On 2012-11-06 11:57, Chris Morley wrote: > On 05/11/2012 20:53, David van der Spoel wrote: >> On 2012-11-05 21:30, Geoff Hutchison wrote: >>>> formation. While the coding is available and straightforward, I don't >>>> know whether the OB policy allows one to read an additional file in >>>> order to get these numbers. >>> >>> These are done through the various "table" classes. See src/data.cpp for >>> examples (i.e., periodic table in OBElementTable). >>> >>> I can't remember -- aren't these basis set and functional-dependent? I >>> think there's a similar problem for computed NMR shifts. >>> >> Yes they are, and I have a small table for the different methods >> implemented in Gaussian, G2,G3,G4,CBS-QB3 for the most common atoms. One >> needs experimental corrections too (sic!). >> >> Ok, I'll dig into the data.cpp. It seems that the data files in /data >> are pretty much in any format... In that case I guess I can just drop >> mine in their as well. >> >>>> 2. If OB in this manner can produce the TRUE heat of formation, it may >>>> cause confusion, because the energy types which are reported based on >>>> Gaussian files now are also called heats of formation - but they are not. >>> >>> I don't think anyone really uses the Gaussian energies. But I don't think >>> this is an insurmountable problem. > > I know that Chris Morley, among others, would be very happy to get > absolute heats of formation. > > Another program I am involved in (Mesmer) does this conversion, but I > think it would be a generally useful addition to OB. The corrections > sound interesting, and might help in making the black art of getting > reliable numbers from comp chem a bit more transparent to non-experts > like me. Does this need a more systematic way of recording the basis > set/method information? When the numbers are used elsewhere this > metadata really should accompany them.
There are series of paper about these methods. They are in principle algorithms where the optimization is done in steps automatically, and finally a single point at high level of theory is done (CCSD(T) for G4). We have stored those corrections for the most common methods and atoms in a text file, and also the experimental data. What will be obtained is the heat of formation at 0K and 298.15K. This will only work for particular methods and for any old QM method. We should probably have a warning when people try to extract energies from a single Gaussian file, since only differences are meaningful really. The methods are described here: http://www.gaussian.com/g_whitepap/thermo.htm > > Chris > > ------------------------------------------------------------------------------ > LogMeIn Central: Instant, anywhere, Remote PC access and management. > Stay in control, update software, and manage PCs from one command center > Diagnose problems and improve visibility into emerging IT issues > Automate, monitor and manage. Do more in less time with Central > http://p.sf.net/sfu/logmein12331_d2d > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
