From owner-nwchem-users@emsl.pnl.gov Mon May 14 12:56:17 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 l4EJuGr3016280 for ; Mon, 14 May 2007 12:56:17 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l4EJuGkl016279 for nwchem-users-outgoing-0915; Mon, 14 May 2007 12:56:16 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 4.7 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AgAAAGQ6SEZCxGT6k2dsb2JhbACPfwIBAQcIBgwf X-IronPort-AV: i="4.14,532,1170662400"; d="scan'208"; a="20159381:sNHT148931706" X-IronPort-AV: i="4.14,532,1170662400"; d="scan'208"; a="20159381:sNHT970219551" DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:Date:From:Subject:To:Cc:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; b=MRA2Ev47g9U1T62fn/LAudg5in0VcURYzIPxsC8KpfYHalKRrAjfPil6uByBgswegEaEzIdwWMllhB4uoZRngJuAZwwxNCnwyDePH8WD5gH+MytAoJR7+4U8ML6nbsxTxglfQ8fnJpLtvB8SBttKnPtYzXr7yVBc3hFN6Bxgnzo=; X-YMail-OSG: 9O9H_9AVM1m2tfX1us1T66zGb3EovDUDJlvhgX8_3A764PGIrszxLyzht6euBN3ifDNFy.EZY2lL._TiA_ZII9l.hBOUuZuSksf1 Date: Mon, 14 May 2007 10:36:27 -0700 (PDT) From: Francesco Pietra Subject: Re: [NWCHEM] Fwd: Vibrational frequencies To: Eric Bylaska Cc: Support ECCE , users nwchem In-Reply-To: <46489141.4030007@pnl.gov> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Message-ID: <102516.2387.qm@web58915.mail.re1.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Eric: Thanks. This is to make clear (if it was not from my previous emails) that the nwch.nwout was from the computer were the code is running. Ecce had lost the capability of collecting data and had no files more in the server directory Output related to this computation. Actually, Ecce does not like this nwch.nwout or ecce.out at all (see my replay to Bert a couple of hours ago. I wonder whether Bert or Gary, or anotheperson in the staff the staff, wants to see the outputs. Just because I am comparing small energy differences among conformers (actually diastereomers deriving from conformational inversion around a chirality axis). In the past days I have withdrawn the manuscript (not for the reasons discussed here, just because I was no more confident about my assumption that ZPE was the same for the different conformers). Thanks francesco --- Eric Bylaska wrote: > 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! 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