MOLCAS manual: Subsections 4.3.1 Editing molecular structures using the GV program. 4.3.2 Visualization of orbitals with gv. 4.3.3 Writing MOLDEN input 4.3 MOLCAS grid and geometry viewer 4.3.1 Editing molecular structures using the GV program. Program GV is used to manipulate molecular structures, build new molecules, etc. It is also used to show orbitals , densities, etc. Here, we shall exemplify how structures are manipulated. The program requires some coordinates to start with. One possible source of initial coordinates is Coord directory, which contains a large number of molecular structures. Change directory to Coord under the main directory of MOLCAS, and run for example molcas gv Water.xyz. In order to make modifications of coordinates we have to select one, two, three or four atoms. Selection is made by clicking on an atom. The first selected atom is covered by blue-colored net, the following selected atoms are covered by magenta-colored net. Any time the user can press 'space' key, or click by middle button on the mouse to remove selection. If only one atom is selected - you can make modifications for this atom, if two atoms are selected - you can modify the bond between atoms, if three atoms are selected you can modify the angle, and for four atoms the dihedral angle. Note, that modifying bond or angle - the first selected atoms will move. Modifications can be done by the following keyboard shortcuts: '+/-', 'PageUp/PageDown',F4. Pressing + or - will modify the value, e.g. if a bond is selected, and user pressed '+' key, the bond length will increase, so the first selected atom will move away from the second atom. Pressing PageUp/PageDown will modify the 'property' of selected object. If only one atom is selected - it will change element name, if bond is selected - it will change the type of the bond (single, double, etc.), and for angle selected, it will change the angle to most common values. If F4 (or '=') key is pressed, user can type the value in a separate input box. If one atom is selected, user can type an element name. If a bond is selected, user can type the lenght of the bond, and finally if an angle is selected - user can type the new value of the angle. Any time a Backspace key can be used to revert modifications (Undo). F2 key can be used to save the coordinate file. The file name will be generated from the original name, by adding a counter. Shift-F2 will overwrite the original file. If an atom is selected it is possible to use Delete or Insert key to delete or insert a new atom. Let make H2O2 molecule started from Water.xyz file. select a H atom press PageUp until the atom becomes oxygen. select another O atom press F4 and type 1.474 followed by Enter press Space bar to un select atoms. select H-O-O press F4 and type 94.8 followed by Enter press Space button select 'new' Oxygen atom press Insert to add H atom near selected atom select two oxygen atoms press F4 and type 94.8 select remaining hydrogen atom to select dihedral angle press F4 and type 111.5 fix O-H bond lenghts. Now we will continue to edit the H2O2 molecule. If we select the O-O bond and change interatomic distance - only one atom will move. If we want to move a group (O-H), we have to mark this group first. There are two different ways to mark atoms into a group. One can do this manually, clicking on an atom with pressed Shift button. Or, it is possible to mark connected (bonded) atoms, in respect to a selected bond. Select an O-O bond and press F7 button. All atoms, which are connected to the first selected atom will be 'marked', and shown as cyan-colored. If you change the length of the O-O bond, all marked group will move accordigly. Note that unselection (Space key, or mouse middle click) will remove selection first, and the second use of unselect button will remove marking of a group. The modified value (of a bond lenght or an angle) is shown on the information line of the screen. Sometime you would like to observe another value during a modification of coordinates. To achive such behavour, select a bond, or an angle, and press F6 button. Now you can make another selection and make modifications in the geometry. But in this case originally selected value will be watched. Pressing Shift-F6 key switches off the watching mode. GV contains a short list of molecular fragments, which can be added to a molecule. Press F3 key, to get a list of available fragmets. Clicking on a picture with a fragment, you will add this fragment into your sceene. If no atoms are selected, the fragment will be added somewhere around the current molecule. If one atom is selected, the fragment will be inserted near the selected atom. Note, that once a fragment has been selected, an Insert key will insert this fragment. Example. Let's make mesitylene (1,3,5-trimethylbenzene). molcas gv Benzene mark (not select) 3 hydrogen atoms Press Delete select C atom, press F3 and click on CH3 icon select another C atom, and press Insert select third C atom, and press Insert To make modifications of coordinates via distances and angles, you might need dummy (reference) atoms. These dummy atoms can be set by End button. If there is no selected atoms, 'End' key will add dummy atoms located on XYZ axeses. If a bond is selected, the dummy atom will be placed in the middle of the bond. For example, if you have a planar molecule, but it is not oriented according to cartesian axeses, you can add dummy atoms on each axis, mark all atoms in the molecule, and select a dihedral angle between the plain of the molecule and desired plane, created by dummy atoms. Program GV can recognize the symmetry elements of a molecule, or apply symmetry operations for all, or marked atoms in the molecule. If no selection is made, F8 key displays symmetry elements of the molecule (D2h subgroup only). If some atoms are selected, F8 key will apply a symmetry operation: in case of only one atoms being selected inversion, in case of a bond, C2 axis, and in case of an angle - a mirror plain. This feature can be used to construct symmetrical molecules. Let us start from a benzene molecule. Delete two hydrogens (in ortho positions), and select two carbon atoms (with broken bonds). Pressing F8 key will duplicate the structure, creating naphtalene. If, during such transformation coordinates of a new atom are very close to another atom - the average coordinates will be used. For example, if you have an almost planar molecule, you can flatten it, by applying a mirror plane symmetry. Also note, that if a part of the molecule is marked, the symmetry operation will be applied only for marked part. GV can be customized. Press F9 key to save current setting. It will create a directory .molcasgv in user HOME directory, with default settings for used colors, initial sizes etc. User can edit this files to reset the default values. 4.3.2 Visualization of orbitals with gv. To visulaize orbitals and density by program GV you have to compute a grid file (.grid) first by using GRID_IT. Orbitals can be browsed by PageUp/PageDown key, or selected by a menu, invoked by the right mouse button. If you know the symmetry and number of an orbital, you would like to display, you can press F4 (or =) key, and press # followed by symmetry and orbital number, e.g. (# 1 3). In order to change isosurface value, you can use + or - key, or press F4 key, and type a desired isosurface value. Sometime you would like to filter orbitals, shown by GV. Pressing Delete key you can hide an orbital. All hidden orbitals will become visible if Insert key is pressed. Alternatevely, you can apply a filter to hide some orbitals by a criteria: symmetry number (s), orbital energy (e), occupation number (o), or typeindex (i). Usage of filters is clear from the following example: Press F4 key and type #: followed by a filter command - #:s14 to display orbitals only from symmetry 1 and 4, #:e-2:1 to display orbitals in an energy range between -2 and 1. When the grid file is loaded, GV displays subspaces (frozen, inactive, RAS1, RAS2, RAS3, secondary, deleted). User can modify the typeindex of the orbital, save (F2 key) the INPORB file (it will have an extension GvOrb), and use this file in the following RASSCF calculation withou having to reorder the orbitals. In order to modify the index of the displayed molecule, user can use a menu, or press one of the keys: fi123sd. Pressing Space key (or middle mouse button) changes the typeindex in a loop. It is possible to display all orbitals of the grid file simultaneously. Press F3 key to get the screen with all orbitals. By default, the background (rainbow colors) for each orbital corresponds to the type index information. Clicking on an individual orbital you can use the same keys to modify it's type, or delete it from the screen. Pressing F3 button again, or Escape will close the multiview mode. Using PageUp/PageDown in multiview mode will increase/decrease the sizes of subscreens. These features of GV can be quite helpful for selecting the different orbital spaces in RASSCF calculations. GV can also be used to compare densities from different GRID_IT calculations. A command molcas gv -a 1.0 scf.grid rasscf.grid will compute a density difference between two grid file. A bit more complicated procedure should be done if you would like to visualize a density difference between two interactive molecules. First, you have to make a BSSE-like calculation, adding dummy atoms (with or without basis) in order to produce identical (in space grids). Let say, we computed 3 grid files A.grid, B.grid, AB.grid. Run molcas gv -a 1.0 A.grid B.grid -out sum.grid. gv will create a file sum.grid which is a sum (due to -a 1.0) of densities. Now, run molcas gv -a -1.0 AB.grid sum.grid to compute the difference AB - (A+B). 4.3.3 Writing MOLDEN input By default the SCF, RASSCF, CASVB, SLAPAF, and MCLR modules generate input in Molden format. The SCF and RASSCF modules generate input for molecular orbital analysis, CASVB for valence bond orbital analysis, SLAPAF for geometry optimization analysis, and the MCLR module generates input for analysis of harmonic frequencies. Molden files can be visualized by gv or by Molden (http://www.caos.kun.nl/˜schaft/molden/molden.html). The generic name of the input file is MOLDEN. However, the actual name is different for the nodes as a reflection on the data generated by each module. Hence, the actual names for MOLDEN in each module are SCF module: $Project.scf.molden RASSCF module: $Project.rasscf.molden for the state-averaged natural orbitals, and $Project.rasscf.x.molden for the state-specific natural spin orbitals, where x is the index of a CI root. CASVB module: $Project.casvb.molden SLAPAF module: $Project.geo.molden MCLR module: $Project.freq.molden