Although it has been touched on previously in the mailing lists, I think we need to clarify what OBMol::_energy contains. It is accessed in OBMol::SetEnergy(double) and by OBMol::GetEnergy().
Note that OBMol::GetEnergy(int) is separate, and is concerned with relative of conformer energies. Its data is kept in OBConformerData. Can we agree that OBMol::_energy is the QM zero-point energy in kcal/mole? (I take this to be the energy released on assembling the molecule from elementary particles, but I may be wrong on this. However it is a large negative number.) This arose because in gaussformat it was also being used for something else (now commented out with Dave Lonie's agreement pending resolution). It is also accessed in: adfformat.cpp, cccformat.cpp, gamessformat.cpp, gulpformat.cpp, mopacformat.cpp, mol2format.cpp, pwscfformat.cpp, vaspformat.cpp, and (reading only) mmodformat.cpp, xyzformat.cpp, cmlformat.cpp Apart from the last (which I wrote), can those closer to these formats confirm that the proposal above would be consistent with them? The comment in the declaration (and the API documentation) for OBMol::GetEnergy()) is "return the heat of formation for this molecule (in kcal/mol)" I understand something different by heat of formation (thermodynamics, defined to be zero for elements). Is "QM zero-point energy" the right expression? Chris ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
