From owner-nwchem-users@emsl.pnl.gov Mon Dec 29 14:59:45 2008 Received: from odyssey.emsl.pnl.gov (localhost.pnl.gov [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id mBTMxiCY001786 for ; Mon, 29 Dec 2008 14:59:45 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id mBTMxiXm001785 for nwchem-users-outgoing-0IhS; Mon, 29 Dec 2008 14:59:44 -0800 (PST) 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: 4.4 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AskBAAPlWEnRVZK3kGdsb2JhbACMQ4ZzPgEBAQEJCQwHEQOpDFiEVy+FW4U0AQMBA4ZBgmU X-IronPort-AV: E=Sophos;i="4.36,297,1228118400"; d="scan'208";a="88471484" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:received:received:message-id:date:from:sender :to:subject:cc:in-reply-to:mime-version:content-type :content-transfer-encoding:content-disposition:references :x-google-sender-auth; bh=vxxnkPi+L3UVrJFPMrFZFdDANvYy2DrwNZZahmSEjyU=; b=kVKKrLzI0IGl2lEL+M1S4fb9gNi0qHjotXXPYWe3E/Ip8bX/oY+e0ckaEVvKzIBpAv vgntaAuZlO+cp7w4zd2+7Njnt8BV51OMFBtEee/SDdsaR0bhHk9MJMmroHWBS4UdnNI6 6YVelkbMzzsxUQ+WLU9mbfqwZSrjhjFif+lAU= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version :content-type:content-transfer-encoding:content-disposition :references:x-google-sender-auth; b=AJRy5eHe3NdpLjpEiVXeaJwcH+Ex2txk2EKyTHk0WLL9L99fMH9EkGN+jHeeYz6sMR 2RyCNkGl8/1AVHUmwaWUOtAly415pm9mFD2tNRkV1ee+6SrBrcVk7YWAH8h5tNF/qp08 uU2u77nKytYhl7OhVd1TlOTLiQXAU+FX0AkpE= Message-ID: Date: Mon, 29 Dec 2008 16:59:42 -0600 From: "Kin-Yiu WONG (Kiniu)" To: "Jeff Hammond" Subject: Re: [NWCHEM] nga_put_common:cannot locate region Cc: "Chang, Christopher" , nwchem-users@emsl.pnl.gov In-Reply-To: <96f4bb620812181800t58574b96mca5c09b4a078e244@mail.gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline References: <96f4bb620812181800t58574b96mca5c09b4a078e244@mail.gmail.com> X-Google-Sender-Auth: b6ba96f78038e058 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk I also got similar problems when I'm working on the interface between NWChem and CHARMM. If Mulliken analysis is not necessary for your calculations, you may simply suppress it in the "scf" section as follows: ***** SCF ... ... NoPrint "mulliken" ... ... End ***** Wishes, Kiniu -- Kin-Yiu WONG (Kiniu), PhD Post-Doctoral Research Associate Department of Chemistry The University of Minnesota at Twin Cities USA Primary Email: kiniu@umn.edu Permanent Email: kiniu@alumni.cuhk.net On Thu, Dec 18, 2008 at 8:00 PM, Jeff Hammond wrote: > You have two problems: > > 1. Mulliken analysis does not work for bq charges. > 2. The vectors file needs the full path specified. > > The job runs fine without bq charges when the vector path is given but > I gather bq is not compatible with Mulliken analysis. > > I have no solution but I assume there is an incompatibility having to > do with bq not being real atoms with a density matrix but being > counted as such in the geometry module. Hopefully someone else will > comment in more detail. > > If you add basis functions for the bq charges, the Mulliken analysis > works. Since the zeta->infinity limit of a Gaussian corresponds to a > delta function, perhaps you can get something useful by using a really > big exponent single zeta basis on the bq "atoms". > > Jeff > > On Thu, Dec 18, 2008 at 7:41 PM, Chang, Christopher > wrote: >> Hi, >> >> With the following input (this is a test job, hence the small basis): >> >> START H2 >> MEMORY total 2000 mb >> SCRATCH_DIR . >> >> title "H2 and point charges, ccpV8Z first s function" >> geometry >> symmetry c1 >> h -0.375 0.000 0.000 >> h 0.375 0.000 0.000 >> bq -1.000 0.500 0.000 charge -2.0 >> bq -1.000 -0.500 0.000 charge 3.0 >> bq 1.000 0.250 0.000 charge -1.0 >> end >> >> basis spherical >> h s >> 13940.8000000 0.00000301 >> 3471.4300000 0.00000544 >> 1903.1800000 0.00001785 >> 623.2860000 0.00007195 >> 290.3600000 0.00012055 >> 126.5850000 0.00052527 >> 44.6955000 0.00201384 >> 16.0038000 0.00687086 >> end >> scf >> vectors output firsts.movecs >> end >> dplot >> gaussian >> title "H2 cc-pV8Z first s function" >> spin total >> vectors firsts.movecs >> limitxyz >> -2.000 2.000 40 >> -1.000 1.000 20 >> -0.500 0.500 10 >> output first_s.cube >> end >> task scf >> task dplot >> ---- >> >> running on a single dual-(single core)die AMD64 node initiated with >> >> mpirun nwchem temp.nwchem >& $PBS_O_WORKDIR/temp.log >> >> I get the following during the post-SCF Mulliken analysis: >> >> ... >> >> Mulliken analysis of the total density >> -------------------------------------- >> 0:0:nga_put_common:cannot locate region: [3:3 ,3:3 ]:: -992 >> 0:0:nga_put_common:cannot locate region: [3:3 ,3:3 ]:: -992 >> Last System Error Message from Task 0:: Inappropriate ioctl for device >> [node083:30698] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD >> with errorcode -992 >> 1:1:nga_put_common:cannot locate region: [4:4 ,4:4 ]:: -992 >> 1:1:nga_put_common:cannot locate region: [4:4 ,4:4 ]:: -992 >> Last System Error Message from Task 1:: No such file or directory >> [node083:30699] MPI_ABORT invoked on rank 1 in communicator MPI_COMM_WORLD >> with errorcode -992 >> >> If I run on only 1 of the 2 chips in the node: >> >> Mulliken analysis of the total density >> -------------------------------------- >> 0:0:nga_put_common:cannot locate region: [3:3 ,3:3 ]:: -992 >> 0:0:nga_put_common:cannot locate region: [3:3 ,3:3 ]:: -992 >> Last System Error Message from Task 0:: Inappropriate ioctl for device >> [node065:04413] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD >> with errorcode -992 >> >> What might be happening here? >> >> Thanks; Chris >> >> > > > > -- > Jeff Hammond > The University of Chicago > http://home.uchicago.edu/~jhammond/ >