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Building LAMMPS Data Files With Car/mdf Files and The Msi2lmp Utility

This document describes how to build LAMMPS data files from structure files (car/mdf files) containing molecular information using the msi2lmp utility. It outlines the components of LAMMPS data files and structure files, describes force field files that contain energy parameters, and provides examples of generating data files for kaolinite and toluene vapor simulations. The msi2lmp tool reads structure files and force field files and automatically generates the corresponding LAMMPS data file for molecular simulations.

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254 views9 pages

Building LAMMPS Data Files With Car/mdf Files and The Msi2lmp Utility

This document describes how to build LAMMPS data files from structure files (car/mdf files) containing molecular information using the msi2lmp utility. It outlines the components of LAMMPS data files and structure files, describes force field files that contain energy parameters, and provides examples of generating data files for kaolinite and toluene vapor simulations. The msi2lmp tool reads structure files and force field files and automatically generates the corresponding LAMMPS data file for molecular simulations.

Uploaded by

adil
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Building LAMMPS data files with

car/mdf files and the msi2lmp utility

Jeffery A. Greathouse

Sandia National Laboratories, Albuquerque, New Mexico

Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company,


for the United States Department of Energy’s National Nuclear Security Administration
under contract DE-AC04-94AL85000.
Outline
► Description of files
 LAMMPS data file
 Structure files (car/mdf) Biosym/Discover
 Force field files (frc) software
 msi2lmp.exe

► Mineral with limited bonding (kaolinite)

► Bonded organic molecule (toluene)

2
LAMMPS Data Files
► http://lammps.sandia.gov/doc/read_data.html

► Typical components (toluene.lammps05)


 Summary of molecular connectivity
 Cell dimensions
 Force field parameters (pair, bond, angle, dihedral,
improper)
 Atom info (molecule #, atom type #, charge, xyz
coordinates)
 Bond info (bonds, angles, etc)

► Examples in LAMMPS distribution

3
Structure Files

► car file (coordinates, atom type, charge)

C1 -0.692663292 -0.094096410 0.003399037 XXXX 1 cp C -0.100


C2 0.080988729 -1.425449986 0.004347065 XXXX 1 cp C -0.100
C3 1.620876319 -1.420834453 0.005671437 XXXX 1 cp C -0.100
C4 2.386905208 -0.085003697 -0.002079692 XXXX 1 cp C -0.100
C5 1.613536848 1.246298529 -0.026904058 XXXX 1 cp C 0.000
C6 0.073572216 1.241704742 -0.004902500 XXXX 1 cp C -0.100
C7 2.379381006 2.581705596 0.007764760 XXXX 1 c3 C -0.300
H1 -1.832488967 -0.097446130 0.009999447 XXXX 1 h H 0.100
H2 -0.486334530 -2.414248925 0.007052748 XXXX 1 h H 0.100
H3 2.193596249 -2.406396682 0.013631449 XXXX 1 h H 0.100
H4 3.526773693 -0.081542221 0.008067005 XXXX 1 h H 0.100
H5 -0.499289128 2.227113274 0.002830637 XXXX 1 h H 0.100
H6 2.624394086 2.906106279 -1.057242639 XXXX 1 h H 0.100
H7 3.346362304 2.450326318 0.597088580 XXXX 1 h H 0.100
H8 1.733495243 3.376908124 0.507943882 XXXX 1 h H 0.100

4
Structure Files

► mdf file (atom type, charge, bonding information)

XXXX_1:C1 C cp ? 0 0 -0.1000 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H1


XXXX_1:C2 C cp ? 0 0 -0.1000 0 0 8 1.0000 0.0000 C3/1.5 C1/1.5 H2
XXXX_1:C3 C cp ? 0 0 -0.1000 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H3
XXXX_1:C4 C cp ? 0 0 -0.1000 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H4
XXXX_1:C5 C cp ? 0 0 0.0000 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C7
XXXX_1:C6 C cp ? 0 0 -0.1000 0 0 8 1.0000 0.0000 C5/1.5 C1/1.5 H5
XXXX_1:C7 C c3 ? 0 0 -0.3000 0 0 8 1.0000 0.0000 C5 H6 H7 H8
XXXX_1:H1 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C1
XXXX_1:H2 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C2
XXXX_1:H3 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C3
XXXX_1:H4 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C4
XXXX_1:H5 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C6
XXXX_1:H6 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C7
XXXX_1:H7 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C7
XXXX_1:H8 H h ? 0 0 0.1000 0 0 8 1.0000 0.0000 C7
5
Force Field Files
► These files are in the Biosym/Discover format and
available in the LAMMPS distribution (…/tools/msi2lmp)
 cff91.frc
 cvff.frc
 cvff_aug.frc
 pcff.frc (pcff.rlb and pcff_templates.dat also needed)
► Information contained in frc files
 Atom types
 Energy expressions and parameters
 Atomic charge assignments (not used by msi2lmp)
► Build you own frc file (clayff.frc)

6
msi2lmp.exe
► Available in LAMMPS distribution (…/tools/msi2lmp)

► Written in C

► Updated as of LAMMPS 2005

► Reads molecular information from structure files and


produces a LAMMPS data file

► Syntax:
msi2lmp.exe root –frc frc_file
root = root name of car/mdf files (toluene.car,
toluene.mdf)
frc_file = Biosym/Discover force field file
7
Example – kaolinite Al2Si2O5(OH)4

► Fully bonded model


 Created with Materials
Studio software
 Atom types assigned
manually

► Nonbonded model for LAMMPS


simulations (except for hydroxyl
groups)

► Build kaolinite data file from


kaolinite.car and kaolinite.mdf
8
Example – toluene vapor
► Atom types and charges
assigned automatically with
Materials Studio software

► All other parameters assigned


automatically from cvff.frc
 pair coeffs
 bond coeffs
 angle coeffs
 dihedral coeffs
 improper coeffs
► Build toluene data file from
toluene.car and toluene.mdf

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