MSI2LMP(1)

Hey bestie 💖 welcome to MSI2LMP(1) from the General Commands Manual — this is the whole converter-for-Materials-Studio-files-to-LAMMPS situation, and yes, we’re gonna get through every single flag together. 🫶

✨ NAME ✨

MSI2LMP — converter for Materials Studio files to LAMMPS.

That’s the whole name vibe: it takes Materials Studio stuff and makes it LAMMPS-ready. 💅

🌈 SYNOPSIS 🌈

The call shape is literally this, bestie — don’t improvise the spelling:

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

🦋 DESCRIPTION 🦋

Okay so MSI2LMP is a tool bundled with LAMMPS to aide in the conversion of simulation inputs from Biovia’s Materials Studio software for use with LAMMPS. It’s a standalone program that generates a LAMMPS data file based on the information in an MS .car file (atom coordinates), an .mdf file (molecular topology and atom types), and an .frc file (forcefield parameters).

The .car and .mdf files are specific to a molecular system, while the .frc file is specific to a forcefield (variant). The only coherency needed between the .frc and .car/.mdf files is the atom types. That’s the whole compatibility bridge, bestie. 🌉

💅 OPTIONS 💅

• -h, -help — Print a detailed help message to the screen and stop. Like a little “help me help you” moment. 🆘
• <ROOTNAME> — This has to be the first argument and it is mandatory. It defines the root of the file names; i.e. for a <ROOTNAME> of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf' in the current working directory. msi2lmp will then read and process those files according to its remaining settings. All other settings are optional and have defaults as listed. So yes: root name first, always. 👑
• -c <I,1,II,2,O,0>, -class <I,1,II,2,O,0> — The -c or -class option selects the force field class, i.e which pair styles and bond styles and so on are required in the LAMMPS input file. Class I or class 1 uses a similar combination of functional forms as the Amber and Charmm force field and supports the force fields cvff and clayff. Class II or class 2 corresponds to the more complex force fields COMPASS and pcff. Class O or class 0 is finally an experimental and incomplete extension and supports generating output for OPLS-AA. So: not all classes are equally complete, and O/0 is explicitly labeled experimental. 🧪
• -f <ffname>, -frc <ffname> — The original page says “The -c or -frc option” right here (yes, really), and this is the option that lets you select the force field parameter file. Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug, pcff, compass_published, cff91, and oplsaa. If the argument is a pathname, i.e. it starts with a . or a /, then this absolute path is used to read the force field; otherwise msi2lmp will look in the folder pointed to by the environment variable $MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current directory. The extension .frc is appended, if missing. Default is to look for the cvff.frc force field file. Cute path drama, but it’s all specified. 🗂️
• -p <loglevel>, -print <loglevel> — Selects the amount of information messages about the progress of the conversion printed to the screen. <loglevel> can be a number from 0 (silent except for errors) to 3 (very detailed). So 0 = quiet queen, 3 = tell me everything. 🗣️
• -i, -ignore — Ignore errors about missing parameters and use 0.0 for the respective force constants, making these no-ops. It’s correct to be used for a few molecules and settings, but often an indication that either the atom type assignment has errors, or the force field file is missing entries. So use it sometimes, but side-eye it when it’s doing too much. 👀
• -n, -nocenter — Do not center the box around the (geometrical) center of the atoms, but around the origin. Default is to recenter. So default = recenter; this flag = origin time. 🎯
• -o, -oldstyle — Write out a data file without style hint comments to be compatible with old LAMMPS versions. Default is to write out those comments. Retro-compatible era, but only when you ask. 🕰️
• -s <x> <y> <z>, -shift <x> <y> <z> — Shift the entire system (box and coordinates) by a vector (default: 0.0 0.0 0.0). Move the whole vibe, box and all. 🚚

🌸 EXAMPLES 🌸

Copy-paste these bad boys exactly:

msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc

msi2lmp benzene-class1 -c I

msi2lmp decane -c 0 -f oplsaa

👑 COPYRIGHT 👑

© 2003--2022 Sandia Corporation

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.

This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

---

That’s the whole page, bestie 💖 — MSI2LMP(1), source/version v3.9.10, dated 2023-03-10, signing off with all the sparkle. 🎀✨