CHARMM c30b1 molvib.doc



File: Molvib ]-[ Node: Top
Up: (commands.doc) -=- Next: Syntax\n

                     The MOLVIB Module of CHARMM

            By K.Kuczera & J.Wiorkiewicz-Kuczera, May 1991


    MOLVIB is a general-purpose vibrational analysis program, suitable
for small to medium sized molecules (say of less than 50 atoms).  For
larger systems the detail of description may be too great.

    The main options are:
 
    - the vibrational problem in internal coordinates (GF)
    - the vibrational problem in cartesian coordinates (GFX)
    - analysis of GAUSSIAN program output (GFX,GAUS)
    - analysis of dependencies in internal coordinate sets (G)
    - canonic force field calculations (KANO)
    - crystal normal mode analysis for k=0 (CRYS)
    - generating cartesian displacements along some interesing
      directions (STEP)
 
    The different options use mostly the same package of subroutines
called in different order. New applications may thus be easily added
when necessary. 
 
    Of special interest is the symbolic PED analysis package, enabling
a clear and condensed overview of the usually complex PED contributions.
 
* Menu:

* Syntax::              Syntax of the MOLVIB command
* Function::            Purpose of each of the keywords
* Input::               MOLVIB Input Description


File: Molvib ]-[ Node: Syntax
Up: Top -=- Previous: Top -=- Next: Function\n[SYNTAX MOLVib command]


    MOLVib NDI1 int NDI2 int NDI3 int 
           [NATOm int] [MAXSymbol int] [NGMAx int] [NBLMax int]
           [IZMAx int] [NOTOpology] [SECOnd] [PRINt]



File: Molvib ]-[ Node: Function
Previous: Syntax -=- Up: Top -=- Next: Input\nThe following section describes the keywords of the MOLVib command.


    NDI1,NDI2,NDI3 are the MOLVIB variables NQ, NIC, NIC0; their definition
      here effectively replaces the MOLVIB 'DIM ' card. Two cases:
    
     a. Molecular vibrations
        NIC0 - number of primitive internal coordinates (PIC's), this
               must correspond to the number of entries following the
               'IC' card
        NIC - number of IC's left after transformation by first U matrix
              If only one U matrix is used, this should be the same
              as NQ; if no U matrices used, NQ=NIC=NIC0
        NQ  - number of vibrational degrees of freedom. Usually this
              is the famous number 3*Nat-6 (3*Nat-5), but also separate 
              symmetry blocks of the vibrational Hamiltonian may be
              entered. 
     b. Crystal vibrations
        NIC0 - no. of primitive molecular coords (MC), i.e. external
               coords + primitive IC's
        NIC  - no. of vibrational degrees of freedom = 3*NAT, where
               NAT is the total no. of atoms in unit cell
        NQ   - here =NIC
 
    NATOm - defines the number of atoms in the system. To be used only in
      conjunction with the NOTO flag. If NOTO is not provided, the number
      of atoms from the PSF will be used in MOLVIB and will override any
      values provided here.

    IZMAx - needed for 'CRYS' option only - specifies maximum number
      of molecules in unit cell. Default is 10.

    MAXSymbol, NGMax, NBLMax - dimensions for PED analysis arrays. They
      specify the maximum number of symbols, coordinate groups and
      symmetry blocks, respectively. Defaults are NQ (NDI1) for all
      three.  It is recommended not to modify these defaults.

    NOTOpology - if flag is present, CHARMM data structures will not
      be used, all information required is to be read in inside the module.
      If flag is absent, cartesian coordinates, atomic masses and cartesian
      force constants from CHARMM may be passed to MOLVIB, as needed.

    SECOnd - calculate second derivatives (force constants in cartesian
      coordinates) and pass them to MOLVIB.
      This is done through a call to the CHARMM routine ENERGY, so all
      preconditions for energy (and second derivative) calculations
      must be met. 

    PRINT - flag for test printout of the CHARMM second derivatives being
      passed to MOLVIB.



File: Molvib ]-[ Node: Input
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                            Input Description

    This data is processed by subroutine MOLINP.  As the CHARMM command
parser is not used, this input does not conform to CHARMM standards, 
       e.g. - parameter substitution will not work
            - the STREAM command will not work, all commands will be read
              from the current input stream
            - OPEN, READ, WRITE, etc. commands will not work
            - most entries are not free format


[SYNTAX MOLVIB input]
      
    The MOLVIB input consists of a series of blocks; each block
consists of a command and an (optional) data structure; i.e. it has
the form: 

     command-spec 
     [data-struc]

     command-spec ::== keyword [<int1>] [<int2>] [<int3>] [<int4>]
                       format: A4,6X,4I5
    
     data-struc ::== one of the MOLVIB input data structures; defined by the
                     keyword.

    The list of currently supported keywords folows. One of the first
group of keywords must be used first in order to define type of
calculation. 


 Keyword        Interpretation

  G     - perform redundancy analysis

  GF    - solve standard Wilson GF problem

  GAUS  - choose GAUSSIAN analysis option

  GFX   - vibrational problem in cartesian coordinates

  KANO  - determine canonical force field

  CRYS  - crystal vibrations for k=0;

  STEP  - generate cartesian displacements in a given


For the remaining keywords, the order is arbitrary:

 Keyword        Interpretation

  CART  - read in cartesian coordinates 

  MASA  - interpret fourth column of cartesian coord input as A numbers

  MASZ  - interpret the above column as Z numbers 

  UMAT  - read in U Matrix for similarity transformation

  FMAT  - read in F matrix

  LX    - read in cartesian eigenvectors 

  IC    - read in internal/external coordinate definitions

  PRNT  - set print level

  TEST  - set print level

  NULL  - control card for 'G   ' option with IGLEV=2

  PED   - read in PED data structure

  SCAL  - read in scale factor for F matrix

  TRRM  - remove translational and rotational contributions to LX

  MNAT  - read in the numbers of atoms for each molecule in unit cell

  IFTR  - specifies the dimension (and type) of F matrix

  SYMM  - read in symmetry blocking data

  EXPF  - read in reference frequencies for the system

  END   - end input section, perform MOLVIB calculations and


This section gives a more detailed explanantion of the keywords and the
assocaited data structures.


 keyword            Interpretation

   G     - perform redundancy analysis
             <int1> == IGLEV
             IGLEV=1 - diagonalize G and write out eigenvalues
                       and eigenvectors
             IGLEV=2 - additionally generate a set of null and
                       independent coordinates orthogonal to the
                       initially specified ones 

  GF     - solve standard Wilson GF problem

  GAUS   - choose GAUSSIAN analysis option

  GFX    - vibrational problem in cartesian coordinates

  KANO - determine canonical force field
             <int1> == ICANO
             ICANO=1 - preliminary run, just to output the FR
                       matrix; one of the other keywords must follow
                       GF, GFX or GAUS - so that FR is evaluated
                       or just read in as part of those processes.
             ICANO=2 - evaluation of the canonic force field FR*
                      N.B. No U matrix allowed here.
                      Give: DIMensions, CARTesian coords, IC's and FMAT.

  CRYS  - crystal vibrations for k=0;
                      <int1> == IZMOL,  <int2> == IFCRYS
                      IZMOL - no. of molecules in unit cell
                      IFCRYS=0 (default) - calculation analogous to GFX

  STEP  - generate cartesian displacements in a given
                      direction.
                      <int1> == IFSTEP
                      <int2> == ISTCOR
                      <int3> == IFFMAT
                      <int4> == IFLMAT
                      Additionally, the card following the 'STEP'
                      card contains the value of STPSIZ (real,free format)
               IFSTEP=1 - cartesian eigenvector no. ISTCOR
               (IFSTEP=2 - internal eigenvector no. ISTCOR, not implemented)
               (IFSTEP=3 - internal coordinate no. ISTCOR, not implemented)
               STPSIZ - step size, e.g. the transformation is 
                  X(I)=X(I)+STPSIZ*LX(I,ISTCOR) for cart. eigenvectors
                  where LX the columns of LX are normalized.
               IFFMAT,IFLMAT - determine the starting point of the 
                       calculation:
               IFFMAT=0 and IFLMAT
                                  =1 - start from LX
                                  =2 - start from LS
               IFLMAT=0 and IFFMAT
                                  =1 - start from FX
                                  =2 - start from FS
 
  CART  - cartesian coordinates for NAT atoms will follow
               <int1> == unused
               <int2> == IFC
               In MOLVIB <int1> usually used to define the number of
                 atoms NAT.  In the CHARMM version, NAT is specified
                 on the MOLVIB command line (if NOTO flag is used) or
                 is read from the PSF (if NOTO is absent).
               IFC - specifies format for cart. coords:
                 IFC=0 free format, four real numbers per line
                   X, Y, Z, and MASS (see below).
                 IFC=1 CHARMM format; only atom entry lines, no titles
                   or NATOM field, mass information in WMAIN field.
                 N.B.
                 For the 'GAUS' option use GAUSSIANxx CMS coordinates.
                 FOR THE 'GFX ' option use GAUSSIANxx coordinates in the
                 Z-matrix orientation.

                 Mass specification : (1) enter mass in amu as fourth real
                 number in  entry line for each atom.  (2) instead of mass
                 place atomic number Z or mass number A as fourth real
                 number  and subsequently use a 'MASZ' or 'MASA'
                 control cards. NB. For 'CRYS' NAT should be equal to
                 no. of atoms in unit cell.
      
  MASA  - interpret fourth column of cartesian coord input
               as atomic mass numbers (A) ; useful for isotopes, e.g.
               a mass of 2.0 will designate D, mass of 15.0 - 15N etc.

  MASZ  - interpret the above column as atomic numbers (Z) 
 
  UMAT  - read in U Matrix for similarity transformation
             <int1> == IFU 
             <int2> == INU 
             <int3> == IUU 
             <int4> == IZU 
             IFU - defines format
              =0 Schachtschneider/Snyder format only supported
             INU = 1/0 - normalize/dont normalize rows of U
             IUU - defines FORTRAN unit for U read
                 if left blank, unit input stream will be used
                 if >0 then the data should be provided in the correct
                   FORTRAN file
             IZU - multiplicity; usually IZU=(no. of molecules in unit
                 cell). IZU.GT.1 turns on autogeneration of U for
                 whole unit cell from the provided values for the first
                 asymmetric unit.
    (see SUBROUTINE RDMAT in MOLVIO)

    Details:
    Two, one or none U matrices may be supplied on input. These are
    (generally) rectangular matrices which perform linear transformations
    on internal coordinate sets, of the type
       S=U*R  ( or S(i) = {sum over j} U(i,j)*R(j) ),
    with S - final, and R initial coordinate sets. The function of the
    U matrix is e.g. to transform from primitive IC' s (of which there
    are NIC0>NQ) to a set of independent IC's NQ in number, or to scale
    the IC's by a factor (useful when trying to reproduce vibrations
    reported in the literature, as different research groups use different
    definitons of angle or dihedral IC's).
    If two U matrices are given, then the IC's (and the B and G matrices)
    are sequentially transformed using first U1, then U2. The F matrix is
    assumed to be expressed in the final IC's on input, and is not 
    transformed (except for the 'KANO' option - see 'IFTR').

 
  FMAT  - read in F matrix, (the second derivatives of energy wrt
          coordinates) 
             <int1> == IFF 
             <int2> == ISF 
             <int3> == IUF 
               IFF - specifies format
                 = 0 - Schatschneider/Snyder format
                 = 1 - GAUSSIANxx format
                   N.B. remember to use 'Z matrix' oriented cartesian
                   coords. 
                 = 2 - CHARMM formatted SECO file format
               IFS = 1/0 - symmetrize/dont symmetrize (upper triangle
                      assumed  on input)
               IUF - FORTAN unit no., as for 'UMAT'
            (see RDMAT, RFORC, RDSECO in MOLVIO)
 
  LX    - read in cartesian eigenvectors 
             <int1> == IFL 
             <int2> == unused 
             <int3> == IUL 
             IFL - specifies format
                = 0 - GAUSSIANxx format (see SUBROUTINE REIGEN)
                  all 3*NAT eigenvectors read in
                  N.B. remember to use 'standard' (or 'CMS') oriented
                  cartesian coordinates
                = 1 - CHARMM binary format (see SUBROUTINE REIGCH)
                 only the NQ=3*NAT-6 "vibrational" eigenvectors
                 are expected by REIGCH; use "WRITE NORM 7 THRU ..."
                 command to achieve this.
                 NB. Binary files are machine specific.
              IUL - FORTAN unit no. from which to read , aas in 'UMAT'
 
  IC    - read in internal/external coordinate definitions;
             <int1> == IZIC
             Five integers will be read from NIC0 lines in free
             format; each line contains:
             ITYP,I,J,K,L - specify type and four atom numbers
             as defined in cartesian coordinates
             Note: it is necessary to add zeros in unused fields.
             IZIC - multiplicity, usually = no. of molecules in unit
                   cell. IZIC.GT.1 turns on autogeneration of 
                   internal/external coordinates for unit cell from
                   the ones provided for the first asymmetric unit.
 
            ITYP=1,2,3,4 - internal coordinates
            ITYP = 1 - I-J  bond stretch
 
                    I --- J
 
            ITYP = 2 - I-J-K  angle bend
 
                       J
                      / \
                     /   \
                    I     K
 
            ITYP = 3 - I-L bond angle with J-K-L plane (Wilson wag)
 
                            K
                           /
                          /
                  I ---  L
                          \
                           \
                            J
 
            ITYP = 4 - angle between IJK abd JKL planes
 
 
                I
                 \
                  \
                   J --- K
                          \
                           \
                            L
 
              For details : a) see SUBROUTINE BMAT
                            b) see Wilson,Decius,Cross section 4.1,
                               substituting their atom numbers with:
               ITYP=1   (12)   -> (IJ)
                    2   (123)  -> (IKJ)   ! thats right !
                    3   (1234) -> (IJKL)
                    4   (1234) -> (IJKL)
 
            A good reference for standard definitions of independent
            internal coordinates for a wide selection of chemical
            groups is:
            P.Pulay,G.Fogarasi,F.Pang & J.E.Boggs, JACS 101, 2550 (1979)
 
        For the 'CRYS' option, the external coordinates are defined
        here; their codes:
             ITYP=11 - x translation
             ITYP=12 - y translation
             ITYP=13 - z translation
             ITYP=14 - x rotation
             ITYP=15 - y rotation
             ITYP=16 - z rotation
 
         In this case the I field should hold the consecutive number
         of the molecule in the unit cell (consistent with MNAT data).
 
  PRNT  - set print level
             <int1> == IPRNT
               IPRNT=0 - minimal printout
               IPRNT=5 - maximum printout [default is 2]
 
  TEST  -  equivalent to 'PRNT' with IPRNT=4
 
  NULL  - control card for 'G   ' option with IGLEV=2
             <int1> == NULL 
             <int2> == NSTRT
              NULL = the number of orthonormal vectors for  the null
                     space to be read from the U2 matrix
              NSTRT = the number of starting vectors for the Gram-Schmidt
                     procedure in the vibrational space

    Note: If any null coordinates are known, they should be orthonormalized
    and placed in the first NULL rows of U2. The program will then write out
    the complete set of orthonormal coordinates spanning the null space,
    starting with the ones provided. If NSTRT.GT.0 a completely independent
    calculation will be performed in the vibrational space. In that case,
    the NULL+1,...NULL+NSTRT rows of U2 should contain the known coordinates
    of the vibrational space orthogonal to each other and the redundancies
    (null space vectors). The program will construct an orthonormal basis of
    the vibrational space which is orthogonal to the redundancies, starting
    with the provided vectors.

  PED  - symbolic PED analysis will be performed
             <int1> == NGRUP
             <int2> == NCUTP
             NGRUP - number of coordinate groups to be defined
             NCUTP - cutoff level; PED contributions below NCUTP % will
               not be printed, for clarity (default is 3%).

             The following cards must contain:
             1. for each group I=1,NGRUP: LGRUP(I),IGRUP(I,J), J=1,LGRUP(I)
                - the number of coords in group and their consecutive numbers
                (these are the final numbers, i.e. after all U matrix
                operations) (20I3)
             2. for each coordinate : IS,SS - its consecutive number (after
                all U matrix operations) and the assigned symbol.
                4(I3,2X,A8,2X) - zero to four entries per line; blank fields
                skipped, negative IS value to end this input section.
                Only the first coord of each group needs a symbol defnition,
                the rest are set to this string; contributions from the whole
                group are added up and printed beside the group symbol.
 
  SCAL   - scale the F matrix Fij' = FACT*Fij;
             the real value of FACT will be read from next line (F10.6).
 
  TRRM   - remove translational and rotational contributions from cartesian
           coordinate vibrational eigenvectors. (currently used only
           for GAUS) 
 
  MNAT  - lines following this card will contain the numbers of atoms
             of the individual molecules comprising the unit cell (or
             molecular aggregate) in 20I3 format.
             Application - makes possible external coordinate use in
             vibrational analysis of mixed crystals or molecular
             aggregates (use CRYS option in both cases).
             The value of IZMOL should already be defined for this card
 
  IFTR  - specifies the dimension (and type) of F matrix
             <int1> == IFTRAN
               = 0 - F is in primitive ICs R, NIC0xNIC0
               = 1 - F is in S1=U1*R, NICxNIC
               = 2 - F is in S2=U2*U1*R coords, NQxNQ
             If card is not given, default IFTRAN=NUMAT is assumed
            (works only for 'KANO' option)

  SYMM  - use symmetry (in symbolic PED analysis only)
              <int1> == NBLOCK
              It is assumed that by use of similarity transformations (the U
              matrices), the vibrational problem has been transformed to 
              such coordinates that the Hamiltonian (G and F) is
              block-diagonal. This usually happens if the coordinates form
              a basis for the irreducible representations of the molecular
              point group.

              The following cards should contain the data:
              IBLOCK(I),I=1,NBLOCK - sizes of consecutive blocks (coordinate
              numbering is as for PED analysis, i.e. after all U matrix
              transformations)
              SBLOCK(I),I=1,NBLOCK - block symbols (e.g. representation names)

  EXPF  - read in reference frequencies for the system
              Frequencies should be in ascending order (if 'SYMM' is
              present, the ordering should be separate within each block).
              The frequencies from MOLVIB will be printed out side-by-side
              with the reference set, differences and an rms deviation will
              computed. (If 'SYMM' is present, a separate analysis will be
              performed for each block).
              Format: free, 1 real value per line.

  END   - end input section, perform MOLVIB calculations and
                      return to CHARMM.
 
 Note: the Schactschneider/Snyder format

    This format is very useful for i/o of sparse matrices (or small and
not so sparse ones). The basic format is: 4(2I3,F12.6) 
The two integer fields specify the row and column number, the real field -
the value of the array element. Any elements not explicitly specified are
set to zero. Each line of input may contain 0-4 entries, blank lines are
ignored, a negative value for the column number terminates input.
See subroutine RDMAT in MOLVIO.

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