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Re: [lammps-users] Using msi2lmp and clayff
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Re: [lammps-users] Using msi2lmp and clayff


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 24 Jun 2017 10:53:53 -0400



On Sat, Jun 24, 2017 at 4:42 AM, neda Sanchuli via lammps-users <lammps-users@lists.sourceforge.net> wrote:
Dear All,

I want to simulate montmorillonite with lammps. First I created .car and .mdf file of the structure with Material Studio and then I used them to create data file with msi2lmp and clayff. But I get this warnings:

Forcefield file name: ../frc_files/clayff.frc
 Output is recentered around geometrical center
 Output contains style flag hints
 System translated by: 0 0 0
 Reading car file: mont.car
 Reading mdf file: mont.mdf

 Building internal coordinate lists
 WARNING inconsistent # of connects on atom 16 type ob
 WARNING inconsistent # of connects on atom 17 type ob
 WARNING inconsistent # of connects on atom 22 type ob
 WARNING inconsistent # of connects on atom 23 type ob
 WARNING inconsistent # of connects on atom 28 type ob
 WARNING inconsistent # of connects on atom 29 type ob
 WARNING inconsistent # of connects on atom 34 type ob
 WARNING inconsistent # of connects on atom 35 type ob

 Reading forcefield file

 Get force field parameters for this system
 Unable to find equivalent type for ao
 Unable to find equivalent type for ob
 Unable to find bond data for ao ob

I searched this problem in mailing lammps, Jeff suggested delete bonds in the Material Studio before using msi2lmp. I have a question. If I delete bonds, would lammps detect which atoms should have nonbonded interactions? Because when I delete bonds, there is no bonds between atoms except O and H.

​you have to look up how interactions in clayff are modeled. the relevant publication describing the force field has to tell you where explicit bonds are needed and where not. from the looks of it (but don't take my word for it), atoms of type ao and of type ob have no explicit bonds between them and other atoms. so, your topology in the .mdf file doesn't seem consistent with the force field and you get the errors as a consequence.

whether a​ pair of atoms interacts is independent of whether there is a bond shown in the visualization.

​axel.​


 
I definitely need help on this from lammps users.

Neda Sanchuli

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.