc++abi.dylib: terminating with uncaught exception of type ErrorUtil::NekError: Level 0 assertion violation Variable index out of range. Abort trap: 6

I want to know can this command run with .chk file? Since we use the parallel computing, our cylinder1_Spherigon_5.chk file contains several .fld files and one info.xml.

Also I want to know for the command in Page 84 of user-guide-4.4.1, what does "bnd" really mean?

Could you help me figure this out? Thank you very much!

Best, Shan _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@imperial.ac.uk South Kensington Campus, Phone: +44 (0)20 7594 5052 Imperial College London, Fax: +44 (0)20 7594 1974 London, SW7 2AZ, UK http://www.imperial.ac.uk/people/s.sherwin/

_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users