diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index d17e9dab19..722c0992ba 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -1472,6 +1472,7 @@ if(BUILD_EXE) add_executable(msi2lmp ${MSI2LMP_SOURCES}) target_link_libraries(msi2lmp m) install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) + install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) endif() diff --git a/doc/msi2lmp.1 b/doc/msi2lmp.1 new file mode 100644 index 0000000000..08a442e1de --- /dev/null +++ b/doc/msi2lmp.1 @@ -0,0 +1,111 @@ +.TH MSI2LMP "v3.9.9" "2018-11-05" +.SH NAME +.B MSI2LMP +\- Converter for Materials Studio files to LAMMPS + +.SH SYNOPSIS +.B msi2lmp + [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift ] + +.SH DESCRIPTION +.PP +.B 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 is 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 (forcefield parameters) +file. 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 .frc and .car/.mdf files are the atom types. +.PP + +.SH OPTIONS +.TP +\fB\\fR +This has to be the first argument and is a +.B mandatory +argument. It defines the root of the file names; i.e. for a +.B +of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf' +in the current working directory. +.B msi2lmp +will then read and process those files according to its remaining settings. +All other settins are optional and have defaults as listed. +.TP +\fB\-c \fR, \fB\-class \fR +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 similar combination of functional forms as Amber +and Charmm force field and support the force fields +.B cvff +and +.B clayff. +Class II or class 2 corresponds to the more complex force fields +.B COMPASS +and +.B pcff. +Class O or class 0 finally is an experimental and incomplete extension +and supports generating output for +.B OPLS-AA +.TP +\fB\-f \fR, \fB\-frc \fR +The \-c or \-frc option allows the selection of the force field parameter +file +.B.frc. +Valid names for 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 +.B 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. +.TP +\fB\-p \fR, \fB\-print \fR, +Selects the amount of information messages about the progress of the +conversion printed to the screen. +.B +can be a number from 0 (silent except for errors) to 3 (very detailed). +.TP +\fB\-i\fR, \fB\-ignore\fR, +Ignore errors about missing parameters and use 0.0 for the respective +force constants making these no-ops. Is correct to be used for a few +molecules and settings, but often an indication, that either the atom +type assignment have errors, or the force field file is missing entries. +.TP +\fB\-n\fR, \fB\-nocenter\fR, +Do not center the box around the (geometrical) center of the atoms, +but around the origin. Default is to recenter. +.TP +\fB\-o\fR, \fB\-oldstyle\fR, +Write out a data file without style hint comments to be compatible +with old LAMMPS versions. Default is to write out those comments. +.TP +\fB-s \fR, \fB-shift \fR, +Shift the entire system (box and coordinates) by a vector +(default: 0.0 0.0 0.0). +.TP + +.SH EXAMPLES + +msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc + +msi2lmp benzene-class1 -c I + +msi2lmp decane -c 0 -f oplsaa + + +.SH COPYRIGHT +© 2003--2019 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. +