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README
msi2lmp.exe
This code has several known limitations listed below under "LIMITATIONS"
(and possibly some unknown ones, too) and is no longer under active
development. Only the occasional bugfix is applied.
Please send any inquiries about msi2lmp to the lammps-users
mailing list and not to individual people.
------------------------------------------------------------------------
OVERVIEW
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 third version was revised in Fall 2011 by Stephanie Teich-McGoldrick
to add support non-orthogonal cells.
The next revision was started in Summer/Fall 2013 by Axel Kohlmeyer to
improve portability to Windows compilers, clean up command line parsing
and improve compatibility with the then current LAMMPS versions. This
revision removes compatibility with the obsolete LAMMPS version written
in Fortran 90.
INSTALLATION & USAGE
This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
program to produce a LAMMPS data file.
1. Building msi2lmp
If you are using CMake to compile LAMMPS, the building
(and installation) of msi2lmp is included in the normal
build process.
Otherwise you can 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.
------------------------------------------------------------------------
LIMITATIONS
msi2lmp has the following known limitations:
- there is no support to select morse bonds over harmonic bonds
- there is no support for auto-equivalences to supplement fully
parameterized interactions with heuristic ones
- there is no support for bond increments
- there is no support for coordinates defined by symmetry operations,
i.e. the .mdf file has to be set up for space group P1
------------------------------------------------------------------------
CHANGELOG
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.
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
V3.6 outputs to LAMMPS 2005 (C++ version).
Contact: Kelly L. Anderson, kelly.anderson@cantab.net
V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car
and .mdf files written by Accelys' Materials Studio GUI. April 2005
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.
V3.2 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.
-----------------------------
msi2lmp v3.9.8 6/10/2016