From owner-nwchem-users@emsl.pnl.gov Mon May 14 09:41:43 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l4EGfges003309 for ; Mon, 14 May 2007 09:41:43 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l4EGfghl003308 for nwchem-users-outgoing-0915; Mon, 14 May 2007 09:41:42 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: i="4.14,532,1170662400"; d="scan'208"; a="31559445:sNHT31636269" Message-ID: <46489141.4030007@pnl.gov> Date: Mon, 14 May 2007 09:41:37 -0700 From: Eric Bylaska User-Agent: Thunderbird 1.5.0.10 (Macintosh/20070221) MIME-Version: 1.0 To: Francesco Pietra CC: Support ECCE , users nwchem Subject: Re: [NWCHEM] Fwd: Vibrational frequencies References: <402610.66703.qm@web58905.mail.re1.yahoo.com> In-Reply-To: <402610.66703.qm@web58905.mail.re1.yahoo.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 14 May 2007 16:41:38.0273 (UTC) FILETIME=[BDFD7510:01C79646] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk The ZPE outputed in NWChem is more correct. The difference seen in the ZPE is probably due to the fact that ECCE is using a calculation in which the scaling constants were (sloppily) only specified to one decimal place. This isn't much of a difference for small molecules, but for larger ones it is... I'm pretty sure I fixed this problem sometime ago including in the ecce output, but somebody probably unfixed it. The old ZPE calculation is still outputed so that people could still compare to their previous calculations with older versions of NWChem. Eric Bylaska Francesco Pietra wrote: > I had to give more credit to the procedure. It has > ended 0, giving ZPE, ZPE correction to energy, and a > lot of other information from nwch.nwout. 54 atoms was > a great effort. > > During the procedure Ecce has lost full connection > with the code. In Viewer, all the part below Energy > disappeared, and there was nothing more in Server > about this computation. I did not notice anything > wrong with ssh, which still allowed slogin. On trying > to reconnect from the Organizer RunMgt it reported > "Error. Unable to spawn copy command ssh/shellcp" and > monitoring was not restored. However, Ecce was still > able to read the tail of nwch.nwout correctly. I > closed Ecce and the computer and restarted everything: > same affairs. > > Does Ecce help analyzing the results of a vibrational > analysis? If so, is it possible to have that now by > copying manually files from the code side? (I see > nwch.nwout ecce.out eccejobmonitor, among many > others). > > At the moment I do not understand the difference > reported between > > ZPE 284.66543896 kcal/mol > > and > > ZPE correction to energy 284.444 kcal/mol > > Thanks > francesco > > > > > --- Francesco Pietra wrote: > > >> Date: Sun, 13 May 2007 01:28:25 -0700 (PDT) >> From: Francesco Pietra >> Subject: Fwd: Vibrational frequencies >> To: users nwchem >> CC: Support ECCE >> >> I forgot to ask if there is a way to restart the >> frequency task mentioned below without loosing to >> much >> (should for any reason the computation should day). >> Thanks >> francesco >> >> --- Francesco Pietra wrote: >> >> >>> Date: Fri, 11 May 2007 23:49:05 -0700 (PDT) >>> From: Francesco Pietra >>> Subject: Vibrational frequencies >>> To: users nwchem >>> CC: Support ECCE >>> >>> I wonder whether I am carrying out correctly a >>> vibrational frequency procedure. >>> >>> I first carried out a DFT/Geometry on a closed >>> >> shell >> >>> 54-atoms molecule, using coordinates from the >>> minimum >>> strain-energy conformation from a global space MM >>> search. The procedure was launched from Ecce, just >>> to >>> be able to observe the geometry course on screen. >>> >> I >> >>> saved only the Ecce-imported files (ecce.out and >>> nwch.nwout), deleting all files for this >>> >> computation >> >>> on the nwchm code machine. >>> >>> Then, I started a vibrational frequency DFT >>> procedure >>> from Ecce (Duplicate for rerun from last >>> >> geometry), >> >>> just to get ZPE, changing the name of the >>> >> procedure, >> >>> at the same basis set level and same density >>> functional. The input looks like >>> >>> Start .... >>> >>> echo >>> >>> Memory 468 mw >>> >>> charge 0 >>> >>> geometry autosym units angstrom >>> ............................. >>> end >>> >>> ecce_print ........ ecce.out >>> >>> basis "ao basis" cartesian print >>> H library "6-31G*" >>> ......... >>> END >>> >>> dft >>> mult 1 >>> XC ... >>> iterations 80 >>> mulliken >>> end >>> >>> task dft energy >>> task dft freq >>> >>> >>> >>> I checked that the last geometry is really being >>> used. >>> Also, the energy procedure was rapidly executed >>> >> and >> >>> the value corresponded to the one previously >>> obtained >>> from DFT/Geometry. >>> >>> My question above is related to the length of the >>> subsequent stages, which are going on atom per >>> >> atom. >> >>> It has just concluded with heavy atoms and now it >>> >> is >> >>> doing the job hydrogen per hydrogen. I see that >>> .movecs and .movecs.hess are recorded on the code >>> machine, besides ecce.out and nwch.nwout. I wonder >>> whether I should have saved all the output files >>> from >>> the code for the previous DFT/Geometry procedure, >>> instead of only the Ecce-imported files: I did not >>> check if there were .movecs files that should have >>> been used, i.e. if restart should have been better >>> carried out directly from the machine where the >>> >> code >> >>> is installed. >>> >>> Thanks >>> francesco pietra >>> >>> >>> >>> >>> > ____________________________________________________________________________________Ready > >>> for the edge of your seat? >>> Check out tonight's top picks on Yahoo! TV. >>> http://tv.yahoo.com/ >>> >>> >> >> >> >> > ____________________________________________________________________________________ > >> TV dinner still cooling? >> Check out "Tonight's Picks" on Yahoo! 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