From owner-chemistry@ccl.net Tue Oct 7 07:14:00 2014 From: "berger : chem.helsinki.fi" To: CCL Subject: CCL: cif file -> full unit cell Message-Id: <-50560-141007012719-9458-JreSi3nAslcdyDEdyKto3A%%server.ccl.net> X-Original-From: berger-$-chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 7 Oct 2014 08:27:05 +0300 MIME-Version: 1.0 Sent to CCL by: berger|a|chem.helsinki.fi Dear Keith and all, thank you fo that suggestion, that is also a great one! I love it already for the name :) best regards Raphael > Sent to CCL by: Keith Refson [krefson[*]gmail.com] > Dear Rafael, > > Nobody has yet mentioned my preferred tool for this - "cif2cell". > > http://sourceforge.net/projects/cif2cell/ > > which is tect-based and will generate output in QE input file format > (and many others to boot). > > Keith Refson > > > On 04/10/14 07:05, berger[*]chem.helsinki.fi wrote: >> >> Sent to CCL by: berger:_:chem.helsinki.fi >> Dear all, >> >> thank you very much for the various very helpful recommendations! I was >> particularly happy with critic2 and mercury. The former allows text >> based >> i/o and has lots of more functionality. especially the suggestion hit by >> incident the very heart of the problem, which I didnt mention. I want to >> generate quantum espresso input. >> >> the other suggestion which was extremely helpful was mercury, it is gui >> based but I could solve the problem with that one within less than 5 >> minutes(including installation). >> >> thank you again all for all your suggestiones! >> Raphael >> >>> Sent to CCL by: "Close, David M." [CLOSED%a%mail.etsu.edu] >>> Prof. Berger: >>> This problem comes up from time to time. I wrote a program based on >>> old >>> crystallographic programs like ORTEP, and ORFEE that allows you to >>> generate as many unit cells as you need, based on the xyz coordinates >>> of >>> the atoms, and the symmetry of the unit cell. The program was >>> drawcrys, >>> and is on the CCL archive. The output can be viewed in GaussView, or >>> ChemCraft, etc. >>> If you don't have a compiled version, I could easily generate output >>> for >>> you if you have the specifications of the unit cell. >>> Regards, Dave Close. >>> >>> -----Original Message----- >>>> From: owner-chemistry+closed==etsu.edu:ccl.net >>>> [mailto:owner-chemistry+closed==etsu.edu:ccl.net] On Behalf Of >>>> berger%a%chem.helsinki.fi >>> Sent: Friday, October 03, 2014 7:44 AM >>> To: Close, David M. >>> Subject: CCL: cif file -> full unit cell >>> >>> >>> Sent to CCL by: berger%x%chem.helsinki.fi Der CCLers, >>> >>> I am searching for a tool (linux/text based prefered) which can read in >>> a >>> CIF file and generate to full unit cell contants from it >>> (prefenentially >>> in crystalographic coordinates). >>> >>> Thank you >>> R. >>> Bergerhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Oct 7 07:49:00 2014 From: "berger|chem.helsinki.fi" To: CCL Subject: CCL: cif file -> full unit cell Message-Id: <-50561-141007012725-9496-bndKMG2E+ks1f/jnrqHIRw-x-server.ccl.net> X-Original-From: berger_-_chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 7 Oct 2014 08:27:09 +0300 MIME-Version: 1.0 Sent to CCL by: berger]![chem.helsinki.fi Dear Keith and all, thank you fo that suggestion, that is also a great one! I love it already for the name :) best regards Raphael > Sent to CCL by: Keith Refson [krefson[*]gmail.com] > Dear Rafael, > > Nobody has yet mentioned my preferred tool for this - "cif2cell". > > http://sourceforge.net/projects/cif2cell/ > > which is tect-based and will generate output in QE input file format > (and many others to boot). > > Keith Refson > > > On 04/10/14 07:05, berger[*]chem.helsinki.fi wrote: >> >> Sent to CCL by: berger:_:chem.helsinki.fi >> Dear all, >> >> thank you very much for the various very helpful recommendations! I was >> particularly happy with critic2 and mercury. The former allows text >> based >> i/o and has lots of more functionality. especially the suggestion hit by >> incident the very heart of the problem, which I didnt mention. I want to >> generate quantum espresso input. >> >> the other suggestion which was extremely helpful was mercury, it is gui >> based but I could solve the problem with that one within less than 5 >> minutes(including installation). >> >> thank you again all for all your suggestiones! >> Raphael >> >>> Sent to CCL by: "Close, David M." [CLOSED%a%mail.etsu.edu] >>> Prof. Berger: >>> This problem comes up from time to time. I wrote a program based on >>> old >>> crystallographic programs like ORTEP, and ORFEE that allows you to >>> generate as many unit cells as you need, based on the xyz coordinates >>> of >>> the atoms, and the symmetry of the unit cell. The program was >>> drawcrys, >>> and is on the CCL archive. The output can be viewed in GaussView, or >>> ChemCraft, etc. >>> If you don't have a compiled version, I could easily generate output >>> for >>> you if you have the specifications of the unit cell. >>> Regards, Dave Close. >>> >>> -----Original Message----- >>>> From: owner-chemistry+closed==etsu.edu:ccl.net >>>> [mailto:owner-chemistry+closed==etsu.edu:ccl.net] On Behalf Of >>>> berger%a%chem.helsinki.fi >>> Sent: Friday, October 03, 2014 7:44 AM >>> To: Close, David M. >>> Subject: CCL: cif file -> full unit cell >>> >>> >>> Sent to CCL by: berger%x%chem.helsinki.fi Der CCLers, >>> >>> I am searching for a tool (linux/text based prefered) which can read in >>> a >>> CIF file and generate to full unit cell contants from it >>> (prefenentially >>> in crystalographic coordinates). >>> >>> Thank you >>> R. >>> Bergerhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Oct 7 08:24:00 2014 From: "Fedor Goumans goumans : scm.com" To: CCL Subject: CCL: Kinetic Modeling Software Message-Id: <-50562-141007040419-14759-uhQ/2i1PnZfP2RtelKC9Vw|a|server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Oct 2014 10:03:28 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans##scm.com] Dear Fred, You could try out POLYRATE and DL-FIND: POLYRATE uses Variational Transition State Theory, which can include tunneling corrections (SCT, LCT or mu-OMT): http://comp.chem.umn.edu/polyrate/ It is also interfaced to a few quantum chemistry codes for running it in 'direct dynamics' mode, using energies, forces and Hessians from those codes. DL-FIND can perform instanton (harmonic quantum transition state formulation using Feynman path integrals) calculations: http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/dlfind.html#instanton which can perform surprisingly well in the deep tunneling regime (where you are undoubtedly at at 2K). Again, DL-FIND is interfaced to many codes and can be hooked on to other codes of your liking as well. I'm sure there other codes out there for running path integral molecular dynamics, quantum instanton, quantum transition state theory, but DL-FIND you can download freely as L-GPL code and through simple registration you can obtain POLYRATE as well. Both are fairly well documented. Hope this helps, Fedor On 10/7/2014 12:41 AM, Fredrick M Mutunga fredrick.mutunga**gmail.com wrote: > Sent to CCL by: "Fredrick M Mutunga" [fredrick.mutunga-x-gmail.com] > Hello Guys, > > Could anyone suggest a suitable program/software which can calculate rate constants for low temperature reactions (temperature ~ 2.0K and pressure ~3.0 Torr)with tunneling corrections. > > > Thanks, > > Fred> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans^-^scm.com http://www.scm.com From owner-chemistry@ccl.net Tue Oct 7 08:59:00 2014 From: "Robin Shannon R.Shannon[a]leeds.ac.uk" To: CCL Subject: CCL: Kinetic Modeling Software Message-Id: <-50563-141007051645-17337-XlltoA4TJBwB7YDvzdVSWg:_:server.ccl.net> X-Original-From: Robin Shannon Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Oct 2014 10:16:36 +0100 MIME-Version: 1.0 Sent to CCL by: Robin Shannon [R.Shannon,,leeds.ac.uk] Hi Fred Assuming you are considering a bimolecular reaction, at such low temperatures even an extremely weak VdW complex (5 kJ mol-1 or less) will be key to the kinetic behavior. Such a complex a weak complex may be difficult to optimize using ab initio methods but there will undoubtedly be one and at 2 K even the weakest of complexes will have a significant lifetime and at 3 torr most systems will be close to capture controlled. Polyrate will do a very good job of each calculation step, capture step using variable reaction coordinate method, and unimolecular (tunneling step) using multi dimensional tunneling. However at such low temperatures, given the VdW complex considerations I have describe above, transition state theory is not really appropriate and a full master equation approach should be used. MESMER (http://www.chem.leeds.ac.uk/mesmer.html) could be used to treat the system and if you have very accurate data from Polyrate calculations, transition state sums of states and tunneling coefficients could be read in. There may be problems going quite as low as 2 K in MESMER though for most systems with a weak well, you could get down to 10 K or below. Best wishes Robin ________________________________________ > From: owner-chemistry+chmrsh==leeds.ac.uk::ccl.net [owner-chemistry+chmrsh==leeds.ac.uk::ccl.net] On Behalf Of Fredrick M Mutunga fredrick.mutunga**gmail.com [owner-chemistry::ccl.net] Sent: 06 October 2014 23:41 To: Shannon, Robin J Subject: CCL: Kinetic Modeling Software Sent to CCL by: "Fredrick M Mutunga" [fredrick.mutunga-x-gmail.com] Hello Guys, Could anyone suggest a suitable program/software which can calculate rate constants for low temperature reactions (temperature ~ 2.0K and pressure ~3.0 Torr)with tunneling corrections. Thanks, Fredhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Oct 7 09:34:01 2014 From: "Viswanath Pasumarthi v.pasumarthi|iitg.ac.in" To: CCL Subject: CCL:G: COSMO File generation using Gaussian 03 Message-Id: <-50564-141007085621-11757-x/DI9dy06er9F1Z7VOcGag],[server.ccl.net> X-Original-From: "Viswanath Pasumarthi" Date: Tue, 7 Oct 2014 08:56:20 -0400 Sent to CCL by: "Viswanath Pasumarthi" [v.pasumarthi/a\iitg.ac.in] Hi, Can you please provide/refer a tutorial giving necessary directions to generate COSMO-RS (.cosmo) file using Gaussian 03? I have been browsing internet for the same but unfortunately couldn't come across any helpful resource. Version: Gaussian 03 Revision C02 Platform: Windows 8.1 Processor: 64-bit Intel Xeon Quad Core -,-3.00 GHz RAM: 8 GB Thank you, Viswanath. From owner-chemistry@ccl.net Tue Oct 7 13:07:00 2014 From: "Andreas Klamt klamt]*[cosmologic.de" To: CCL Subject: CCL:G: COSMO File generation using Gaussian 03 Message-Id: <-50565-141007114148-21408-Ytgnc2ok7/q3WsmzsFq7Ug*|*server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 07 Oct 2014 17:41:42 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt*o*cosmologic.de] Hi Viswanath, as far as I know, you just have to specify the keyword COSMORS or COSMO-RS. This does the required setting for C-PCM calculation most close to our BP-TZVP/COSMO calculations in TURBOMOLE. But this keyword was deactivated in some revisions of Gaussian 03!!! Mike Frisch wanted to remove it for ever, but for what reason ever, it is active again in newer Gaussian versions. Andreas Am 07.10.2014 14:56, schrieb Viswanath Pasumarthi v.pasumarthi|iitg.ac.in: > Sent to CCL by: "Viswanath Pasumarthi" [v.pasumarthi/a\iitg.ac.in] > Hi, > > Can you please provide/refer a tutorial giving necessary directions to > generate COSMO-RS (.cosmo) file using Gaussian 03? I have been browsing > internet for the same but unfortunately couldn't come across any helpful > resource. > > Version: Gaussian 03 Revision C02 > Platform: Windows 8.1 > Processor: 64-bit Intel Xeon Quad Core ~ 3.00 GHz > RAM: 8 GB > > Thank you, > Viswanath.> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt|cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt