forked from lijiext/lammps
refactor msi2lmp documentation to emphasize lack of active development
- put a note into the manual - reorder contents of the README file - request for information should be sent to lammps-users - add list of known missing features
This commit is contained in:
Axel Kohlmeyer
parent
2f32fb7f8b
commit
dd90c860ee
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@ -369,15 +369,18 @@ supports it. It has its own WWW page at
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msi2lmp tool :h4,link(msi)
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The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from BIOVIA's Materias Studio files (formerly Accelrys'
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The msi2lmp sub-directory contains a tool for creating LAMMPS template
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input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
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Insight MD code, formerly MSI/Biosym and its Discover MD code).
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This tool was written by John Carpenter (Cray), Michael Peachey
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(Cray), and Steve Lustig (Dupont). Several people contributed changes
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to remove bugs and adapt its output to changes in LAMMPS.
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See the README file for more information.
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This tool has several known limitations and is no longer under active
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development, so there are no changes except for the occasional bugfix.
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See the README file in the tools/msi2lmp folder for more information.
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:line
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@ -1,98 +1,50 @@
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Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
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Please send any inquiries about msi2lmp to the lammps-users mailing list.
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06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
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msi2lmp.exe
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Improved whitespace handling in parsing topology and force field
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files to avoid bogus warnings about type name truncation.
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This code has several known limitations listed below under "LIMITATIONS"
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(and possibly some unknown ones, too) and is no longer under active
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development. Only the occasional bugfix is applied.
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24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
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Please send any inquiries about msi2lmp to the lammps-users
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mailing list and not to individual people.
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Added check to make certain that force field files
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are consistent with the notation of non-bonded parameters
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that the msi2lmp code expects. For Class 1 and OPLS-AA
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the A-B notation with geometric mixing is expected and for
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Class 2 the r-eps notation with sixthpower mixing.
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------------------------------------------------------------------------
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11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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OVERVIEW
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Refactored ReadMdfFile.c so it more consistently honors
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the MAX_NAME and MAX_STRING string length defines and
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potentially handles inputs with long names better.
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This is the third version of a program that generates a LAMMPS data file
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based on the information in MSI .car (atom coordinates), .mdf (molecular
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topology) and .frc (forcefield) files. The .car and .mdf files are
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specific to a molecular system while the .frc file is specific to a
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forcefield version. The only coherency needed between .frc and
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.car/.mdf files are the atom types.
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27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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The first version was written by Steve Lustig at Dupont, but required
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using Discover to derive internal coordinates and forcefield parameters
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Added TopoTools style type hints as comments to all Mass, PairCoeff,
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BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
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This should make it easier to identify force field entries with
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the structure and force field map in the data file later.
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The second version was written by Michael Peachey while an intern in the
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Cray Chemistry Applications Group managed by John Carpenter. This
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version derived internal coordinates from the mdf file and looked up
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parameters in the frc file thus eliminating the need for Discover.
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06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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The third version was written by John Carpenter to optimize the
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performance of the program for large molecular systems (the original
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code for deriving atom numbers was quadratic in time) and to make the
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program fully dynamic. The second version used fixed dimension arrays
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for the internal coordinates.
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Fixed a bug in handling of triclinic cells, where the matrices to
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convert to and from fractional coordinates were incorrectly built.
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The third version was revised in Fall 2011 by Stephanie Teich-McGoldrick
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to add support non-orthogonal cells.
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26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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The next revision was started in Summer/Fall 2013 by Axel Kohlmeyer to
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improve portability to Windows compilers, clean up command line parsing
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and improve compatibility with the then current LAMMPS versions. This
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revision removes compatibility with the obsolete LAMMPS version written
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in Fortran 90.
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Implemented writing out force field style hints in generated data
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files for improved consistency checking when reading those files.
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Also added writing out CGCMM style comments to identify atom types.
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INSTALLATION & USAGE
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08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed a memory access violation with Class 2 force fields.
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Free all allocated memory to better detection of memory errors.
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Print out version number and data with all print levels > 0.
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Added valgrind checks to the regression tests
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08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed a memory access violation with Class 2 force fields.
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Free all allocated memory to better detection of memory errors.
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Print out version number and data with all print levels > 0.
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Added valgrind checks to the regression tests
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02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Added rudimentary support for OPLS-AA based on
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input provided by jeff greathouse.
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18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Added support for writing out image flags
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Improved accuracy of atom masses
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Added flag for shifting the entire system
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Fixed some minor logic bugs and prepared
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for supporting other force fields and morse style bonds.
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12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed the bug that caused improper coefficients to be wrong
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Cleaned up the handling of box parameters and center the box
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by default around the system/molecule. Added a flag to make
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this step optional and center the box around the origin instead.
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Added a regression test script with examples.
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1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Cleanup and improved port to windows.
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Removed some more static string limits.
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Added print level 3 for additional output.
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Make code stop at missing force field parameters
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and added -i flag to override this.
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Safer argument checking.
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Provide short versions for all flags.
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23 Sep 2011
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added support for triclinic boxes
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see msi2lmp/TriclinicModification.pdf doc for details
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-----------------------------
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msi2lmp V3.6 4/10/2005
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This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
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This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
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program to produce a LAMMPS data file.
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1. Building msi2lmp
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@ -178,50 +130,111 @@ see msi2lmp/TriclinicModification.pdf doc for details
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-- the LAMMPS data file is written to <ROOTNAME>.data
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protocol and error information is written to the screen.
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****************************************************************
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*
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* msi2lmp
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*
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* This is the third version of a program that generates a LAMMPS
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* data file based on the information in MSI .car (atom
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* coordinates), .mdf (molecular topology) and .frc (forcefield)
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* files. The .car and .mdf files are specific to a molecular
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* system while the .frc file is specific to a forcefield version.
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* The only coherency needed between .frc and .car/.mdf files are
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* the atom types.
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*
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* The first version was written by Steve Lustig at Dupont, but
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* required using Discover to derive internal coordinates and
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* forcefield parameters
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*
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* The second version was written by Michael Peachey while an
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* intern in the Cray Chemistry Applications Group managed
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* by John Carpenter. This version derived internal coordinates
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* from the mdf file and looked up parameters in the frc file
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* thus eliminating the need for Discover.
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*
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* The third version was written by John Carpenter to optimize
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* the performance of the program for large molecular systems
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* (the original code for deriving atom numbers was quadratic in time)
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* and to make the program fully dynamic. The second version used
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* fixed dimension arrays for the internal coordinates.
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*
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* The current maintainer is only reluctantly doing so because John Mayo no longer
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* needs this code.
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*
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* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
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* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
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* for number_of_dihedrals, etc. could be unpredictable in these systems.
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*
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* V3.3 was generated in response to a strange error reading a MDF file generated by
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* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c
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* seems to have fixed the problem.
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*
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* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
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* written by Accelys' Materials Studio GUI.
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*
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* V3.6 outputs to LAMMPS 2005 (C++ version).
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*
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* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
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*
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* April 2005
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------------------------------------------------------------------------
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LIMITATIONS
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msi2lmp has the following known limitations:
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- there is no support to select morse bonds over harmonic bonds
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- there is no support for auto-equivalences to supplement fully
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parameterized interactions with heuristic ones
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- there is no support for bond increments
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------------------------------------------------------------------------
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CHANGELOG
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06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
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Improved whitespace handling in parsing topology and force field
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files to avoid bogus warnings about type name truncation.
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24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
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Added check to make certain that force field files are consistent with
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the notation of non-bonded parameters that the msi2lmp code expects.
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For Class 1 and OPLS-AA the A-B notation with geometric mixing is
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expected and for Class 2 the r-eps notation with sixthpower mixing.
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11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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Refactored ReadMdfFile.c so it more consistently honors the MAX_NAME
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and MAX_STRING string length defines and potentially handles inputs
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with long names better.
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27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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Added TopoTools style type hints as comments to all Mass, PairCoeff,
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BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
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This should make it easier to identify force field entries with
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the structure and force field map in the data file later.
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06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed a bug in handling of triclinic cells, where the matrices to
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convert to and from fractional coordinates were incorrectly built.
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26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Implemented writing out force field style hints in generated data
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files for improved consistency checking when reading those files.
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Also added writing out CGCMM style comments to identify atom types.
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08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed a memory access violation with Class 2 force fields. Free all
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allocated memory to better detection of memory errors. Print out
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version number and data with all print levels > 0. Added valgrind
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checks to the regression tests.
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02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Added rudimentary support for OPLS-AA based on input provided
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by jeff greathouse.
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18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Added support for writing out image flags. Improved accuracy of atom
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masses. Added flag for shifting the entire system. Fixed some minor
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logic bugs and prepared for supporting other force fields and morse
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style bonds.
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12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Fixed the bug that caused improper coefficients to be wrong. Cleaned up
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the handling of box parameters and center the box by default around the
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system/molecule. Added a flag to make this step optional and center the
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box around the origin instead. Added a regression test script with
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examples.
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1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
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Cleanup and improved port to windows. Removed some more static string
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limits. Added print level 3 for additional output. Make code stop at
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missing force field parameters and added -i flag to override this.
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Safer argument checking. Provide short versions for all flags.
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23 Sep 2011
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added support for triclinic boxes
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V3.6 outputs to LAMMPS 2005 (C++ version).
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Contact: Kelly L. Anderson, kelly.anderson@cantab.net
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V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car
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and .mdf files written by Accelys' Materials Studio GUI. April 2005
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V3.3 was generated in response to a strange error reading a MDF file
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generated by Accelys' Materials Studio GUI. Simply rewriting the input
|
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part of ReadMdfFile.c seems to have fixed the problem.
|
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|
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V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
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systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
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for number_of_dihedrals, etc. could be unpredictable in these systems.
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-----------------------------
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msi2lmp v3.9.8 6/10/2016
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