Re: [OpenBabel-Devel] Updates to the Gaussian reading for Thermochemistry
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. 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
Re: [OpenBabel-Devel] Updates to the Gaussian reading for Thermochemistry
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.sehttp://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
[OpenBabel-Devel] Updates to the Gaussian reading for Thermochemistry
Hi, I'm working on implementing the Gaussian Thermochemistry model into OB. For this one needs to extract three values from three different lines of the file, and post-process them. The simple route, which works fine, is to put these into OBPairData and extract the three values in in my external program. In order to get true heats of formation however, the sum of these numbers should be corrected for the atomic heats of formation. My program does this, but I think it would be great if OpenBabel could do this as well. There's a catch however, or rather, two. 1. In order to do this a database file has to be read (implemented in my program as a text file) holding the additional atomic heats of 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. 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. Comments? -- 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.sehttp://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
Re: [OpenBabel-Devel] Updates to the Gaussian reading for Thermochemistry
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. 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. So, in short, this sounds like a great addition. Thanks, -Geoff -- 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
Re: [OpenBabel-Devel] Updates to the Gaussian reading for Thermochemistry
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. So, in short, this sounds like a great addition. Thanks, -Geoff -- 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.sehttp://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
