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Stephanie Teich-McGoldrick (Sandai) is the current maintainer
of the msi2lmp tool. She can be contacted at steichm at sandia.gov
1 Jul 2013
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 msi2lmp3
Use the Makefile in the src directory. It is
currently set up for gcc. One will have to modify
it to use a different compiler.
2. Testing the program
There are three pairs (.car and .mdf) files in the
test directory: crambin, nylon and phen3_cff97. The
atom types in crambin and nylon are cvff (Class I) atom
types and those in phen3_cff97 are cff9x (Class II) atom types.
Two forcefield files, cvff.frc and cff91.frc, are needed
generate lammps data files for these three test files. To
run it you would:
% setenv BIOSYM_LIBRARY ../biosym_frc_files
% ../src/msi2lmp.exe nylon -class I -frc cvff > data.nylon
% ../src/msi2lmp.exe crambin -class I -frc cvff > data.crambin
% ../src/msi2lmp.exe phen3_cff97 -class II -frc cff91 > data.phen3_cff97
Three files should be generated: data.nylon, data.crambin
and data.phen3_cff97. These can be compared against
data.x in the directory correct. If there are differences,
first recompile the program with no optimization and try again.
If there are still differences, send email to jec@mayo.edu
Note: you will see many "Unable to find..." parameters messages
in the phen3_cff97 test case. Most of those parameters
exist in cff95.frc, but not in cff91.frc
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 {-2001} {-print #} {-class #} {-frc FRC_FILE}
-- 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.
-- -class (or -c)
# is the class of forcefield to use (I or 1 = Class I e.g., CVFF)
(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 $BIOSYM_LIBRARY (or %BIOSYM_LIBRARY% on Windows).
If $BIOSYM_LIBRARY is not set, ../biosym_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 $BIOSYM_LIBRARY
or ../biosym_frc_files)
-frc cff/cff91 (assumes cff91.frc is in cff)
-frc /usr/local/biosym/forcefields/cff95
(assumes cff95.frc is in /usr/local/biosym/forcefields/)
By default, the program uses $BIOSYM_LIBRARY/cvff.frc or ../biosym_frc_files/cvff.frc
-- the LAMMPS data file is written to ROOTNAME.lammps{01/05},
protocol and error information is written to the screen.
****************************************************************
*
* Msi2lmp3
*
* 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
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