[I'm moving this to jmol-developers, please follow discussion there]
El 29 Jun 2009 a las 10:45, Riccardo Sabatini escribió:
> Hi,
>
> i'm a PhD student from italy and i'm writing a modelling
> application for nano-structures that will be used as an editing tools
> for a DFT code developed by my college (and others...).
>
> I started to use Jmol as a viewer and i'm writing to the list
> 'cause i found some problems and i'd like the have a discussion about
> my integration strategy. I first explain the approach used in the code
> (the code will be released as open source, if anyone need to see the
> source i'll be glad to share).
>
> The software will be able to open files containg several
> different atomic configurations. All the editing and modelling part is
> done with tables of atomic positions and with other tools (not visual)
> and JMol is used only as a visualization tool and as a picking tools
> (trough findNearestAtomIndex(x, y)).
>
> In the DFT calculation is very common to import tens, or even
> hunderds, of different configurations and then scroll along all of
> them. Plus in the software i'm finishing i've implemented a way to
> store objects or visualization details (specific atoms color,
> distances....) in a specific configuration. To let this work properly
> and without annoying time delays i've implemented this conceptual
> architecture.
>
> ------------------------------------------------
>
> 1) loads the new conf [not jmol]
> 2) if the conf is connected to the one visualized (same atoms, same
> cell):
> 2.a) delete drawing objects "draw ID * DELETE" [evalString() method]
> 2.b) store the view point getProperty("getProperty",
> "orientationInfo", "") [evalString() method]
> 2.b) calculate the translation vector for each atom
> 2.c) translate the atomos with "atomno=***; translateSelected
> {x,y,z}" [evalString() method]
> 2.d) paint the objects contained in the new conf [evalString()
> method]
> 2.e) restore the viewpoint and other view directives
> contained in the new conf [evalString() method]
>
> 3) if the conf is completely new
> 3.a) produce a new string in the XYZ format and send it to
> the code trough openStringInline() method
> 3.b) paint new objects [evalString() method]
> 3.c) set the conf. specific visualization options
> [evalString() method]
>
> ------------------------------------------------
>
> Now, BEFORE and AFTER any evalString() and openStringInline()
> i've decided to check if jmol object was running or busy trough a very
> easy call
>
> public void waitUntilFree() {
>
> while (jmolViewer.isScriptExecuting()) {
> try {
> Thread.sleep(100);
> } catch (InterruptedException e) {
> e.printStackTrace();
> }
> }
>
> }
>
> This architecture works quite good and let's me scroll very fast
> between different configurations (new ones and the ones only with the
> atoms displaed in new positions). But still some problems appear when
> a configuration has some obects to draw. Sometimes the code breaks and
> gives this specific error
>
> Exception in thread "QueueThread0" java.lang.NullPointerException
> at org.jmol.viewer.Viewer.loadShape(Unknown Source)
>
> This happens when i try to send in the openStringInline() method
> and i can't reproduce it with everytime. Sometimes happens, some other
> times the code works flawlessy !!
>
> Do you have any idea why this error comes out ?
> And, in general, do you have any reccomandations how to implement
> in a better way the integration between jmol, maybe with threads ?
> And, very last question, i saw in the last cvs version the
> findNearestAtomIndex(x, y) was not anymore a public function and i had
> to redeclare it, is there any plans to remove it ? I REALLY REALLY
> hope not, it's extremeluy important for integratin jmol !!
>
> Thanks for the help,
>
> Riccardo
>
>
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