1MSI2LMP(1) General Commands Manual MSI2LMP(1)
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6 MSI2LMP - Converter for Materials Studio files to LAMMPS
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10 msi2lmp <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>]
11 [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
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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.
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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 -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 -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 -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 -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 -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 -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 -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 EXAMPLES
85 msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
87 msi2lmp benzene-class1 -c I
89 msi2lmp decane -c 0 -f oplsaa
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95 © 2003--2022 Sandia Corporation
96 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 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.
1052018-11-05 v3.9.9 MSI2LMP(1)