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Re: [lammps-users] LAMMPS library: Gather specific atoms and insert small molecules
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Re: [lammps-users] LAMMPS library: Gather specific atoms and insert small molecules


From: Stephan Grein <stephan.grein@...5733...>
Date: Thu, 31 Aug 2017 16:42:22 +0200

Dear LAMMPS users,
dear Steve and Axel,

I'm following up on this old post on the list.
Trying to get all coordinates for a given
type, e.g. 2, I put this in my LAMMPS script:

group MYGRP type 2
variable MYCOORDS atom x
variable MYCOUNT equal count(MYGRP)

Using the functions from library.cpp by

double* pnatoms = (double*) lammps_extract_variable(lmp, "MYCOUNT", NULL);
												int natoms = (int)(*pnatoms);
										   										double* coords = (double*)
lammps_extract_variable(lmp, "MYCOORDS", "MYGRP");

However, coords contains only zeros, e.g. 0.0, 0.0, 0.0.
Apparently I'm doing something wrong, but I'm not sure what.

Maybe somebody can point me in the right direction.

Best regards,
Stephan

Am 13/04/16 um 17:00 schrieb Steve Plimpton:
> Just see the variable doc page for all the syntax.
> My email was just meant to be an idea, not
> all the details of the correct syntax.  Ditto
> for the lib interface function you need to use
> to eval a variable.
> 
> Steve
> 
> On Tue, Apr 12, 2016 at 9:50 AM, Stephan Grein
> <stephan.grein@...5733...
> <mailto:stephan.grein@...5733...>> wrote:
> 
>     Dear Steve,
> 
>     thanks so much!
> 
>     Am 12/04/16 um 17:27 schrieb Steve Plimpton:
>     > variable equal x x[id][0]
> 
>     This sounds interesting.
>     I'm not sure how to define this
>     in my script, sorry!
> 
>     Would I do like that:
>     myAtomNameToTrack equal x x[myAtomId][0]
> 
>     Then using:
>     lammps_extract_variable(lmp, "myAtomNameToTrack", NULL);
> 
>     Right? TIA.
> 
>     Best,
>     S.
> 
> 


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