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Re: [lammps-users] problem with "fix thermal/conductivity"
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Re: [lammps-users] problem with "fix thermal/conductivity"


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 3 Aug 2017 10:47:14 -0400



On Thu, Aug 3, 2017 at 10:25 AM, Neda Rafiee <ne.rafiee@...4739.....> wrote:
Dear Axel ,
Could you please explain with more details what I should do for re-compiling Lammps? Is there anything I could do before making lammps? any change in ./configure? Currently, I installed the 24Jul2017 Development version of lammps from this link:
http://lammps.sandia.gov/download.html
I will be thankful if you can explain what I should do to update this version. Is there any updated source file I can try or any repository, etc?

​everything you are asking about is answered in the LAMMPS manual. there is no "configure" script for LAMMPS; for most cases "make mpi" or "make serial" should work out of the box, only in special (documented!) cases or for enabling additional compile time features, you need to make changes to makefiles with a text editor.

please note, that in the development version there is a change in the installation via python convenience scripts (Make.py has been removed and replaced), that is currently not fully and consistently documented. the standard "manual" installation is unchanged and works as described.
we expect to have a new stable version released within the next couple of weeks, as soon as the documentation has been reviewed and​ adjusted for that and the python convenience scripts properly tested.

axel.

 
Regards,
Neda

On Thu, Aug 3, 2017 at 6:18 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Thu, Aug 3, 2017 at 9:32 AM, Neda Rafiee <ne.rafiee@...444...> wrote:
Dear Axel,
Thanks a lot. Actually, after I checked with "lmp_mpi -h",  I understood that I don't have thermal/conductivity among the fix styles in my compilation folder. I should say that I installed Lammps on my institutional cluster so I cannot update it because of administrative laws. What can I do now to make it work?

​there is no alternative to re-compiling LAMMPS.​

 
Thanks

On Thu, Aug 3, 2017 at:09 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Thu, Aug 3, 2017 at 4:58 AM, Neda Rafiee via lammps-users <lammps-users@...42...e.net> wrote:
Dear all,
I have a problem with the style of "fix  thermal/conductivity". When I use this command, this error appears:  "unknown fix style thermal/conductivity"
I checked the mailing list archive and I found that the problem may be due to the MISC package. 
So, I used "make package-status" and I saw that both MISC and USER-MISC packages are installed. what would be my problem then?

​having the package installed is only one prerequisite. ​you also have to have updated your compilation and have to actually use that updated binary.
you can verify that, by looking at the output of ./lmp_mpi -h in your compilation folder and compare that to the output that you get when you a -h flag to your simulation run command. also, these days, you have to watch out for non-ascii characters, e.g. when you cut-n-paste text verbatim from the manual, as many pdf viewers and webbrowsers have a tendency to replace certain ascii characters with similar looking non-ascii versions for a more visually appealing text rendering.

axel.

 
Thanks

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.




--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.




--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.