diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index 03611c7cdb..d95c4f0cd4 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -369,15 +369,18 @@ supports it. It has its own WWW page at msi2lmp tool :h4,link(msi) -The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from BIOVIA's Materias Studio files (formerly Accelrys' +The msi2lmp sub-directory contains a tool for creating LAMMPS template +input and data files from BIOVIA's Materias Studio files (formerly Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS. -See the README file for more information. +This tool has several known limitations and is no longer under active +development, so there are no changes except for the occasional bugfix. + +See the README file in the tools/msi2lmp folder for more information. :line diff --git a/tools/msi2lmp/README b/tools/msi2lmp/README index a20f6e893f..db9b1aca5e 100644 --- a/tools/msi2lmp/README +++ b/tools/msi2lmp/README @@ -1,98 +1,50 @@ -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 + msi2lmp.exe -Improved whitespace handling in parsing topology and force field -files to avoid bogus warnings about type name truncation. +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. -24 Oct 2015 Axel Kohlmeyer +Please send any inquiries about msi2lmp to the lammps-users +mailing list and not to individual people. -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 +OVERVIEW -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. +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. -27 May 2014 Axel Kohlmeyer +The first version was written by Steve Lustig at Dupont, but required +using Discover to derive internal coordinates and forcefield parameters -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. +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. -06 Mar 2014 Axel Kohlmeyer +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. -Fixed a bug in handling of triclinic cells, where the matrices to -convert to and from fractional coordinates were incorrectly built. +The third version was revised in Fall 2011 by Stephanie Teich-McGoldrick +to add support non-orthogonal cells. -26 Oct 2013 Axel Kohlmeyer +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. -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. +INSTALLATION & USAGE -08 Oct 2013 Axel Kohlmeyer - -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 - -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 - -Added rudimentary support for OPLS-AA based on -input provided by jeff greathouse. - -18 Jul 2013 Axel Kohlmeyer - -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 - -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 - -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 +This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT program to produce a LAMMPS data file. 1. Building msi2lmp @@ -178,50 +130,111 @@ see msi2lmp/TriclinicModification.pdf doc for details -- the LAMMPS data file is written to .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 +------------------------------------------------------------------------ + +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 + +------------------------------------------------------------------------ + +CHANGELOG + +06 Oct 2016 Axel Kohlmeyer + +Improved whitespace handling in parsing topology and force field +files to avoid bogus warnings about type name truncation. + +24 Oct 2015 Axel Kohlmeyer + +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 + +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 + +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 + +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 + +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 + +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 + +Added rudimentary support for OPLS-AA based on input provided +by jeff greathouse. + +18 Jul 2013 Axel Kohlmeyer + +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 + +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 + +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 +