forked from lijiext/lammps
add manpage for msi2lmp
This commit is contained in:
Axel Kohlmeyer
parent
3b43fc3ea7
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a6c9a782a4
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@ -1472,6 +1472,7 @@ if(BUILD_EXE)
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add_executable(msi2lmp ${MSI2LMP_SOURCES})
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target_link_libraries(msi2lmp m)
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install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
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install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
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endif()
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@ -0,0 +1,111 @@
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.TH MSI2LMP "v3.9.9" "2018-11-05"
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.SH NAME
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.B MSI2LMP
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\- Converter for Materials Studio files to LAMMPS
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.SH SYNOPSIS
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.B msi2lmp
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<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
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.SH DESCRIPTION
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.PP
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.B MSI2LMP
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is a tool bundled with LAMMPS to aide in the conversion of simulation
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inputs from Biovia's Materials Studio software for use with LAMMPS.
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It is a standalone program that generates a LAMMPS data file based on
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the information in an MS .car file (atom coordinates), an .mdf file
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(molecular topology and atom types) and an .frc (forcefield parameters)
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file. The .car and .mdf files are specific to a molecular system while
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the .frc file is specific to a forcefield (variant). The only coherency
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needed between .frc and .car/.mdf files are the atom types.
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.PP
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.SH OPTIONS
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.TP
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\fB\<ROOTNAME>\fR
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This has to be the first argument and is a
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.B mandatory
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argument. It defines the root of the file names; i.e. for a
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.B <ROOTNAME>
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of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
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in the current working directory.
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.B msi2lmp
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will then read and process those files according to its remaining settings.
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All other settins are optional and have defaults as listed.
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.TP
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\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
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The \-c or \-class option selects the force field class, i.e which pair
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styles and bond styles and so on are required in the LAMMPS input file.
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Class I or class 1 uses similar combination of functional forms as Amber
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and Charmm force field and support the force fields
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.B cvff
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and
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.B clayff.
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Class II or class 2 corresponds to the more complex force fields
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.B COMPASS
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and
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.B pcff.
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Class O or class 0 finally is an experimental and incomplete extension
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and supports generating output for
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.B OPLS-AA
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.TP
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\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
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The \-c or \-frc option allows the selection of the force field parameter
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file
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.B<ffname>.frc.
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Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
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pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
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i.e. it starts with a '.' or a '/', then this absolute path is used to read
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the force field, otherwise
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.B msi2lmp
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will look in the folder pointed to by the environment variable
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$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
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directory. The extension '.frc' is appended, if missing.
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Default is to look for the cvff.frc force field file.
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.TP
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\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
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Selects the amount of information messages about the progress of the
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conversion printed to the screen.
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.B <loglevel>
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can be a number from 0 (silent except for errors) to 3 (very detailed).
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.TP
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\fB\-i\fR, \fB\-ignore\fR,
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Ignore errors about missing parameters and use 0.0 for the respective
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force constants making these no-ops. Is correct to be used for a few
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molecules and settings, but often an indication, that either the atom
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type assignment have errors, or the force field file is missing entries.
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.TP
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\fB\-n\fR, \fB\-nocenter\fR,
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Do not center the box around the (geometrical) center of the atoms,
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but around the origin. Default is to recenter.
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.TP
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\fB\-o\fR, \fB\-oldstyle\fR,
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Write out a data file without style hint comments to be compatible
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with old LAMMPS versions. Default is to write out those comments.
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.TP
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\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
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Shift the entire system (box and coordinates) by a vector
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(default: 0.0 0.0 0.0).
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.TP
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.SH EXAMPLES
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msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
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msi2lmp benzene-class1 -c I
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msi2lmp decane -c 0 -f oplsaa
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.SH COPYRIGHT
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© 2003--2019 Sandia Corporation
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This package is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License version 2 as
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published by the Free Software Foundation.
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This package is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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