I think that would required a different way of storing the internals of what Jmol is dealing with. It would allow one to put each of the structures in a certain 'context', as opposed to having a single list of structures/vibrations.
It seems to me that Jmol should continue to store the different 'models'
as flat models ... but we need to supplement these models with additional
information.
Some computational packages allow one to do calculations on a series of molecules (usually the idea is that the same atoms are present but in different arrangements, or using different levels of calculation). Each of those calculations can give rise to a series of structures for that particular molecule. I think that that if one were to be retain that relationship, one would need to have a hierarchical way of storing the structures.
Maybe this is something beyond the scope of what Jmol is intended for, but I was under the impression that the CML file format would allow for that, i.e., you could have something like (not focusing on meta-information about each of these structures) the following for a calculation that had two starting geometries (m1 and m2) for which two steps of geometry optimizations were done (called s1 and s2 here):
<cml id="calculation"> <molecule id="m1"> <atomArray>...</atomArray> <cml id="s1"> <atomArray>.....</atomArray></cml> <cml id="s2"><atomArray >.....<//atomArray></cml> </molecule > < molecule id="m2"> <atomArray>...</atomArray> <cml id="s1"><atomArray >.....</ atomArray></cml> <cml id="s2"><atomArray >.....</ atomArray></cml> </molecule > </cml>
It is important that one needs to specify what the meaning of a particular atomArray is. Since I believe there is no restriction on the number of atomArrays per cml node (it is hard to get that information from the cmlCore/HTMLDOCS) one may have to associate a convention with an atomArray, as opposed to the cml node itself. (By the way, why does an atomArray not have an id attribute? This way we can not refer back to a particular atom in a particular atomArray in the particular molecule). One could use something like convention="vibration" to denote the interpretation of the xyz3 attribute as a vector for the vibration and a ref attribute to refer back to the atom CML element that this is a vibration for. This actually with a convention="force" could also allow for the specification of the force (or gradient) on an atom in a particular nuclear arrangement.
I am not sure what you mean with models here. Each molecule node could be considered to represent a molecule (but that is not even strictly necessary. CML is very flexible). I go with the assumption that with a model you mean a arrangement of atoms that are to dealt with as an ensemble (i.e., allow for multiple molecules that are together at one point in time, each atom with a unique index/id).The biggest problem is that I don't understand these models or what the hierarchy (if any) looks like.
Restricting ourselves to talking about vibrations for a minute ...
Q: Is there just one 'input' model?
Usually there is one nuclear arrangement for which a set of frequencies exists. Each frequency is basically an energy value which has vectors associated with it for each atom in the nuclear arrangement.
CML would allow for specifications of multiple 'input' models, each of which could have a set of vibrations associated with them.
Q: Is there just one 'refined/optimized' output model?I am not really sure what you mean with an output model. To me one just has a model. Internally each vibration for a particular input model could be considered a model in itself, but the nuclear coordinates of those are the same as the input model that one has the vibrations for.
Q: Are there N vibrational frequency models?One usually reports for non-linear molecules one has 3N-6, and for linear ones 3N-5 vibrations. The 5 and 6 refer to degrees of freedom of the molecule that have to do with translation and rotation (3 each for a non-linear one and 3 and 2, respectively, for a linear molecule).
The energies of the vibrations (usually expressed in units of cm-1) are positive if the molecule is at a minumum in energy for that vibration or imaginary (sometimes reported as negative values instead) if that vibration is at a maximum in the energy. (Basically the frequency is square-root of the second derivative of the energy to the particular nuclear coordinate [which is the vectors that represent the vibrations].
One caveat. Some programs (e.g., NWChem) do not take the dummy atoms out of the calculations of the frequencies and also does not take out the rotations and vibrations, for 6 atoms with 2 dummy atoms it will report 3x(6+2)-6 = 18 frequencies, while a program like Gaussian will report only the real atoms and no rotation/translate, i.e, 3x6-6 = 12 frequencies.
I think the take home message is, let the parsing of the file determine how many frequencies are encountered, and do not expect a certain number :-_
Q: Other that the resonant frequency name, what properties are interestingAs Peter replied (while I was writing this), symmetry labels can be things like A1g, B1, etc, (i.e, just short strings).
for each of these models?
Another interesting property is the IR intensity (as Gaussian calls it).
Partly back to Peter's reply.
Q: Are there other models that exist?
At each stage of a geometry optimization it may output something else that is of interest: the gradient of the energy (i.e., the dE/dx, dE/dy and dE/dz) which is related to the forces on the atom that exist in that specific nuclear arrangement.
Miguel
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