Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
It looks Avogadro2 will be using Chemical JSON whenever possible to transfer data. Do you think this would be possible with cclib? http://wiki.openchemistry.org/Chemical_JSON Right now, there aren't really specifications for computational data (MO, basis, etc.) in Chemical JSON. So CML would probably be fine, or some push to standardize these data representations in Chemical JSON. (I'd be happy to help with either of these.) -Geoff -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
Albert, I think CML will continue to be very much a first class citizen too. JSON feels much easier to change/augment, and Python support for JSON is very good - it would be great to add it, but I don't think it is critical. We could add some simple Python glue too, the format is super-simple. With Open Babel we ended up using CML, MDL and XYZ to get data into Avogadro 2. Marcus On Thu, Dec 18, 2014 at 9:59 AM, Defusco III, Albert A defu...@pitt.edu wrote: Hi Karol, It looks Avogadro2 will be using Chemical JSON whenever possible to transfer data. Do you think this would be possible with cclib? http://wiki.openchemistry.org/Chemical_JSON Albert -- Albert DeFusco, Ph.D. Research Assistant Professor Technical Director, Center for Simulation and Modeling University of Pittsburgh Pittsburgh, PA 15260 412-648-3094 http://www.pitt.edu/~defusco http://www.sam.pitt.edu On Dec 17, 2014, at 11:22 PM, Karol Langner karol.lang...@gmail.com wrote: One of the things I want to do soon is give cclib the ability to output CML. That would be an easy way to communicate between programs in a standard format. Karol On Fri, Dec 12, 2014 at 12:33 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: It sounds like you think of these things as exclusive, and I don't see why they should be. The current state of the code is https://github.com/OpenChemistry/avogadrolibs/tree/master/avogadro/quantumio That is, these things are *separate* from “regular” IO. Reading files and finding quantum data are currently in different parts of the code. Now, one may question whether “regular” and quantum IO *should* be separate. But I’m not talking about throwing away existing code - I believe Albert was saying that rather than adding X new implementations to avogadrolibs/avogadro/quantumio, it would be helpful to have an interface to cclib for parsing quantum data. is demonstrably much more efficient than going through Open Babel for regular input for example. We can certainly tweak defaults, so the I certainly wasn’t talking about changing the current pattern for regular IO, although I’d certainly suggest that the interface could merge “import” and “open” commands. In the case of CML or other formats that Avogadro directly handles, preference can go to the internal implementation, and other formats could be handled through Open Babel. I’d be happy to make that change. I thought the discussion was about Summer of Code projects, and certainly improving quantum IO would be great. (Adding features to read and visualize other “cube” formats would be nice too.) -Geoff -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
One of the things I want to do soon is give cclib the ability to output CML. That would be an easy way to communicate between programs in a standard format. Karol On Fri, Dec 12, 2014 at 12:33 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: It sounds like you think of these things as exclusive, and I don't see why they should be. The current state of the code is https://github.com/OpenChemistry/avogadrolibs/tree/master/avogadro/quantumio That is, these things are *separate* from “regular” IO. Reading files and finding quantum data are currently in different parts of the code. Now, one may question whether “regular” and quantum IO *should* be separate. But I’m not talking about throwing away existing code - I believe Albert was saying that rather than adding X new implementations to avogadrolibs/avogadro/quantumio, it would be helpful to have an interface to cclib for parsing quantum data. is demonstrably much more efficient than going through Open Babel for regular input for example. We can certainly tweak defaults, so the I certainly wasn’t talking about changing the current pattern for regular IO, although I’d certainly suggest that the interface could merge “import” and “open” commands. In the case of CML or other formats that Avogadro directly handles, preference can go to the internal implementation, and other formats could be handled through Open Babel. I’d be happy to make that change. I thought the discussion was about Summer of Code projects, and certainly improving quantum IO would be great. (Adding features to read and visualize other “cube” formats would be nice too.) -Geoff -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
On Thu, Dec 11, 2014 at 11:36 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I think Albert was talking about a glue layer for quantum io, not for regular input. Regular input is probably best handled through Open Babel, since that already handles bond perception, typing, etc. Right now, Avogadro v1 and v2 have separate code for reading basis set and MO information from various formats. Instead, such information (which is only performed when computing orbitals, etc) could be handled through a python call and cclib parsing. It sounds like you think of these things as exclusive, and I don't see why they should be. Maybe we just need to chat, and flesh out what is meant a little more. If what was done for Open Babel is considered a glue layer for regular input, then what I meant in my reply was that it sounded like a great idea and that we even have a template for such a layer. We could certainly expand what can be brought in by such a layer, but I have some motivation to keep some of the other IO work present as it is demonstrably much more efficient than going through Open Babel for regular input for example. We can certainly tweak defaults, so the richest approach would be offered automatically. Marcus -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
Hi guys, Would good project be to re-wire Avogadro to use cclib instead of relying on the quantumio in Avogadro2? I'm very much in favor of adding visualization capabilities for QuantumEspresso and CP2K. Albert -- Albert DeFusco, Ph.D. Research Assistant Professor Technical Director, Center for Simulation and Modeling University of Pittsburgh Pittsburgh, PA 15260 412-648-3094 http://www.pitt.edu/~defusco http://www.sam.pitt.edu On Dec 8, 2014, at 5:32 PM, avogadro-devel-requ...@lists.sourceforge.net wrote: Personally, I'd like to see more interoperability between the open-source chemistry apps, including avogadro, openbabel and cclib Indeed, I think one big push is for Avogadro v2 to use cclib to read QM file formats (e.g., MO coefficients, basis set, etc.) rather than implementing them all in C++. As for Open Babel and cclib, I think some of that is simply a matter of not repeating the wheel - i.e., leaving QM-specific data in cclib, but certainly a lot more is important here. I think these are good ideas. I?ll go create a wiki page somewhere to start storing some of them. -Geoff P.S. I don?t think it would be hard for Avogadro as a whole to get approved, since we?ve had 3 students working on Avogadro-related code in previous years. I do agree that an umbrella organization might be helpful. Albert DeFusco, Ph.D. Research Assistant Professor Technical Director, Center for Simulation and Modeling University of Pittsburgh Pittsburgh, PA 15260 412-648-3094 http://www.pitt.edu/~defusco http://www.sam.pitt.edu -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu wrote: Hi guys, Would good project be to re-wire Avogadro to use cclib instead of relying on the quantumio in Avogadro2? I'm very much in favor of adding visualization capabilities for QuantumEspresso and CP2K. You don't need to rewire, the Open Babel plugin reuses all of the readers/writers advertised. That pattern could be used to reuse the cclib readers/writers, offering the option of what reader to use if there is more than one. I think it would be great to add that capability. Marcus -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2
I think Albert was talking about a glue layer for quantum io, not for regular input. Regular input is probably best handled through Open Babel, since that already handles bond perception, typing, etc. Right now, Avogadro v1 and v2 have separate code for reading basis set and MO information from various formats. Instead, such information (which is only performed when computing orbitals, etc) could be handled through a python call and cclib parsing. I'm very much in favor of such an approach, since cclib handles a greater variety of quantum data *and* a greater variety of formats than Avogadro does presently (e.g., MO symmetries, energy scans). As far as CP2K, Quantum Espresso and the like, I think these would require some cclib support for periodic boundary conditions. I think there was also some push on the solid-state side to use XCrysDens format (http://www.xcrysden.org/doc/XSF.html http://www.xcrysden.org/doc/XSF.html) as something like Molden format in molecular chemistry. -Geoff On Thu, Dec 11, 2014 at 7:29 PM Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu mailto:defu...@pitt.edu wrote: Hi guys, Would good project be to re-wire Avogadro to use cclib instead of relying on the quantumio in Avogadro2? I'm very much in favor of adding visualization capabilities for QuantumEspresso and CP2K. You don't need to rewire, the Open Babel plugin reuses all of the readers/writers advertised. That pattern could be used to reuse the cclib readers/writers, offering the option of what reader to use if there is more than one. I think it would be great to add that capability. Marcus -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net mailto:Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
