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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: Tue, 19 Sep 2017 19:08:50 +0200


Am 15/09/17 um 20:56 schrieb Axel Kohlmeyer:
> 
> 
> On Fri, Sep 15, 2017 at 1:48 PM, Stephan Grein
> <stephan.grein@...5733...
> <mailto: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.​

Thanks for pointing that out.

This might seem like a silly question:
If I don't need extra atom types for my molecule
I want to add via the molecule command I could just
use the atom types provided from my "main molecule"
which I loaded before with the read_data command.
There is probably no automation I could make use of.
Correct? (Just want to make sure I don't miss
something or do unneccesary work). TIA.

Best wishes,
Stephan


> 
> 
> ​axel.​
> 
>  
> 
> 
>     Best regards,
>     Stephan
> 
> 
>     >
>     > ​axel​
>     >
>     >  
>     >
>     >
>     >     Thanks in advance.
>     >
>     >     Best regards,
>     >     Stephan
>     >
>     >
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>     >
>     >
>     > --
>     > Dr. Axel Kohlmeyer  akohlmey@...24... <mailto:akohlmey@...29....>
>     <mailto:akohlmey@...24... <mailto:akohlmey@...24...>>
>     >  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/ <https://math.temple.edu/~queisser/>
>     phone: +1 (215) 434-5843
> 
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer  akohlmey@...24... <mailto:akohlmey@...24...>
>  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.


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