1MSI2LMP(1)                  General Commands Manual                 MSI2LMP(1)
2
3
4

NAME

6       MSI2LMP - Converter for Materials Studio files to LAMMPS
7
8

SYNOPSIS

10       msi2lmp  <ROOTNAME>  [-class  <I|1|II|2|O|0>] [-frc <path to frc file>]
11       [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
12
13

DESCRIPTION

15       MSI2LMP is a tool bundled with LAMMPS to aide in the conversion of sim‐
16       ulation  inputs  from  Biovia's  Materials Studio software for use with
17       LAMMPS.  It is a standalone program that generates a LAMMPS  data  file
18       based on the information in an MS .car file (atom coordinates), an .mdf
19       file (molecular topology and atom types) and an .frc (forcefield param‐
20       eters)  file.  The .car and .mdf files are specific to a molecular sys‐
21       tem while the .frc file is specific to  a  forcefield  (variant).   The
22       only  coherency  needed  between  .frc and .car/.mdf files are the atom
23       types.
24

OPTIONS

26       <ROOTNAME>
27              This has to be the first argument and is a  mandatory  argument.
28              It  defines the root of the file names; i.e. for a <ROOTNAME> of
29              benzene, you have to provide the files 'benzene.car'  and  'ben‐
30              zene.mdf'  in  the current working directory.  msi2lmp will then
31              read and process those files according  to  its  remaining  set‐
32              tings.   All  other  settings  are optional and have defaults as
33              listed.
34
35       -c <I,1,II,2,O,0>, -class <I,1,II,2,O,0>
36              The -c or -class option selects the force field class, i.e which
37              pair styles and bond styles and so on are required in the LAMMPS
38              input file.  Class I or class  1  uses  similar  combination  of
39              functional forms as Amber and Charmm force field and support the
40              force fields cvff and clayff.  Class II or class  2  corresponds
41              to  the  more complex force fields COMPASS and pcff.  Class O or
42              class 0 finally is an experimental and incomplete extension  and
43              supports generating output for OPLS-AA
44
45       -f <ffname>, -frc <ffname>
46              The  -c  or  -frc option allows the selection of the force field
47              parameter file Valid names for <ffname> with  this  distribution
48              are: cvff, clayff, cvff_aug, pcff, compass_published, cff91, and
49              oplsaa. If the argument is a pathname, i.e. it starts with a '.'
50              or  a  '/',  then  this  absolute path is used to read the force
51              field, otherwise msi2lmp will look in the folder pointed  to  by
52              the  environment  variable  $MSI2LMP_LIBRARY. If the variable is
53              not set, then it will look in the current directory. The  exten‐
54              sion '.frc' is appended, if missing.  Default is to look for the
55              cvff.frc force field file.
56
57       -p <loglevel>, -print <loglevel>,
58              Selects the amount of information messages about the progress of
59              the  conversion printed to the screen.  <loglevel> can be a num‐
60              ber from 0 (silent except for errors) to 3 (very detailed).
61
62       -i, -ignore,
63              Ignore errors about missing parameters and use 0.0 for  the  re‐
64              spective  force  constants making these no-ops. Is correct to be
65              used for a few molecules and settings, but often an  indication,
66              that  either  the atom type assignment have errors, or the force
67              field file is missing entries.
68
69       -n, -nocenter,
70              Do not center the box around the  (geometrical)  center  of  the
71              atoms, but around the origin. Default is to recenter.
72
73       -o, -oldstyle,
74              Write out a data file without style hint comments to be compati‐
75              ble with old LAMMPS versions. Default is to write out those com‐
76              ments.
77
78       -s <x> <y> <z>, -shift <x> <y> <z>,
79              Shift  the  entire system (box and coordinates) by a vector (de‐
80              fault: 0.0 0.0 0.0).
81
82
83
84       EXAMPLES
85
86              msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
87
88              msi2lmp benzene-class1 -c I
89
90              msi2lmp decane -c 0 -f oplsaa
91
92
93
95       © 2003--2022 Sandia Corporation
96
97       This package is free software; you can redistribute it and/or modify it
98       under  the  terms  of  the GNU General Public License version 2 as pub‐
99       lished by the Free Software Foundation.
100
101       This package is distributed in the hope that it  will  be  useful,  but
102       WITHOUT  ANY  WARRANTY;  without  even  the  implied  warranty  of MER‐
103       CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  General
104       Public License for more details.
105
106
107
108
1092018-11-05                          v3.9.9                          MSI2LMP(1)
Impressum