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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: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 15 Sep 2017 14:56:36 -0400



On Fri, Sep 15, 2017 at 1:48 PM, Stephan Grein <stephan.grein@...5733...> wrote:
>
>     3) create_atoms can create/distribute
>     random atoms. I need however to create
>     small molecules and distribute them
>     randomly. The small molecule structure
>     is known a-priori, however I need to
>     insert let's say 10 randomly in my
>     simulation box.
>
>
> with a recent enough version of LAMMPS, ​create_atoms can also create
> molecules that have been previously defined with the molecule command
> and read from a suitable file.

Follow up on this:
If I would add a new ion type to my system,
I would have to specify obviously all the
interactions with the other types in my system.
Correct? So would it be better to prepare the
ion in a let's say dummy PDB file and convert
it to a LAMMPS input data with e.g. topotools
and then use read_data?

​the read_data command takes options like: ​extra/atom/types 
where you can reserve space for these atom types.

the basic rules in LAMMPS related to this are simple:
- number of atom/bond/angle/dihedral/improper types per atom, max bonds/angles/dihedrals/impropers per atom, max special per atom are locked in, when the simulation cell is created. this happens with either create_box, read_data or read_restart.
- this cannot be changed after that as it would require to redo the box creation. a new box can only be created after the clear command, which reinstantiates the LAMMPS class from scratch.

​no need to use a dummy atom, tho.​


​axel.​

 

Best regards,
Stephan


>
> ​axel​
>
>  
>
>
>     Thanks in advance.
>
>     Best regards,
>     Stephan
>
>
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> --
> Dr. Axel Kohlmeyer  akohlmey@...24... <mailto:akohlmey@...43...4...>
>  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

--
Stephan Grein
Department of Mathematics
Temple University
1805 N Broad Street, Room 513
Philadelphia, PA 19122-6094, USA
https://math.temple.edu/~queisser/
phone: +1 (215) 434-5843




--
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.