Jmol.___JmolVersion="14.20.1"
bug fix: ADF reader not accepting Xx.name atom ids
This reads N.test as symbol="N" and name="N.text"
On Mon, Jul 3, 2017 at 7:20 AM, Georg Eickerling <
georg.eickerl...@physik.uni-augsburg.de> wrote:
> Dear all,
>
> this is some kind of feature addon for the Jmol filters:
>
> The ADF filter obviously assumes all element symbols to be simple
> strings. This is not always true following the ADF user guide
>
> https://www.scm.com/doc.2016/ADF/Input/Atomic_coordinates.
> html?highlight=atoms
>
> were "atom types" are
>
> ***************************
> AtomType
>
> The name of an atom type. It must begin with the standard one- or
> two-character symbol for the chemical element (e.g. H, He, Li,...).
> Optionally it may be appended by .text, where text is any string (not
> containing delimiters). Examples: H, Mn.3, Cu.dz-new.
> ***************************
>
> This feature is for example used in NMR coupling calculations when
> re-defining special basis sets for some of the coupling atoms.
>
> At the moment, the jmol parser apparently simply ignores atoms with
> names such as "H.b" so they are just lacking in the final structure. I
> suggest the following one line fix:
>
> ADFReader.java
>
> starting from line 159:
>
> while (rd() != null && !line.startsWith(" -----")) {
> tokens = getTokens();
> if (tokens.length < 5)
> break;
> String symbol = tokens[1];
> /* +++++++++++++ADD THIS++++++++++++++ */
> if(symbol.contains("."))
> {
> symbol = symbol.split("\\.")[0];
> }
> /* +++++++++++++ADD THIS++++++++++++++ */
> if (JmolAdapter.getElementNumber(symbol) < 1)
> nXX++;
> else
> addAtomXYZSymName(tokens, pt0, symbol, null);
> }
>
> This will just split off the things after the period and proceed with
> the element symbol as usual and works for me on my local files with
> "H.b" atoms.
>
>
> best
>
> Georg
>
>
>
>
>
>
>
>
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> PD Dr. Georg Eickerling
> Universität Augsburg
> Institut für Physik
> Lehrstuhl für Chemische Physik und Materialwissenschaften
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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