lammps/tools/msi2lmp/README

Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
Please send any inquiries about msi2lmp to the lammps-users mailing list.

06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>

Improved whitespace handling in parsing topology and force field
files to avoid bogus warnings about type name truncation.

24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>

Added check to make certain that force field files
are consistent with the notation of non-bonded parameters
that the msi2lmp code expects. For Class 1 and OPLS-AA
the A-B notation with geometric mixing is expected and for
Class 2 the r-eps notation with sixthpower mixing.

11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>

Refactored ReadMdfFile.c so it more consistently honors
the MAX_NAME and MAX_STRING string length defines and 
potentially handles inputs with long names better.

27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>

Added TopoTools style type hints as comments to all Mass, PairCoeff,
BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
This should make it easier to identify force field entries with
the structure and force field map in the data file later.

06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>

Fixed a bug in handling of triclinic cells, where the matrices to
convert to and from fractional coordinates were incorrectly built.

26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Implemented writing out force field style hints in generated data
files for improved consistency checking when reading those files.
Also added writing out CGCMM style comments to identify atom types.

08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Fixed a memory access violation with Class 2 force fields.
Free all allocated memory to better detection of memory errors.
Print out version number and data with all print levels > 0.
Added valgrind checks to the regression tests

08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Fixed a memory access violation with Class 2 force fields.
Free all allocated memory to better detection of memory errors.
Print out version number and data with all print levels > 0.
Added valgrind checks to the regression tests

02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Added rudimentary support for OPLS-AA based on
input provided by jeff greathouse.

18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Added support for writing out image flags
Improved accuracy of atom masses
Added flag for shifting the entire system
Fixed some minor logic bugs and prepared
for supporting other force fields and morse style bonds.

12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Fixed the bug that caused improper coefficients to be wrong
Cleaned up the handling of box parameters and center the box
by default around the system/molecule. Added a flag to make
this step optional and center the box around the origin instead.
Added a regression test script with examples.

1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>

Cleanup and improved port to windows.
Removed some more static string limits.
Added print level 3 for additional output.
Make code stop at missing force field parameters
and added -i flag to override this.
Safer argument checking.
Provide short versions for all flags.

23 Sep 2011

added support for triclinic boxes
see msi2lmp/TriclinicModification.pdf doc for details

-----------------------------

 msi2lmp V3.6 4/10/2005

 This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
 program to produce a LAMMPS data file.

 1. Building msi2lmp

    Use the Makefile in the src directory. It is
    currently set up for gcc. You will have to modify
    it to use a different compiler.

 2. Testing the program

    There are several pairs of input test files in the format generated
    by materials studio or compatible programs (one .car and one .mdf
    file each) in the test directory. There is also a LAMMPS input to
    run a minimization for each and write out the resulting system as
    a data file. With the runtests.sh script all of those inputs are
    converted via msi2lmp, then the minimization with LAMMPS is run
    and the generated data files are compared with the corresponding
    files in the reference folder. This script assumes you are on a 
    unix/linux system and that you have compile a serial LAMMPS executable
    called lmp_serial with make serial. The tests are groups by the
    force fields they use.

 3. To run the program

    The program is started by supplying information at the command prompt
    according to the usage described below.  

    USAGE: msi2lmp.exe <ROOTNAME> {-print #} {-class #} {-frc FRC_FILE}
                {-ignore} {-nocenter} {-shift # # #}

   -- msi2lmp.exe is the name of the executable
   -- <ROOTNAME> is the base name of the .car and .mdf files
   -- -2001
         Output lammps files for LAMMPS version 2001 (F90 version)
         Default is to write output for the C++ version of LAMMPS

   -- -print (or -p)
	 # is the print level  0 - silent except for error messages
	                       1 - minimal (default)
                               2 - verbose (usual for developing and
                                   checking new data files for consistency)
                               3 - even more verbose (additional debug info)

   -- -ignore (or -i)     ignore errors about missing force field parameters
                          and treat them as warnings instead.

   -- -nocenter (or -n)   do not recenter the simulation box around the
                          geometrical center of the provided geometry but
                          rather around the origin

   -- -oldstyle (or -o)   write out a data file without style hints
                          (to be compatible with older LAMMPS versions)

   -- -shift (or -s)      translate the entire system (box and coordinates)
                          by a vector (default: 0.0 0.0 0.0)

   -- -class  (or -c)
        # is the class of forcefield to use (I  or 1 = Class I e.g., CVFF)
                                            (O  or 0 = OPLS-AA)
                                            (II or 2 = Class II e.g., CFFx)
        default is -class I

   -- -frc    (or -f) specifies name of the forcefield file (e.g., cff91)
 
     If the file name includes a directory component (or drive letter 
     on Windows), then the name is used as is. Otherwise, the program
     looks for the forcefield file in $MSI2LMP_LIBRARY (or %MSI2LMP_LIBRARY%
     on Windows). If $MSI2LMP_LIBRARY is not set, ../frc_files is used
     (for testing). If the file name does not end in .frc, then .frc
     is appended to the name.

     For example,  -frc cvff (assumes cvff.frc is in $MSI2LMP_LIBRARY
                              or ../frc_files)

                   -frc cff/cff91 (assumes cff91.frc is in cff)

                   -frc /usr/local/forcefields/cff95
                       (assumes cff95.frc is in /usr/local/forcefields/)

     By default, the program uses $MSI2LMP_LIBRARY/cvff.frc  or
      ../frc_files/cvff.frc depending on whether MSI2LMP_LIBRARY is set.

  -- the LAMMPS data file is written to <ROOTNAME>.data
     protocol and error information is written to the screen.

****************************************************************
*
* msi2lmp
*
* This is the third version of a program that generates a LAMMPS
* data file based on the information in MSI .car (atom
* coordinates), .mdf (molecular topology) and .frc (forcefield) 
* files. The .car and .mdf files are specific to a molecular
* system while the .frc file is specific to a forcefield version.
* The only coherency needed between .frc and .car/.mdf files are
* the atom types. 
*
* The first version was written by Steve Lustig at Dupont, but
* required using Discover to derive internal coordinates and
* forcefield parameters
*
* The second version was written by Michael Peachey while an
* intern in the Cray Chemistry Applications Group managed
* by John Carpenter. This version derived internal coordinates
* from the mdf file and looked up parameters in the frc file
* thus eliminating the need for Discover.
*
* The third version was written by John Carpenter to optimize
* the performance of the program for large molecular systems
* (the original  code for deriving atom numbers was quadratic in time)
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* The current maintainer is only reluctantly doing so because John Mayo no longer
* needs this code.
*
* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
* for number_of_dihedrals, etc. could be unpredictable in these systems.
*
* V3.3 was generated in response to a strange error reading a MDF file generated by
* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c 
* seems to have fixed the problem.
*
* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
* written by Accelys' Materials Studio GUI.
*
* V3.6 outputs to LAMMPS 2005 (C++ version).
*
* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
* 
* April 2005