git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14219 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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.
+
+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

tools/msi2lmp/frc_files/README

+Set the environment variable MSI2LMP_LIBRARY or copy cvff.frc and cff9*.frc
+or any other *.frc files (which you have license to use) to this directory
+for use with msi2lmp.
+
+Note that LAMMPS does not distribute Accelrys (or old BioSym)
+force field files, since they are proprietary.  All the
+files in this directory that are part of the LAMMPS distribution
+are are openly available files that are in the public domain.
+
+

tools/msi2lmp/frc_files/clayff.frc

+!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             
+

tools/msi2lmp/frc_files/oplsaa.frc

+!BIOSYM forcefield          1
+
+! This is a modified version of msi2lmp for use specifically wtih the
+! OPLS force field. No out-of-plane or cross-terms are included.
+! Atom types from SPC water and CLAYFF are also included.
+
+
+#atom_types     cvff
+
+> Masses from CRC 1973/74 pages B-250.
+
+!Ver  Ref  Type    Mass      Element  Connections   Comment
+!---- ---  ----  ----------  -------  -----------------------------------------
+ 1.0   1    HC     1.007970    H           1        H, RH, alkanes
+ 1.0   1    HO     1.007970    H           1        H(O), ROH
+ 1.0   1    HS     1.007970    H           1        H(S), RSH
+ 1.0   1    HM     1.007970    H           1        H(C), CH3OH
+ 1.0   1    CT    12.011150    C           4        Aliphatic C
+ 1.0   1    OH    15.999400    O           2        O, ROH
+ 1.0   1    SH    32.064000    S           2        S, RSH
+ 1.0   1    S     32.064000    S           2        S, RSR
+ 1.0   1    CG    12.011150    C           1        Graphite C
+ 1.0   1    CL    35.453000    Cl          1        Cl, RCl
+ X.X   X    CC    12.011150    C           3        Carbonate ion C, AMBER
+ X.X   X    OC    15.035060    O           1        Carbonate ion O, AMBER
+
+
+#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
+
+
+
+#quadratic_bond cvff
+
+> E = K2 * (R - R0)^2
+
+!Ver  Ref     I     J          R0         K2
+!---- ---    ----  ----     -------    --------
+ 2.3  23     CT    CT        1.529     268.0
+ 2.3  23     CT    HC        1.09      340.0
+ 2.3  23     CT    OH        1.410     320.0
+ 2.3  23     CT    SH        1.810     222.0
+ 1.0   1     HO    OH        0.96      553.0
+ 1.0   1     HS    SH        1.336     274.0
+ 1.0   1     CT    S         1.810     222.0
+ 1.0   1     CT    CL        1.781     245.0
+ X.X   X     CC    OC        1.21      648.0
+
+
+
+#quadratic_angle        cvff
+
+> E = K2 * (Theta - Theta0)^2
+
+!Ver  Ref     I     J     K       Theta0         K2
+!---- ---    ----  ----  ----    --------     -------
+ 2.3  23     CT    CT    CT      112.7        58.35
+ 2.3  23     CT    CT    HC      110.7        37.50
+ 2.3  23     CT    CT    OH      109.5        50.00
+ 2.3  23     HC    CT    HC      107.8        33.00
+ 2.3  23     CT    OH    HO      108.5        55.00
+ 2.3  23     HC    CT    OH      109.5        35.00
+ 1.0   1     CT    CT    SH      108.6        50.00
+ 1.0   1     CT    SH    HS      96.0         44.00
+ 1.0   1     HC    CT    SH      109.5        35.00
+ 1.0   1     CT    CT    S       114.7        50.00
+ 1.0   1     CT    S     CT       98.9        62.00
+ 1.0   1     HC    CT    S       109.5        35.00
+ 1.0   1     CT    CT    CL      109.8        69.0
+ 1.0   1     HC    CT    CL      107.6        51.0
+ X.X   X     OC    CC    OC      127.0        79.1
+
+
+#bond-bond      cvff
+
+> E = K(b,b') * (R - R0) * (R' - R0')
+
+!Ver  Ref     I     J     K       K(b,b')
+!---- ---    ----  ----  ----     -------
+ 1.0   1     c     o     c'        0.0000
+
+#bond-angle     cvff
+
+> E = K * (R - R0) * (Theta - Theta0)
+
+!Ver  Ref     I     J     K       K(b,theta) K(b',theta)
+!---- ---    ----  ----  ----     ---------- -----------
+ 1.0   1     c     o     c'       57.0000     57.0000
+
+#torsion_1      opls
+
+> E = 0.5*K1*[1 + cos(Phi)] + 0.5*K2*[1 + cos(2*Phi)] + 0.5*K3*[1 + cos(3*Phi)] + 0.5*K4*[1 + cos(4*Phi)]
+
+!Ver  Ref     I     J     K     L        K1           K2        K3       K4
+!---- ---    ----  ----  ----  ----      -------      ------    ------   -----
+ X.X  XX     HC    CT    CT    HC        0.0          0.0       0.318    0.0
+ X.X  XX     HC    CT    CT    CT        0.0          0.0       0.366    0.0  
+ X.X  XX     CT    CT    CT    CT        1.740       -0.157     0.279    0.0
+ X.X  XX     HC    CT    OH    HO        0.0          0.0       0.450    0.0
+ X.X  XX     CT    CT    OH    HO       -0.356       -0.174     0.492    0.0
+ X.X  XX     HC    CT    CT    OH        0.0          0.0       0.468    0.0
+ X.X  XX     CT    CT    CT    OH        1.711       -0.500     0.663    0.0
+ X.X  XX     HC    CT    SH    HS        0.0          0.0       0.451    0.0
+ X.X  XX     CT    CT    SH    HS       -0.759       -0.282     0.603    0.0
+ X.X  XX     HC    CT    CT    SH        0.0          0.0       0.452    0.0
+ X.X  XX     CT    CT    CT    SH        1.876        0.0       0.0      0.0
+ X.X  XX     HC    CT    CT    S         0.0          0.0       0.452    0.0
+ X.X  XX     CT    CT    S     CT        0.925       -0.576     0.677    0.0
+ X.X  XX     HC    CT     S    CT        0.0          0.0       0.647    0.0
+ X.X  XX      S    CT    CT    CL        0.0          0.0       0.452    0.0
+ X.X  XX     CL    CT    CT    CL        0.250       -0.250     0.0      0.0
+ X.X  XX     HC    CT    CT    CL        0.0          0.0       0.400    0.0
+
+
+#angle-angle-torsion_1  cvff
+
+>  E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi)
+!Ver  Ref     I     J     K     L      K(Ang,Ang,Tor)
+!---- ---    ----  ----  ----  ----    --------------
+ 1.0   1     *     c     c     *        -10.5000
+
+#out_of_plane   cvff
+
+> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
+
+!Ver  Ref     I     J     K     L           Kchi        n           Chi0
+!---- ---    ----  ----  ----  ----      -------      ------     -------
+ 2.3   0     hn    n     c     c'        10.0           2       180.0
+ X.X   X     OC    CC    OC    OC         1.1           2       180.0
+
+
+#out_of_plane-out_of_plane      cvff
+
+> E = Koo * Chi * Chi'
+
+!Ver  Ref     I     J     K     L           Koo
+!---- ---    ----  ----  ----  ----      -------
+ 1.0   1     c     c'    n     o'         0.0100
+
+#angle-angle    cvff
+
+> E = K * (Theta - Theta0) * (Theta' - Theta0')
+
+!                   J'    I'    K'
+!Ver  Ref     I     J     K                 K
+!---- ---    ----  ----  ----  ----      -------
+ 1.0   1     c     c     c     c         -7.9000
+
+
+
+#morse_bond     cvff_auto
+
+> E = D * (1 - exp(-ALPHA*(R - R0)))^2
+
+!Ver  Ref     I     J          R0         D           ALPHA
+!---- ---    ----  ----     -------    --------      -------
+ 2.0  18     c3m_   c3m_      1.5100     88.0000      1.9150
+
+#quadratic_bond    cvff_auto
+
+> E = K2 * (R - R0)^2
+
+!Ver  Ref     I     J          R0         K2
+!---- ---    ----  ----     -------    --------
+ 2.0  18     c3m_   c3m_      1.5100    322.7158
+
+
+#quadratic_angle      cvff_auto
+
+> E = K2 * (Theta - Theta0)^2
+
+!Ver  Ref     I     J     K       Theta0         K2
+!---- ---    ----  ----  ----    --------     -------
+ 2.0  18     c3m_  c3m_  c3m_     60.0000     46.0000
+
+
+
+
+#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     HC      7152.557      29.297
+ 1.0   1     HO      0.0           0.0
+ 1.0   1     HS      0.0           0.0
+ 1.8  14     HM      7152.557      29.297
+ 1.0   1     CT      892114.214    485.302
+ 1.0   1     OH      578580.831    627.244
+ 2.3  25     SH      4006270.2     2001.567
+ 2.3  25     S       4006270.2     2001.567
+ 1.0   1     CG      531140.879    343.824
+ 1.0   1     CL      2863704.82    1853.765299
+ X.X   X     CC      819971.66216  531.10286
+ XX    X     OC      379876.39852  564.88598
+
+
+
+#bond_increments        cvff
+
+!Ver  Ref     I     J       DeltaIJ     DeltaJI
+!---- ---    ----  ----     -------     -------
+ 2.3  23     no    o-        0.1684     -0.1684
+

tools/msi2lmp/frc_files/pcff.rlb

+VERSION
+elib

tools/msi2lmp/src/CheckLists.c

+#include "msi2lmp.h"
+
+void CheckLists() {
+  int i;
+
+  for (i=0; i < total_no_bonds; i++) {
+    if ((atoms[bonds[i].members[0]].type != bondtypes[bonds[i].type].types[0])
+        || (atoms[bonds[i].members[1]].type != bondtypes[bonds[i].type].types[1])) {
+      fprintf(stderr,"Warning atom types in bond %d are inconsistent with bond type %d\n",i,bonds[i].type);
+    }
+  }
+
+  for (i=0; i < total_no_angles;i++) {
+    if ((atoms[angles[i].members[0]].type != angletypes[angles[i].type].types[0])
+        || (atoms[angles[i].members[1]].type != angletypes[angles[i].type].types[1])
+        || (atoms[angles[i].members[2]].type != angletypes[angles[i].type].types[2])) {
+      fprintf(stderr,"Warning atom types in angle %d are inconsistent with angle type %d\n", i,angles[i].type);
+    }
+  }
+
+  for (i=0; i < total_no_dihedrals; i++) {
+    if ((atoms[dihedrals[i].members[0]].type != dihedraltypes[dihedrals[i].type].types[0])
+        || (atoms[dihedrals[i].members[1]].type != dihedraltypes[dihedrals[i].type].types[1])
+        || (atoms[dihedrals[i].members[2]].type != dihedraltypes[dihedrals[i].type].types[2])
+        || (atoms[dihedrals[i].members[3]].type != dihedraltypes[dihedrals[i].type].types[3])) {
+      fprintf(stderr,"Warning atom types in dihedral %d are inconsistent with dihedral type %d\n",i,dihedrals[i].type);
+    }
+  }
+
+  for (i=0; i < total_no_oops; i++) {
+
+    if ((atoms[oops[i].members[0]].type != ooptypes[oops[i].type].types[0])
+        || (atoms[oops[i].members[1]].type != ooptypes[oops[i].type].types[1])
+        || (atoms[oops[i].members[2]].type != ooptypes[oops[i].type].types[2])
+        || (atoms[oops[i].members[3]].type != ooptypes[oops[i].type].types[3])) {
+      fprintf(stderr,"Warning atom types in oop %d are inconsistent with oop type %d\n",i,oops[i].type);
+    }
+  }
+}

tools/msi2lmp/src/Forcefield.h

+/******************************
+*
+*   This is the header file for the routine that reads the forcefield file
+*   into memory in order to speed up searching.
+*
+*   It defines the data structures used to store the force field in memory
+*/
+
+#define MAX_NO_MEMS 6
+#define MAX_NO_PARAMS 8
+
+struct FrcFieldData {
+  float  ver;                /* Version number of forcefield entry */
+  int    ref;                /* Reference within forcefield */
+  char   ff_types[MAX_NO_MEMS][5];
+  double ff_param[MAX_NO_PARAMS];
+};
+
+struct FrcFieldItem {
+  char keyword[25];
+  int  number_of_members;    /* number of members of item */
+  int  number_of_parameters; /* number of parameters of item */
+  int  entries;              /* number of entries in item list */
+  struct FrcFieldData *data; /* contains all eqiuv and param data */
+};
+
+extern struct FrcFieldItem ff_atomtypes, equivalence, ff_vdw, ff_bond, ff_morse, ff_ang, ff_tor, ff_oop,
+  ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13;
+
+/* prototypes */
+extern void InitializeItems(void);
+extern void ClearFrcItem(struct FrcFieldItem *item);
+extern void SearchAndFill(struct FrcFieldItem *item);
+extern const char *SearchAndCheck(const char *);
+

tools/msi2lmp/src/InitializeItems.c

+/*
+*   This function fills in the keyword field, the number of members for each
+*   item and the number of parameters for each item
+*
+*/
+
+#include "msi2lmp.h"
+#include "Forcefield.h"
+
+#include <string.h>
+
+void InitializeItems(void)
+{
+  /* ATOM TYPES */
+  strcpy(ff_atomtypes.keyword,"#atom_types");
+  ff_atomtypes.number_of_members = 1;
+  ff_atomtypes.number_of_parameters = 1;
+
+  /* EQUIVALENCE */
+
+  strcpy(equivalence.keyword,"#equivalence");
+  equivalence.number_of_members = 6;
+  equivalence.number_of_parameters = 0;
+
+  /* NON-BOND */
+
+  strcpy(ff_vdw.keyword,"#nonbond");
+  ff_vdw.number_of_members = 1;
+  ff_vdw.number_of_parameters = 2;
+
+  /* BOND */
+
+  ff_bond.number_of_members = 2;
+  if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
+    strcpy(ff_bond.keyword,"#quadratic_bond");
+    ff_bond.number_of_parameters = 2;
+  }
+
+  if (forcefield & FF_TYPE_CLASS2) {
+    strcpy(ff_bond.keyword,"#quartic_bond");
+    ff_bond.number_of_parameters = 4;
+  }
+
+  /* MORSE */
+
+  if (forcefield & FF_TYPE_CLASS1) {
+    ff_morse.number_of_members = 2;
+    strcpy(ff_morse.keyword,"#morse_bond");
+    ff_morse.number_of_parameters = 3;
+  }
+
+  /* ANGLE */
+
+  ff_ang.number_of_members = 3;
+  if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
+    strcpy(ff_ang.keyword,"#quadratic_angle");
+    ff_ang.number_of_parameters = 2;
+  }
+
+  if (forcefield & FF_TYPE_CLASS2) {
+    strcpy(ff_ang.keyword,"#quartic_angle");
+    ff_ang.number_of_parameters = 4;
+  }
+
+  /* TORSION */
+
+  ff_tor.number_of_members = 4;
+  if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
+    strcpy(ff_tor.keyword,"#torsion_1");
+    ff_tor.number_of_parameters = 3;
+  } 
+
+  if (forcefield & FF_TYPE_CLASS2) {
+    strcpy(ff_tor.keyword,"#torsion_3");
+    ff_tor.number_of_parameters = 6;
+  }
+
+  /* OOP */
+
+  ff_oop.number_of_members = 4;
+  if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
+    strcpy(ff_oop.keyword,"#out_of_plane");
+    ff_oop.number_of_parameters = 3;
+  }
+
+  if (forcefield & FF_TYPE_CLASS2) {
+    strcpy(ff_oop.keyword,"#wilson_out_of_plane");
+    ff_oop.number_of_parameters = 2;
+  }
+
+  if (forcefield & FF_TYPE_CLASS2) {
+    /* BOND-BOND */
+
+    strcpy(ff_bonbon.keyword,"#bond-bond");
+    ff_bonbon.number_of_members = 3;
+    ff_bonbon.number_of_parameters = 1;
+
+    /* BOND-ANGLE */
+
+    strcpy(ff_bonang.keyword,"#bond-angle");
+    ff_bonang.number_of_members = 3;
+    ff_bonang.number_of_parameters = 2;
+
+    /* ANGLE-TORSION */
+
+    strcpy(ff_angtor.keyword,"#angle-torsion_3");
+    ff_angtor.number_of_members = 4;
+    ff_angtor.number_of_parameters = 6;
+
+    /* ANGLE-ANGLE-TORSION */
+
+    strcpy(ff_angangtor.keyword,"#angle-angle-torsion_1");
+    ff_angangtor.number_of_members = 4;
+    ff_angangtor.number_of_parameters = 1;
+
+    /* END-BOND-TORSION */
+
+    strcpy(ff_endbontor.keyword,"#end_bond-torsion_3");
+    ff_endbontor.number_of_members = 4;
+    ff_endbontor.number_of_parameters = 6;
+
+    /* MID-BOND-TORSION */
+
+    strcpy(ff_midbontor.keyword,"#middle_bond-torsion_3");
+    ff_midbontor.number_of_members = 4;
+    ff_midbontor.number_of_parameters = 3;
+
+    /* ANGLE-ANGLE */
+
+    strcpy(ff_angang.keyword,"#angle-angle");
+    ff_angang.number_of_members = 4;
+    ff_angang.number_of_parameters = 1;
+
+    /* BOND-BOND-1-3 */
+
+    strcpy(ff_bonbon13.keyword,"#bond-bond_1_3");
+    ff_bonbon13.number_of_members = 4;
+    ff_bonbon13.number_of_parameters = 1;
+  }
+}

tools/msi2lmp/src/Makefile

+
+TARGET	 = msi2lmp.exe
+
+SRCS     = msi2lmp.c \
+           ReadCarFile.c \
+           ReadMdfFile.c \
+	   MakeLists.c \
+           ReadFrcFile.c \
+           InitializeItems.c \
+	   SearchAndFill.c \
+           GetParameters.c \
+	   CheckLists.c \
+           WriteDataFile.c
+
+OBJS     = $(SRCS:.c=.o)
+
+HEADERS  = msi2lmp.h Forcefield.h
+
+CC       = gcc
+CFLAGS   = -O -Wall -W -g 
+LDFLAGS  =
+FRCFILE  = cvff.frc
+FRCFILE2 = cff91.frc
+README   = README
+MKFILE   = Makefile
+
+$(TARGET) : $(OBJS)
+	$(CC) $(LDFLAGS) $(CFLAGS) -o $(TARGET) $(OBJS) -lm
+
+.c.o:
+	$(CC) $(CFLAGS) -c $<
+clean:
+	rm -f $(OBJS) $(TARGET)
+
+# dependencies
+CheckLists.o: CheckLists.c msi2lmp.h
+GetParameters.o: GetParameters.c msi2lmp.h Forcefield.h
+InitializeItems.o: InitializeItems.c msi2lmp.h Forcefield.h
+MakeLists.o: MakeLists.c msi2lmp.h
+msi2lmp.o: msi2lmp.c msi2lmp.h
+ReadCarFile.o: ReadCarFile.c msi2lmp.h
+ReadFrcFile.o: ReadFrcFile.c msi2lmp.h Forcefield.h
+ReadMdfFile.o: ReadMdfFile.c msi2lmp.h
+SearchAndFill.o: SearchAndFill.c msi2lmp.h Forcefield.h
+WriteDataFile.o: WriteDataFile.c msi2lmp.h Forcefield.h