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

Copy cvff.frc and cff9*.frc or any other

.frc files you have licensed to this 

directory for use with msi2lmp. 

!CLAYFF forcefield

#atom_types	cvff

!Ver  Ref  Type    Mass      Element  Connections   Comment

!---- ---  ----  ----------  -------  -----------------------------------------

 1.0   1    st     28.08550    Si          4  

 1.0   1    ao     26.98154    Al          6     

 1.0   1    at     26.98154    Al          4   

 1.0   1   mgo     24.30500    Mg          6   

 1.0   1   cao     40.08000    Ca          6

 1.0   1   feo     55.84700    Fe          6

 1.0   1   lio     6.941000    Li          6

 1.0   1    ob    15.99940      O          2

 1.0   1  obss     15.99940     O          3   

 1.0   1  obts     15.99940     O          2   

 1.0   1  obos     15.99940     O          2   

 1.0   1   ohs     15.99940     O          2   

 1.0   1    oh     15.99940     O          2

 1.0   1   oh-     15.99940     O          1

 1.0   1    o*     15.99940     O          2

 1.0   1    ho     1.007970     H          1   

 1.0   1    h*     1.007970     H          1

 1.0   1    Na     22.99000    Na          0

 1.0   1     K     39.10        K          0 

 1.0   1    Cs     132.9100    Cs          0

 1.0   1    Ca     40.07980    Ca          0

 1.0   1    Ba     137.3300    Ba          0 

 1.0   1    Mg      24.3050    Mg          0

 1.0   1    Sr      87.6200    Sr          0

 1.0   1    Pb     207.2000    Pb          0

 1.0   1    Cl     35.45300    Cl          0

#equivalence	cvff 

> Equivalence table for any variant of cvff 

!		         	  Equivalences

!                 -----------------------------------------

!Ver  Ref   Type  NonB     Bond    Angle    Torsion    OOP

!---- ---   ----  ----     ----    -----    -------    ----

 1.0   1    h     h        h        h        h         h   

#auto_equivalence	cvff_auto

!		         	  Equivalences

!                 -----------------------------------------                       

!Ver  Ref   Type  NonB Bond   Bond     Angle    Angle     Torsion   Torsion      OOP      OOP 

!                      Inct           End atom Apex atom End Atoms Center Atoms End Atom Center Atom

!---- ---   ----  ---- ------ ----  ---------- --------- --------- -----------  -------- ----------- 

 2.0  18    h     h     h     h_       h_       h_        h_        h_           h_       h_

#hbond_definition	cvff 

#morse_bond	cvff 

> E = D * (1 - exp(-ALPHA*(R - R0)))^2

!Ver  Ref     I     J          R0         D           ALPHA

!---- ---    ----  ----     -------    --------      -------

 2.3  23     no    o-        1.2178    140.2486      2.0000

#quadratic_bond	cvff 

> E = K2 * (R - R0)^2

!Ver  Ref     I     J          R0         K2    

!---- ---    ----  ----     -------    -------- 

 2.1  28      oh   ho        1.0000    553.9350

 2.1  28     ohs   ho        1.0000    553.9350

#quadratic_angle	cvff 

> E = K2 * (Theta - Theta0)^2

!Ver  Ref     I     J     K       Theta0         K2        

!---- ---    ----  ----  ----    --------     -------

 2.3  23     cp    cp    c'      120.0000     34.6799

#torsion_1      cvff_auto

> E = Kphi * [ 1 + cos(n*Phi - Phi0) ]

!Ver  Ref     I     J      K      L           Kphi        n           Phi0

!---- ---    ----  ----   ----   ----      -------      ------     -------

 2.0  18     *     c_     n3n_   *          0.0500        3         0.

#out_of_plane	cvff_auto

> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]

!Ver  Ref     I     J     K     L           Kchi        n           Chi0

!---- ---    ----  ----  ----  ----      -------      ------     -------

 2.0  18     *     c'_   *      *        10.0000        2       180.0000

#nonbond(12-6)	cvff 

@type A-B

@combination geometric

> E = Aij/r^12 - Bij/r^6

> where  Aij = sqrt( Ai * Aj )

>        Bij = sqrt( Bi * Bj )

!Ver  Ref     I           A             B 

!---- ---    ----    -----------   -----------

 1.0   1    st           12.3645       0.00954

 1.0   1    ao          196.1446       0.03230

 1.0   1    at           12.3645       0.00954

 1.0   1   mgo         1636.3265       0.07688

 1.0   1   cao         17814.73	       0.5987 

 1.0   1   feo           702.54	       0.0504

 1.0   1   lio           112.01	       0.0201

 1.0   1    ob       629358.0000     625.50000

 1.0   1  obss      629358.0000     625.50000

 1.0   1  obts      629358.0000     625.50000

 1.0   1  obos      629358.0000     625.50000

 1.0   1   ohs      629358.0000     625.50000

 1.0   1    oh      629358.0000     625.50000

 1.0   1   oh-      629358.0000     625.50000

 1.0   1    o*      629358.0000     625.50000

 1.0   1    ho        0.00000001       0.00000

 1.0   1    h*        0.00000001       0.00000

 1.0   1    Na       14763.1719      87.65132

 1.0   1    K        754506.86       549.37

 1.0   1    Cs       3998193.96	    1264.63

 1.0   1    Ca      125966.6068     224.46969

 1.0   1    Ba      1799606.56	    582.25

 1.0   1    Mg      1369.00	     69.22

 1.0   1    Sr      1185860.37	    688.73

 1.0   1    Pb      861150.71	    638.08

 1.0   1    Cl      21081006.97     2905.31

#bond_increments        cvff

!Ver  Ref     I     J       DeltaIJ     DeltaJI

!---- ---    ----  ----     -------     -------

 2.3  23     no    o-        0.1684     -0.1684