> In other words, is there a standard specification for > vibrations similar to the standardised formats PDB, > MOL, XYZ, etc for atoms, coords, bonds, ...
I don't think so.
CML addresses this by capturing the eigenvalues and eigenvectors of a compChem calculation. This is a 3N-6 array of values (related to the frequencies) and a (3N-6)*(3N-6) matrix of vibrations. N is no of atoms. (3N-5 for linear molecules). Sometimes the full 3N is output, the first 6 values being imaginary
John's question prompted me to write a short tech note regarding support for XYZ files in Jmol v10.
Jmol supports extended XYZ files which may contain formal charges and/or force vectors.
XYZ files also can contain multiple models. So one could have multiple vibrational frequencies stored in an XYZ file with vectors for each frequency.
XYZ files have a name line, followed by an atom count line, followed by atom records.
The atom records contain an element symbol followed by decimal/numeric fields. Fields are separate by one or more spaces/tabs.
The first three numeric fields represent the cartesian coordinates in angstroms.
{elementSymbol} x.coord y.coord z.coord
If there is one additional field (symbol + 4 numeric fields), it is assumed to be a formal charge.
{elementSymbol} x.coord y.coord z.coord f.charge
If there are three additional fields, (symbol + 6 numeric fields) then the three additional fields are assumed to be vectors
{elementSymbol} x.coord y.coord z.coord x.vect y.vect z.vect
If there are four additional fields (symbol + 7 numeric fields) then the 4 additional fields are assumed to be a formal charge followed by the vector values
{elementSymbol} x.coord y.coord z.coord f.charge x.vect y.vect z.vect
Is this documented anywhere. I suspect it to be rather fragile.
P.
Miguel
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