Add Huub's discussion to the SVN

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Kurt Glaesmann 2010-11-10 16:56:11 +00:00
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========= Dummy centers vs Ghost centers ==========
==== The Characters
Originally dummy centers (named "x") were a mathematical trick to specify
zmatrices for tricky molecules. E.g. benzene, or linear molecules.
Because of their role it is alright to delete dummy centers. This was
introduced at some point to clean up zmatrices. After deleting the dummies
the autoz function would be used to regenerate a zmatrix.
Ghost centers (named "bq" after the ghost Banquo from William
Shakespeare's Macbeth) were introduced to calculate BSSE
free energies. These centers have basis sets, but no charge and
no electrons.
==== The conflict
The way the deletion is implemented means that different things happen
depending on how dummy centers are named. Due to a different choice
of internal coordinates this could lead to a different optimization path.
==== The resolution
To fix this all centers starting with "x" but not "xe" are deleted and a new
zmatrix generated. Bq centers by their nature should not be deleted, and they
now won't be.
==== The dénouement
Not clear to me at present is what happens if the original input
zmatrix contains constraints. I don't see how these can be handled so that they
would always survive the elimination of the dummy centers. Of course one could
replace the dummy centers by ghost centers without a basis set to deal with
such a case. The dft_bsse test case has been updated to match the new approach.