web site: http://www.cmbi.kun.nl/~schaft/molden/molden.html



2 FILES
     MOLDEN reads two files, these are:

     Inputfile

          File holding the title and keyword lines ( FORTRAN unit 5 )

     GAMESS/GAUSSIAN Outputfile

          A file  produced  by running GAMESS/GAUSSIAN.  The name  of this
          file must be defined with  the keyword FILE .  This must  be the
          output of a single GAMESS/GAUSSIAN run.   Care must be taken not
          to turn off printing  of vectors and/or basis set in the case of
          GAMESS.   In  the  case  of  GAUSSIAN   printing  of  basis  set
          information  has  to  be  turned on by  the  use  of the keyword
          GFINPUT.  Printing of MO coefficients has to be turned on by use
          of the keyword IOP(6/7=1).  ( FORTRAN unit 30 )


     MOLDEN writes two files, these are:

     Outputfile

          Results file.  ( FORTRAN unit 6 )

     plotfile

          The Plotter/Screen File called plot ( FORTRAN unit 15 ).  At the
          end of the MOLDEN run, a Screen file can be displayed by :

                                - simply typing 'CAT PLOT' on Unix
                     machines
                                                'TYPE PLOT.DAT' on VAX
                     machines

          Depending on the configuration of the Plotter, the Plot file can
          be displayed  in the same way or  has  to  be sent to a  queue (
          usually by a SUBMIT command or an lpr command ).


     INPUTFILE

          The layout of Inputfile for a MOLDEN job is as follows;

               <Title line>                    ( 80 columns maximum )
               <First line of key words>       ( 80 columns maximum )
               <Second line of key words>      ( 80 columns maximum )

          Both capitals and lowercase can be used.  The keywords taking no
          parameters usually can be abbreviated to four characters.


2 SPECIFICATION_OF_TERMINAL/PLOTTER_TYPE
     The following commands specify which terminal or plotter driver is to
     be used.

     TEK4014

          Syntax:  TEK4014

          The   Tektronix4014  graphics  language   is  considered  to  be
          something of  a  standard.   A lot  of  graphical terminals  can
          emulate tek4014 although you probably need to tell your terminal
          it is to do so.  Some PC's having a VT100 terminal emulation can
          also  emulate tek4014  (it runs at least  on an ATARI  and in an
          impaired way on a Macintosh)  (some HP terminals with a  tek4014
          emulation run tek4014 faster than the HP language)  XWINDOWS has
          an  application xterm  in  which you  can turn  on a tek window.
          (Under  Unix  this command is  usually  located in the directory
          /usr/bin/X11)


     HPGL

          Syntax:  HPGL

          HPGL  stands  for Hewlett  Packard  Graphics  Language.  The  HP
          plotters  all   speak  this  language.    Also  HP  laserwriters
          understand HPGL.


     HP2392A

          Syntax:  HP2392A

          Most HP terminals with graphics capability probably will be able
          to understand these escape codes.


     POSTSCRIPT

          Syntax:  POSTSCRIPT

          Most Laserwriters understand POSTSCRIPT.  Although sometimes you
          have to tell them it is not getting plain text but POSTSCRIPT.


     XWINDOWS

          Syntax:  XWINDOWS

          Most   workstations   have  XWINDOWS  capability  (See   section
          INSTALLATION GUIDE  how  to  install  MOLDEN  with  an  XWINDOWS
          driver).  Before running MOLDEN you have  to define  the display
          you will  be working  on.   On Unix machines just  type;  SETENV
          DISPLAY :0 when  you  want to  use  the  display  of the machine
          MOLDEN   is  executing  on,  and  for  instance  SETENV  DISPLAY
          CAMMS3.CAOS.KUN.NL:0 when  you  want  to use  the display of the
          remote machine with internet address CAMMS3.CAOS.KUN.NL.  On VAX
          machine, the same is accomplished by  typing  SET DISPLAY/CREATE
          /NODE=CAMMS3.CAOS.KUN.NL/TRANS=TCPIP.  A window will  be created
          at run time, holding the picture.  A  rectangular part  of  this
          picture can be magnified by  pressing the left  mouse button and
          holding it down  while  dragging it untill the rectangle has the
          required size.   Pressing the  middle mouse  button subsequently
          will undo  the magnification.   Pressing the  right mouse button
          will end the MOLDEN session.  When the cursor is  in the  MOLDEN
          window, the arrow keys can be used to rotate the 3-d picture and
          I  and  D  keys  will  respectively  Increase  and  Decrease the
          vertical scale op the 3-d plot.  The letter M is a toggle, which
          turns on/off the displaying of the molecule in the 3-d picture.


     FIGURE

          Syntax:  FIGURE

          Figure is a Graphics language developed by the Genetics Computer
          Group.   With it  goes a  package  that can convert Figure  to a
          variety of graphics/plotter languages.


     SILLY

          Syntax:  SILLY

          The Silicon Graphics 3D version  is requested through the use of
          the keyword  SILLY.   This  is  an  experimental  version.  (See
          section INSTALLATION GUIDE on how to install this version.)


2 DEFINITION_OF_DENSITY
     The following keys define ;

          whether the total electron density has to be plotted or  the sum
          of the  density  owing  to  some specified  molecular  orbitals.
          (OCCU, VALENCE)

          whether  the  electron  density  or  the  value of an  molecular
          orbital itself has to be plotted (HOMO, LUMO, PSI, PHASE)

          whether the  molecular density minus spherically averaged atomic
          density has  to  be plotted (BONDS)  or whether for O,F,S and Cl
          oriented ground state atomic  densities have to  be substracted.
          (BONDS in combination with ORIENT)

          whether the  interatomic  overlap  density  has  to  be  plotted
          (OVERLAP)   or the  atomic  part of difference density (ATOMIC).
          These are  the two  components  that  make up the density matrix
          used by BONDS (possibly in combination with ORIENT)


     ATOMIC

          Syntax:  ATOMIC

          Specifies  that the  electron density of the free atoms is to be
          subtracted from the molecular electron density as  with  the use
          of  the  keyword BONDS,  only  now  the  contribution  from  the
          interatomic  overlap  is  set  to  zero.   In  fact  the density
          matrices used by ATOMIC and OVERLAP together make up the density
          matrix used by BONDS.  The density map predominantly will have a
          negative  value,  since  some  of  the atomic  density has  been
          transferred to interatomic  overlap density.  However lone pairs
          usually show  up  as  positive contributions in the density map.
          (As with  BONDS it can be  used in combination with  the keyword
          ORIENT)

          See also BONDS, ORIENT and OVERLAP !!


     BONDS

          Syntax:  BONDS

          Not to  be  used  in conjunction  with  HOMO, LUMO, PSI or OCCU.
          BONDS subtracts the spherically averaged atomic density from the
          molecular density .  The result is a plot whose average value is
          zero, and  shows where the electrons  have come from and gone to
          when the  bonds are formed.  However  a problem can arise.  Most
          atomic ground states are not spherically  symmetric.  Oxygen for
          example has a  3P ground  state  f.i.  Px2Py1Pz1.   The electron
          density now is maximal along the x-axis, so that in fact when an
          atom in the  molecular  environment  has  retained a lot  of its
          ground state character  it  will have a preferable  orientation.
          Subtracting a spherically symmetric atom Px4/3Py4/3Pz4/3 in this
          case  can  result  in  subtracting  too  much  in  the  y and  z
          directions and  too little in the x  direction.  As a result the
          density  difference  plot  may  show  a  misleading  decrease in
          electron density along for example a C-O axis.  In this case the
          keyword  ORIENT  must  be  used.(See  also  ORIENT, OVERLAP  and
          ATOMIC)  This effect  is usually most pronounced  for  the atoms
          O,F,S,  and Cl, whereas  for  example  Carbon  in the  molecular
          environment  usually  has   a  lot   of   spherically  symmetric
          character.

          BONDS can only be used when one of the following  basissets have
          been  employed;  STO3G,  3-21G,  4-31G, 6-31G,  optionally  with
          polarisation  functions ( *, or ** ).   They may differ per atom
          however  and  the  atoms must be  in the  range Hydrogen  up  to
          Chlorine.

          HINT : for contour plots CUT=0.1 is recommended
                 for 3d plots MULT=20 is recommended


     HOMO

          Syntax:  HOMO

          For closed-shell systems  with  non-degenerate  Highest Occupied
          Molecular Orbitals,  the keyword HOMO can  be used to produce an
          intensity map of  the highest  occupied  molecular orbital.  For
          other systems, the keyword PSI should be used.


     LUMO

          Syntax:  LUMO

          For closed-shell systems  with non-degenerate Lowest  Unoccupied
          Molecular orbitals, the keyword LUMO can  be used to  produce an
          intensity map of the lowest  unoccupied  molecular orbital.  For
          other systems, the keyword PSI should be used.


     OCCU

          Syntax:  for example;  OCCU = (1-22/0,9/1.0,10/2 )

          When  the  user  wants   to  explicitly   define  an  electronic
          configuration for a system,  overriding  the occupancies read in
          from  the GAMESS/ GAUSSIAN output file,  the keyword OCCU has to
          be used.  Taking the occupancies read in from the outputfile  as
          a starting  point, the  orbital  occupancies in the example  are
          modified in the following way, in sequential order;

                                             ORBITAL      OCCUPANCY

                                              1-22            0
                                               9              1
                                              10              2

          For  the use  with Unrestricted Hartree Fock  wavefunctions  the
          keywords OCCA (for the alpha electrons)  and OCCB (for the beta
          electrons)  have to be used.


     ORIENT

          Syntax:  ORIENT or ORIENT = (n1,n2/n.nn/n.nn,...)

          To be used in conjunction with the keyword BONDS  and  not to be
          used  in  conjunction  with  HOMO,  LUMO,  PSI  or OCCU.   BONDS
          subtracts the the  spherically averaged atomic density  from the
          molecular density .  The result is a plot whose average value is
          zero, and  shows where the electrons have come  from and gone to
          when the bonds are  formed.  However  a problem can arise.  Most
          atomic ground states are NOT  spherically symmetric.  Oxygen for
          example  has a  3P  ground  state f.i.   Px2Py1Pz1  the electron
          density now is maximal along the x-axis ,so that in fact when an
          atom in the  molecular environment has  retained  a  lot of  its
          ground state  character it will  have  a preferable orientation.
          Subtracting a spherically symmetric atom Px4/3Py4/3Pz4/3 in this
          case  can  result  in  subtracting  too  much in  the  y  and  z
          directions and too little in the  x  direction.  As a result the
          density  difference  plot  may  show  a  misleading  decrease in
          electron density along  for example  a C-O axis.  This effect is
          usually most  pronounced for the atoms O,F,S, and Cl, wheras for
          example Carbon in the molecular environment usually has a lot of
          spherically symmetric character.

          When using ORIENT without parameters, the atomic density (DATOM)
          of O,F,S and Cl atoms will be  oriented in  such a way  that the
          sum  of  (DMOL(i,j)-DATOM(i,j))2  (delta  squared on  the output
          file)  is  at a minimum.  (DMOL  being the  atomic  part  of the
          molecular density matrix  and  i  and  j  run  over the Px,Py,Pz
          Atomic orbitals).  This is done per atom.

          When using  ORIENT =  (N1,N2,..)  only the  specified  atoms are
          oriented.   For  all  others  the  spherically  averaged  atomic
          density is used.  Checked  is whether  atom number N1,N2 etc are
          O,F,S or Cl atoms.

          When  using   ORIENT  =  (N1,N2/N.NN/N.NN,...)    the  automatic
          orientation mechanism is overridden for atom  N2.  Instead it is
          oriented using the  two angles supplied on the keyword after the
          slashes (alfa  and beta  on  the output file).  For  example the
          atomic ground state  density  of  Oxygen  has an  oval symmetry,
          having one direction in  which 2 electrons  participate and  two
          perpendicular directions  in which 1 electron each participates.
          The supplied angles define the direction of the unique axis.  If
          the atom in  the molecular  environment  has lost  a  lot of its
          ground state  character the  automatic orientation mechanism can
          give physically meaningless orientations.  In  the ultimate case
          when the  oxygen has a pure spherical O2- character,  the use of
          oriented ground state  densities is clearly erroneous.  When the
          atomic part of the molecular  density matrix shows one direction
          in which 1 electron participates and two directions in which 1.5
          electrons each participate, the automatic  orientation mechanism
          may provide a direction which  results in a decrease in electron
          density at the middle of a bond axis.   Here orientation by hand
          can  result  in  a density-difference  plot  with  the  expected
          increase in electron density at the middle of a bond axis.

          ORIENT can only be used when one of the following basissets have
          been  employed  ;   STO3G, 3-21G,  4-31G, 6-31G  optionally with
          polarisation  functions (*, or  **).  They may  differ  per atom
          however and the atoms  must  be  in the  range  Hydrogen  up  to
          Chlorine.

          HINT : for contour plots CUT = 0.1 is recommended
                 for 3d plots MULT = 20 is recommended

          (see also Chemical Deformation Densities,  W.H.E.   Schwarz,  K.
          Ruedenberg   and   L.    Mensching,   J.    Am.    Chem.    Soc.
          1989,111,6926-6933, where  the orientation used  here  is termed
          'naive' )


     OVERLAP

          Syntax:  OVERLAP

          The  interatomic overlap density will be  plotted.  This is done
          by setting the atomic  part of  the Molecular density  matrix to
          zero.  The density map  will predominantly have  positive values
          with maxima roughly at midway the bond axes.


     PHASE

          Syntax:  PHASE

          PHASE is  used  to to reverse the sign  of  a Molecular Orbital.
          Used in conjuction with PSI.


     PSI

          Syntax:  PSI = NN

          A specified molecular orbital is to be plotted (see also PHASE).


     VALENCE

          Syntax:  VALENCE

          Since the  inclusion  of  non-valence  electrons  in  ab  initio
          calculations  results  in  the predominance of  the  inner shell
          electron   density  on   the   total   electron   density,   the
          interpretation  of  the   chemically  more  interesting  valence
          electron density  is clouded.  The use of VALENCE results in non
          occupying  those molecular  orbitals which predominantly contain
          inner-shell  electron density.  It only works when your molecule
          exclusively consists  of  atoms  from  H to  Ar.  Otherwise  you
          should use the keyword OCCU.



2 DEFINITION_OF_THE_PLOTPLANE
     The plane of the plot is essentially defined by :

          The center of the plot ((PX,PY,PZ)  on the MOLDEN outputfile )

          The vector perpendicular  to  the plane of  the plot ((CX,CY,CZ)
          on the MOLDEN outputfile )

          The EDGE keyword specifying the size of the square plot


     The center and vector  perpendicular to  the plane  of  the  plot can
     either be specified ;

          directly in cartesian coordinates  by using the absolute form of
          the keywords CENTER and LINE.

          indirectly,  by using the coordinates of the atoms  on the PLANE
          and ROT keywords ( or the atomic form of the keywords CENTER and
          LINE).

     The use of CENTER/LINE and  PLANE(/ROT)   are mutually exclusive.  Of
     these, the PLANE(/ROT)  keywords are  the most  flexible and  easy to
     use.  PLANE defines  the plane of the  plot by specifing  three atoms
     and optionally this plane  can then be rotated round the  axis formed
     by two of these three atoms by use of the keyword ROT.  The remaining
     atom will then no longer lie in the plane of the plot.

     Finally,  when  having  defined  the  plane of  the  plot  by  either
     CENTER/LINE or  PLANE(/ROT)   the plane can be  translated  along the
     vector perpendicular to the plane by use of the keyword LIFT.


     PLANE

          Syntax:  PLANE = (N,N,N)

          This keyword is  essential, it defines  the  plane of  the plot.
          For example  PLANE=(1,2,3)  means the  first  three atoms in the
          coordinate list define the plane of the plot.  The center of the
          triangle will  be taken as  center of  the  plot.   The keywords
          CENTER/LINE and PLANE are mutually exclusive.


     ROT

          Syntax:  ROT = (N,N,NNN.NN)

          This keyword is optional, it can only be use in conjunction with
          the keyword PLANE.   For example, when previously having defined
          the  plane of the  plot by  the first three atoms (PLANE=(1,2,3)
          ), this plane  can  be  rotated round the axis formed by atoms 2
          and 3 by 45 degrees, by using ROT=(2,3,45.0), atom 1 will now no
          longer be part of  the plane  of the plot .   The  center of the
          plot has  been shifted to  the point midway the line  connecting
          atoms 2 and 3.


     CENTER

          Syntax:  CENTER = NN or CENTER = (N.NN,N.NN,N.NN)

          This keyword is essential, it defines the center of the plot Two
          formats are provided to define  the center:  (A)  an atom number
          can be  used, and (B)  an absolute  cartesian coordinate  can be
          specified.  Irrespective of which  option is used, the center of
          the plot  will be  converted  internally into absolute cartesian
          coordinates.

          Atomic

          Syntax:  CENTER =  N.  The location of atom N is  defined as the
          center of the plot.   Thus  if atom n has  cartesian coordinates
          (x=0.5, y=1.4, z=-0.8)  then  the center of the plot is  (x=0.5,
          y=1.4, z=-0.8).  Dummy atoms  are  not counted, so if  any dummy
          atoms were  used  in the  definition  of the geometry, the atoms
          will  have  been  renumbered  (see   the   MOLDEN  output  file;
          coordinates section for the new numbering )

          Absolute

          Syntax:  CENTER = (N.NN,N.NN,N.NN)   .The location of the center
          of the  plot is defined  as being (n.nn,n.nn,n.nn).   Of course,
          before such a  center  can be defined,  the user must  know  the
          cartesian coordinates of the atoms in the molecule.


     LINE

          Syntax:  LINE = NN or LINE = (N.NN,N.NN,N.NN)

          This  keyword is essential, it defines a vector perpendicular to
          the plane of  the plot.  Two formats are provided to  define the
          axis perpendicular to the  plane of the plot.  These formats use
          radically different concepts, so  users are  cautioned to verify
          that  they  understand  both