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Subsections


4.7 Analyzing Results: Output Files and the LUSCUS Program

MOLCAS provides a great deal of printed information in output files, and the printing level is controlled by the environmental variable MOLCAS_PRINT. By default this value is set to two, but can be modified by environmental variable MOLCAS_PRINT Typical MOLCAS output contains the program header and input information, conditions of the calculation, the number of steps to achieve convergence, the energies and wave functions, and final results, including in many cases the molecular orbital coefficients as well as an analysis of the properties for the computed states.


4.7.1 LUSCUS: Grid and Geometry Visualization

MOLCAS developers have developed a graphical interface that can be used both to create input for the MOLCAS program and to analyze the results in a graphical manner by visualizing molecular orbitals, density plots, and other output properties.

The first version of the code has the name GV (stands for Grid Viewer, or Geometry Visualization. By an accident, the name also matches the nicknames of the main developers). GV program uses a very limited set of graphic libraries, and thus has very primitive user interface.

The next generation of GV program has the name LUSCUS. Luscus re-uses the code of GV, and so GV users can use the same key combinations to operate with LUSCUS. At the same time, LUSCUS provides a user-friendly interface, and contains many new options, compared to GV.

LUSCUS can be obtained from https://sourceforge.net/projects/luscus/.

LUSCUS can read the files only in one format: Luscus internal format (.lus). This format contains two sections: XYZ cartesian coordinates, and XML formated data. It means that a standard XYZ file is a valid file in LUSCUS format.

Files with different formats, e.g. molden files, can be understood by LUSCUS since they can be converted to LUSCUS format by a corresponding plug-in. For instance, opening a file with the extension .molden, LUSCUS automatically runs a plug-in to convert a file from molden format to LUSCUS format. Saving a LUSCUS file as a Molcas orbital file will automatically run a converter from LUSCUS format to Orbital format.

  • luscus xyz_file: reads coordinates from a cartesian coordinate file.

    A molecule can be visualized and modified with the use of the left-button of the mouse and the keyboard. Below are some of the most useful commands.

      Left mouse click: Select atoms (if two, a bond is selected, if three a bond angle, if four a dihedral angle
      Left mouse + Shift click: Mark/unmark atoms to/from the group
      Middle mouse/Space: Remove selection, or marking
      Insert key: Insert atom
      PageUp, PageDown: Alter type of selected atom or bond
      Delete/Supress key: Delete a selected atom
      +/-: Change a value of selected bond/angle in steps
      Backspace: Undo last action
      Home: Set selected atom to center of coordinates
      F8 key: Find or apply symmetry

  • luscus molden_file: reads (check the comment about plug-in) from MOLDEN files such as wavefunction.molden, freq.molden, and geo.molden.

    Note that MOLCAS produces molden files with several extensions, so it is recommended to visualize these files by using Luscus.

  • luscus grid_file: reads coordinates and densities and molecular orbitals from a binary grid_file.

    This file is generated by GRID_IT and, by default, placed in the $WorkDir directory with the name $Project.lus. The program allows displaying total densities, molecular orbitals, and charge density differences.

    If MOLCAS and Luscus are installed locally, Luscus can also be called from user input as shown in the following example:



    &GATEWAY
      coord  =  acrolein.xyz
      basis  =  ANO-L-MB
    &SEWARD
    &SCF
    &GRID_IT
    ALL

    *  running  external  GUI  program  luscus

    !  luscus  $Project.lus

    *  User  has  to  select  active  space  and  save  GvOrb  file!

    &RASSCF
    Fileorb=$CurrDir/$Project.GvOrb

    Note, that in the example above, the GRID_IT program will generate a $Project.lus file which LUSCUS then uses, eliminating the need for defining $Project.lus and allowing this file to be overwritten. rasscf will read starting orbitals from the $Project.GvOrb file.


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Next: 5. Problem Based Tutorials Up: 4. Quickstart Guide for Previous: 4.6 Basic Examples