[Nek5000-users] usr file - Vol 62, Issue 9

Sun Apr 13 20:16:49 CDT 2014

I just built a flow chart based on case expansion. I hope it useful for all beginner later.

Zhenyu
-----原始邮件-----
发件人: nek5000-users at lists.mcs.anl.gov
发送时间: 2014-04-14 08:30:27 (星期一)
收件人: nek5000-users at lists.mcs.anl.gov
抄送:
主题: Re: [Nek5000-users] usr file - Vol 62, Issue 9

Dear Murph,

I carried on along your suggested way and at least got some expected results

for case expanson.

Thank you very much for your guidance.

Yours,

Zhenyu

-----原始邮件-----
发件人:nek5000-users at lists.mcs.anl.gov
发送时间: 2014-04-13 23:47:28 (星期日)
收件人:nek5000-users at lists.mcs.anl.gov
抄送:
主题: Re: [Nek5000-users] usr file - Vol 62, Issue 9

Zhenyu,

Hi...  In general, you do the following:

Use an existing run files as templates to start with.  You need the .rea, SIZE, .box, and .usr files.  Rename the rea,box, and usr files to a unique name for your run, like your_run.rea, your_run.box, your_run.usr.

Edit the .box file to define your grid, geometry, and BCs.

Edit the .rea file with all the basic run parameters.  If you have an .rea template that is ascii (without the .re2 option) and it has geometry information at the end, ignore this information as it will be regenerated.
Edit the SIZE file to set your array sizes and GLL DOF (this must also be set correctly in .rea).
Edit the .usr file per instructions, including the information for boundary conditions if applicable.

Then, you generate a new .rea file with the grid geometry by running genbox:  "genbox ./your_run.box".  This will create the files box.rea and box.tmp.  You rename box.rea to your_run.rea.  This will overwrite the one you edited with a new one with all your changes in the settings sections intact, and new geometry information at the end.  Delete box.tmp.

Next, you run genmap to create a new map file:  "genmap ./your_run".  This will create the new map file.

Next, compile the code with:  "./makenek ./your_run".  If successful, you will get a new binary copy of nek5000.

Then you run with one of the scripts like:  "./nekbmpi ./your_run 24"

You will probably get a lot of errors initially based on improper makenek setting for your compiler and target platform, geometry issues, etc...  Read all the documentation and look at the examples to figure this stuff out for your application...

See Ya,

Murph
mlodea at oakland.edu

ForwardedMessage.eml
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Subject:
[Nek5000-users] How to create .usr file |
|
From:
nek5000-users at lists.mcs.anl.gov |
|
Date:
4/10/2014 10:49 AM |
|
To:
Nek5000-users at lists.mcs.anl.gov |

Dear All,

I am trying nek5000 under ubuntu.

As  a beginner, I just wonder which is the best way to create the .usr file, should I copy one from the examples and change it for my case or use a tool just like genbox, genmap, etc. to generate it? I have the same question for creation of SIZE

By the way,  I can only find the usage of prenek and demonstrative cases from the old manual of nekton, what is the current way of generating meshes for public uses?

Thank you very much in advance.

Zhenyu

ForwardedMessage.eml
|
Subject:
Re: [Nek5000-users] How to create .usr file |
|
From:
nek5000-users at lists.mcs.anl.gov |
|
Date:
4/9/2014 11:17 AM |
|
To:
nek5000-users at lists.mcs.anl.gov |

Hi Zhenyu,

The *.usr is to be copied from the examples and change it according to your needs like Boundary condition and Initial condition.

The SIZE file too should be copied (change the number of element per processor according to yours) .

See the example 'Expansion ' --> mkmesh file, which will give you an insight about how to write a script to create a mesh using prenek.

Best Regards,
Kamal.

On 10/04/2014 16:49, nek5000-users at lists.mcs.anl.gov wrote:

Dear All,

I am trying nek5000 under ubuntu.

As  a beginner, I just wonder which is the best way to create the .usr file, should I copy one from the examples and change it for my case or use a tool just like genbox, genmap, etc. to generate it? I have the same question for creation of SIZE

By the way,  I can only find the usage of prenek and demonstrative cases from the old manual of nekton, what is the current way of generating meshes for public uses?

Thank you very much in advance.

Zhenyu

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