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Importing l matrices

PGOPHER can import the required geometry and l matrix directly from normal modes as output by selected ab initio programs. To do this select "File", "Import", "l matrix..." from the main menu, and then navigate to the required file. See Predicting the Photoelectron Spectrum of H2O using ab initio Calculations for a worked example.

When importing l matrices, particularly from from more than one source, it is important to check that the axis system and mode and atom numbering is consistent between the states. The l Matrix Window and Dushinsky Transformation Window provide plots that can help to check for this. Nuclei and modes can be re-ordered by right clicking on the nucleus or mode in the constants tree and selecting "Move Up/Down" (for a move that affects only one electronic state) or Global Shift Up/Down for a move that affects all states within the molecule. The l matrix in its non mass-weighted form should be orthogonal - the "Operate" button in the l Matrix Window contains tools to test and correct this, and the centre of mass.

The point group is not read from the imported file, but defaults to C1. The correct point group can be entered manually, if required, in which case the symmetry of each electronic state and mode must also be entered manually. The modes will not necessarily be in the standard order; use the Global Shift Up/Down or Sort menu items to fix this.

The file formats listed below are currently supported; the format used is detected automatically.

Molden Format

This format is the input to the Molden program, which can be produced by several ab initio programs, either directly or with the help of a post processing program. The format is documented on the Molden website; note that only the [FREQ], [FR-COORD] and [FR-NORM-COORD] sections are read. Note that after version 7.1.370 average atomic weights are assumed, rather than exact masses. The normal modes will be normalized on input, but should be otherwise checked as above.


The xml files produced by the more recent versions of Molpro can be imported directly; the output of the FREQUENCIES command is all that is required. Note that after version 7.1.370 average atomic weights are assumed, rather than exact masses, and a different set of co-ordinates is taken from the xml file. Alternatively the PUT,MOLDEN,file command can be used to write output in Molden format.


The log files produced by Gaussian, or other programs producing the same format, can also be imported directly, though as the format is not formally defined some files may fail to import. Note that the the default in Gaussian is only to give normal modes to 2 decimal places, which is rather low. The Gaussian option freq=hpmode is recommended (if available) to increase the precision