#482 loss of feature in rev 12

closed-fixed
Miguel
5
2010-05-21
2010-05-21
No

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....

Discussion

  • Bob Hanson

    Bob Hanson - 2010-05-21

    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

     
  • Bob Hanson

    Bob Hanson - 2010-05-21

    duh. I see it now -- Jmol!

     
  • Bob Hanson

    Bob Hanson - 2010-05-21

    duh. I see it now -- Jmol!

     
  • Bob Hanson

    Bob Hanson - 2010-05-21
    • status: open --> closed-fixed
     
  • Bob Hanson

    Bob Hanson - 2010-05-21

    OK, that's fixed -- just had two lines switched order in ModelLoader.

    Thanks,
    Bob

     

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