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Re: [cclib-devel] Basis set handling improvements
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From: Benjamin S. <bs...@un...> - 2011-01-19 17:21:11
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Adam and Noel, Thanks for the great feedback! I'll poke around in avogadro (we'll see how rusty my C++ is...) and see how they store the data. I think it's critically important for the data to be accessible as possible; if the basis set is locked up in some gruesome data construct, it likely will never see the light of day. This is probably going to be one of the harder bits to do properly. As an aside, I had read something once about the idea of integrating cclib into avogadro (on avogadro's wiki?), but I don't know if anything ever became of that. Ben On Jan 19, 2011, at 5:05 AM, ccl...@li... wrote: > Send cclib-devel mailing list submissions to > ccl...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cclib-devel > or, via email, send a message with subject or body 'help' to > ccl...@li... > > You can reach the person managing the list at > ccl...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cclib-devel digest..." > > > Today's Topics: > > 1. Re: Basis set handling improvements (Noel O'Boyle) > 2. Re: Basis set handling improvements (Karol M. Langner) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Jan 2011 15:55:58 +0000 > From: "Noel O'Boyle" <bao...@gm...> > Subject: Re: [cclib-devel] Basis set handling improvements > To: Adam Tenderholt <ate...@gm...> > Cc: cclib-dev List <ccl...@li...> > Message-ID: > <AANLkTimAep3oTbnQajmkf5yjgC3_9R1ib2iW=12...@ma...> > Content-Type: text/plain; charset=ISO-8859-1 > > Sounds great. You might want to coordinate with Avogadro here, as they > already have code in the dev version (it's in C++ of course) to do > something similar. This would save you some work. Also you can see > what data structure they are using. > > - Noel > > On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> wrote: >> Hey Ben (and everyone else), >> >> It's great that you're thinking about undertaking such an interesting >> addition to cclib. It's definitely something that I wanted to get >> around to working on, but I've just been plenty busy with research and >> such. Anyhow, I have a couple of thoughts about your approach. >> >> You should try to put the basis sets in a format that makes it easy to >> eventually convert to the densities that may be of some interest. Can >> this be done with matrix operations in numpy? >> >> There's also the promise of OpenCL. This might not help in the >> short-term since I don't think that there are drivers that take >> advantage of GPUs (my laptop for instance can only work with the CPU), >> but it seems like a good long-term approach. One of my former >> colleagues has written a Mac application that renders orbitals from >> Gaussian calculations on the fly. I don't really know what his plans >> are for his program, but I don't think he plans on developing it >> commercially. If you're interested, I can see what he thinks and put >> you two in contact. >> >> Adam >> >> >> On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> wrote: >>> Hello, and I hope everyones holidays were nice and relaxing! >>> >>> I've been thinking about improving the basis set handling in cclib which, as I'm sure everyone knows, looks to be a bit of an undertaking. My eventual goal is to have the handling robust enough to provide methods to generate cube (or whichever format) files of orbitals, densities, etc. >>> >>> Personally, my motivation (aside from learning how basis sets are handled in various packages) is to play around with orbital transformations, and being able to plot them would be beyond useful. In addition, this would open up doors to possibly visualizing time-dependent results (such as density differences and transition densities). >>> >>> I'm attacking the problem using a bottom up sort of approach, by working out how to store the basis set information at the primitive gaussian (or slater, I'm trying to be agnostic) level. So far I've sketched out a few simple classes (bear with me, I'm new to this OO stuff). >>> >>> >>> Some thoughts: >>> >>> Have each atom possess a list of shells. Each shell is composed of primitive functions, each with a contraction coefficient and exponent. This part seems easy-ish; I think I've figured out the parsing of ORCA's basis set output. I haven't looked at Gaussian in a while, but I remember it being reasonable. As long as a package has an option to print out the basis set in some sort of sane format, we should be OK. >>> >>> A tricky bit is how to handle the 2l+1 m_l components of each shell. None of the packages I've looked at so far have documented the m_l ordering. We can always ask the developers if need be, and I think I've figured it out for ORCA by looking at the output. >>> >>> >>> I've attached some code I put together (I haven't tested any of it, just thinking out loud), but I'm not sure if attachments work on the mailing list. If not I'll just pop it up on dropbox or something. >>> >>> Best, >>> Ben >>> >>> >>> >>> Benjamin Stein >>> University of New Mexico >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Protect Your Site and Customers from Malware Attacks >>> Learn about various malware tactics and how to avoid them. Understand >>> malware threats, the impact they can have on your business, and how you >>> can protect your company and customers by using code signing. >>> http://p.sf.net/sfu/oracle-sfdevnl >>> _______________________________________________ >>> cclib-devel mailing list >>> ccl...@li... >>> https://lists.sourceforge.net/lists/listinfo/cclib-devel >>> >>> >> >> ------------------------------------------------------------------------------ >> Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how you >> can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> > > > > ------------------------------ > > Message: 2 > Date: Tue, 18 Jan 2011 22:04:16 +0100 > From: "Karol M. Langner" <kar...@gm...> > Subject: Re: [cclib-devel] Basis set handling improvements > To: ccl...@li... > Cc: Adam Tenderholt <ate...@gm...>, Noel O'Boyle > <bao...@gm...> > Message-ID: <201...@gm...> > Content-Type: text/plain; charset="iso-8859-1" > > I was just going to mention Avogadro, too. I think Marcus there is > separating part of the cube-generating code into a standalone library. > > On Tuesday 18 January 2011 16:55:58 Noel O'Boyle wrote: >> Sounds great. You might want to coordinate with Avogadro here, as >> they already have code in the dev version (it's in C++ of course) to >> do something similar. This would save you some work. Also you can >> see what data structure they are using. >> >> - Noel >> >> On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> > wrote: >>> Hey Ben (and everyone else), >>> >>> It's great that you're thinking about undertaking such an >>> interesting addition to cclib. It's definitely something that I >>> wanted to get around to working on, but I've just been plenty busy >>> with research and such. Anyhow, I have a couple of thoughts about >>> your approach. >>> >>> You should try to put the basis sets in a format that makes it >>> easy to eventually convert to the densities that may be of some >>> interest. Can this be done with matrix operations in numpy? >>> >>> There's also the promise of OpenCL. This might not help in the >>> short-term since I don't think that there are drivers that take >>> advantage of GPUs (my laptop for instance can only work with the >>> CPU), but it seems like a good long-term approach. One of my >>> former colleagues has written a Mac application that renders >>> orbitals from Gaussian calculations on the fly. I don't really >>> know what his plans are for his program, but I don't think he >>> plans on developing it commercially. If you're interested, I can >>> see what he thinks and put you two in contact. >>> >>> Adam >>> >>> On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> > wrote: >>>> Hello, and I hope everyones holidays were nice and relaxing! >>>> >>>> I've been thinking about improving the basis set handling in >>>> cclib which, as I'm sure everyone knows, looks to be a bit of an >>>> undertaking. My eventual goal is to have the handling robust >>>> enough to provide methods to generate cube (or whichever format) >>>> files of orbitals, densities, etc. >>>> >>>> Personally, my motivation (aside from learning how basis sets are >>>> handled in various packages) is to play around with orbital >>>> transformations, and being able to plot them would be beyond >>>> useful. In addition, this would open up doors to possibly >>>> visualizing time-dependent results (such as density differences >>>> and transition densities). >>>> >>>> I'm attacking the problem using a bottom up sort of approach, by >>>> working out how to store the basis set information at the >>>> primitive gaussian (or slater, I'm trying to be agnostic) level. >>>> So far I've sketched out a few simple classes (bear with me, I'm >>>> new to this OO stuff). >>>> >>>> >>>> Some thoughts: >>>> >>>> Have each atom possess a list of shells. Each shell is composed >>>> of primitive functions, each with a contraction coefficient and >>>> exponent. This part seems easy-ish; I think I've figured out the >>>> parsing of ORCA's basis set output. I haven't looked at Gaussian >>>> in a while, but I remember it being reasonable. As long as a >>>> package has an option to print out the basis set in some sort of >>>> sane format, we should be OK. >>>> >>>> A tricky bit is how to handle the 2l+1 m_l components of each >>>> shell. None of the packages I've looked at so far have documented >>>> the m_l ordering. We can always ask the developers if need be, >>>> and I think I've figured it out for ORCA by looking at the >>>> output. >>>> >>>> >>>> I've attached some code I put together (I haven't tested any of >>>> it, just thinking out loud), but I'm not sure if attachments work >>>> on the mailing list. If not I'll just pop it up on dropbox or >>>> something. >>>> >>>> Best, >>>> Ben > > -- > written by Karol Langner > Tue Jan 18 22:04:15 CET 2011 > > > > ------------------------------ > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > > ------------------------------ > > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > > > End of cclib-devel Digest, Vol 48, Issue 7 > ****************************************** Benjamin Stein University of New Mexico |
