[Jmol-developers] [ jmol-Bugs-3005028 ] loss of feature in rev 12

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Bugs item #3005028, was opened at 2010-05-20 20:29
Message generated for change (Comment added) made by hansonr
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Category: User interface
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Miguel (migueljmol)
Summary: loss of feature in rev 12

Initial Comment:
This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules).

Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago).  Sigh....

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>Comment By: Bob Hanson (hansonr)
Date: 2010-05-21 10:35

Message:
duh. I see it now -- Jmol!

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Comment By: Bob Hanson (hansonr)
Date: 2010-05-21 10:32

Message:
Rene, it's the .PATH property:

    atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY,
        "Calculation "+calculationNumber+
        (scanPoint>=0?(SmarterJmolAdapter.PATH_SEPARATOR+"Scan Point
"+scanPoint):"")+
        SmarterJmolAdapter.PATH_SEPARATOR+path);

as far as I know, that should still work. For example, I see for one of
the test files:


auxiliaryinfo.properties.PATH_SEPARATOR	";"
auxiliaryinfo.properties.PATH_KEY	".PATH"
modelinfo.models[1].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[2].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[3].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[4].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[5].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[6].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[7].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[8].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[9].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[10].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[11].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[12].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[13].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"
modelinfo.models[14].modelProperties..PATH	"Calculation
1;FrequenciesFrequencies"

and for another:

modelinfo.models[1].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[2].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[3].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[4].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[5].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[6].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[7].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[8].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[9].modelProperties..PATH	"Calculation 1;Input"
modelinfo.models[10].modelProperties..PATH	"Calculation 1;Standard"
modelinfo.models[11].modelProperties..PATH	"Calculation 2;Input"
modelinfo.models[12].modelProperties..PATH	"Calculation 2;Standard"
modelinfo.models[13].modelProperties..PATH	"Calculation
2;FrequenciesFrequencies"
modelinfo.models[14].modelProperties..PATH	"Calculation
2;FrequenciesFrequencies"
modelinfo.models[15].modelProperties..PATH	"Calculation
2;FrequenciesFrequencies"


These are exactly the same properties that are shown using Jmol 10.9, so
maybe it's just how you are extracting them. What are you using to view
this hierarchy?

Bob
maybe there is 

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