From owner-chemistry@ccl.net Mon Nov 23 03:49:01 2009 From: "Ulrike Salzner salzner%x%gmail.com" To: CCL Subject: CCL:G: ground states of open-shell atoms Message-Id: <-40759-091123034005-29219-xjgjFhMcfDCqeif7H39hEg-*-server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=00151773e6ba9cdbd0047904e014 Date: Mon, 23 Nov 2009 09:36:01 +0200 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner**gmail.com] --00151773e6ba9cdbd0047904e014 Content-Type: text/plain; charset=ISO-8859-1 Dear Collegues, a couple days ago, I had a discussion with a theoretical physicist about natural occupation numbers in atoms. He is investigating systems with up to ten spin orbitals and checking all inequalities that should hold. He also showed me results from "SDPA-GMP" calculations for the triplet P1 and triplet P0 terms of carbon. The natural orbital occupations for the former were 0.9999997, 0.9999994, 0.9763837, 0.9763834,0.674538 (three times), and 0.007872 (three times). To me this seems perfectly reasonable, if the first two spin orbitals are the alpha and beta 1s electrons, the next two are 2s electrons, and the two p-electrons are evenly distributed among the three p-orbitals, considering the 15 microstates that can be formed for two p-electrons in three orbitals for C. For the first excited state of beryllium, the single p-electron was not distributed over the three p-orbitals but resided in one of them. This seems strange to me.The physicist said that distributing the electron evenly over three degenerate orbitals will violate the inequalities, which must hold and he asked me what a standard quantum chemical code would produce. So I tried CASSCF on carbon with Gaussian03 with (4,4) and (6,9) active spaces. In both cases, I got two singly occupied and one empty p-orbital. I did not expect this and now I am at a loss. What is correct? How do I make a proper calculations of open-shell atoms. When I search the internet, I find only references to HF calculations. I am sure there must be extensive literature on this. I would be very grateful for a good reference to learn about such calculations. Thanks, Ulrike Salzner -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --00151773e6ba9cdbd0047904e014 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Collegues,
a couple days ago, I had a discussion with a theoretical physicist about natural occupation numbers in atoms. He is investigating systems with up to ten spin orbitals and checking all inequalities that should hold. He also showed me results from "SDPA-GMP" calculations for the triplet P1 and triplet P0 terms of carbon. The natural orbital occupations for the former were 0.9999997, 0.9999994, 0.9763837, 0.9763834,= 0.674538 (three times), and 0.007872 (three times). To me this seems perfectly reasonable, if the first two spin orbitals are the alpha and beta 1s electrons, the next two are 2s electrons, and the two p-electrons are evenly distributed among the three p-orbitals, considering the 15 microstates that can be formed for two p-electrons in three orbitals for C.= For the first excited state of beryllium, the single p-electron was not distributed over the three p-orbitals but resided in one of them. This seems strange to me.The physicist said that distributing the electron evenl= y over three degenerate=A0 orbitals will violate the inequalities, which must hold and he asked me what a standard quantum chemical code would produce. So I tried CASSCF on carbon w= ith Gaussian03 with (4,4) and (6,9) active spaces. In both cases, I got two singly occupied and one empty p-orbital. I did not expect this and now I am at a loss. What is correct? How do I make a proper calculations of open-shell atoms. When I search the internet, I find only references to HF calculations. I am sure there must be extensive liter= ature on this. I would be very grateful for a good reference to learn about such calculations.
Thanks,
Ulrike Salzner

--
Assoc. Prof. Ulrike S= alzner
Department of Chemistry
Bilkent University
06800 Bilkent, A= nkara
--00151773e6ba9cdbd0047904e014-- From owner-chemistry@ccl.net Mon Nov 23 04:49:00 2009 From: "Herbert Fruchtl herbert.fruchtl::st-andrews.ac.uk" To: CCL Subject: CCL: Which program to optimize the crystal structure of transition metal complex? Message-Id: <-40760-091123044348-24112-R5yhVjSN3QD3cGxMFS2cAA_+_server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Nov 2009 09:42:50 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl#%#st-andrews.ac.uk] They use MgO because a simple example is just as good, if not better, for demonstrating how it works, and can be reproduced without using a lot of computer time. I have done 50 atoms in a unit cell on a few cluster nodes with CASTEP. Other plane wave codes (including several free ones) are very similar in performance. If you want to go to large numbers of atoms and have some sparsity (e.g. protein crystals), have a look at SIESTA (or DMOL3 if you have too much money). HTH, Herbert Jose Alberto Fernandes jafernandes{}ua.pt wrote: > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes:-:ua.pt] > Hello all > > This subject is also interesting to me. Every possible program I find presents MgO as an example, and this seems to me a limitation of those programs (little asymetrical units). I want to do calculations with 50 atoms in the asymetrical unit, at DFT level. Do those programs work with that? > > Best regards > > > Jose Fernandes > > > > > > > >> "irfan ahmad irfaahmad|*|gmail.com" wrote: >> >> Sent to CCL by: irfan ahmad [irfaahmad,+,gmail.com] >> >> --0016e64f44f0cdce760478e520e5 >> Content-Type: text/plain; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> >> You can try material studio. I hope it can help you >> >> On 11/21/09, Mariusz Radon mariusz.radon[]gmail.com > t> >> wrote: >>> >>> Sent to CCL by: Mariusz Radon [mariusz.radon^gmail.com] >>>> My propositions are Turbomole and Orca (...) >>> What I am looking for is a program being able to optimize the *crystal >>> structure* (solid state), not only a single molecule in vacuo (I know >>> that Turbomole and Orca master in it...). In the other words: I would >>> like to optimize the molecules in the crystal and the parameters of >>> the unit cell, simultaneously. I don't think these features are really >>> implemented in Turbomole or Orca (or maybe I am wrong?) >>> >>> My question is still open for your suggestions! >>> >>> Best regards, >>> Mariusz Radon >>> >>> >>> >>> On Sat, Nov 21, 2009 at 9:27 AM, Adam Kubas adam.kubas]*[kit.edu >>> wrote: >>>> Sent to CCL by: Adam Kubas [adam.kubas^kit.edu] >>>> Dear Mariusz, >>>> >>>> My propositions are Turbomole and Orca - first is the fastest DFT code >>>> I've ever seen with wide range of options to control spin state of >>>> optimized compound but you have to buy it (free demo is available). >>>> The second program is a free package and is easily to use. >>>> >>>> 2009/11/20 Mariusz Radon mariusz.radon(0)gmail.com >> ccl.net>: >>>>> Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com] >>>>> Dear Colleagues, >>>>> >>>>> I am looking for a program being able to optimize the crystal >>>>> structure of transition metal complex (molecular structure and unit >>>>> cell parameters) at DFT level. An important point is that I must be >>>>> able to control the spin state of the complex, because I would like to >>>>> perform such optimizations for different spin states in order to >>>>> capture the influence of the spin state on the molecular structure and >>>>> packing in the crystal. >>>>> >>>>> Could you recommend me any program capable to achieve this goal >>>>> (preferably, but not necessarily free software)? Thank you in advance >>>>> very much. >>>>> >>>>> Best regards, >>>>> Mariusz Radon >>>> >>>> -- >>>> Adam Kubas >>>> Karlsruher Institut f=FCr Technologie (KIT) >>>> Institut f=FCr Physikalische Chemie >>>> Abteilung f=FCr Theoretische Chemie >>>> Geb. 30.45, Kaiserstra=DFe 12, D-76131 Karlsruhe >>>> http://www.ipc.uni-karlsruhe.de/theochem/ >>>> ---------------------------------------------------------------------- >>>> Office: >>>> Institut f=FCr Nanotechnologie >>>> Raum: 640/0-333 >>>> Hermann-von-Helmholtz-Platz 1 >>>> 76344 Eggenstein-Leopoldshafen >>>> Tel.: +49 7247 82-8834 >>>> http://www.int.kit.edu >>>> >>>> KIT - Universit=E4t des Landes Baden-W=FCrttemberg und >>>> nationales Gro=DFforschungszentrum in der Helmholtz-Gemeinschaft >>>> >>>> >>>> >>>> - This is automatically added to each message by the mailing script >>> -> >>>> >>> >>> >>> -- >>> Mariusz Radon, PhD student >>> Department of Theoretical Chemistry >>> Jagiellonian University >>> http://www.chemia.uj.edu.pl/~mradon >>> mradon /at/ chemia.uj.edu.pl >>> (PGP public key available on the website) >>> >>> >>> >>> - This is automatically added to each message by the mailing script -> >>> >>> >> >> --=20 >> AHMAD IRFAN >> PhD Scholar >> Northeast Normal University >> Changchun, Jilin Province >> P.R. China >> 13596043265 >> >> --0016e64f44f0cdce760478e520e5 >> Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> >> You can try material studio. I hope it can help you

>>
On 11/21/09, >> Mariusz Radon mariusz.radon[]gmail.com>> <owner-chemistry_+_ccl.net>> > wrote: >>
> px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
Sent to CCL by: Mariusz Rado= >> n [mariusz.radon^gmail.com]
> My pro= >> positions are Turbomole and Orca (...)
>>
What I am looking for is a program being able to optimize the *crystal<= >> br>structure* (solid state), not only a single molecule in vacuo (I know>> that Turbomole and Orca master in it...).=A0=A0In the other words: I would= >>
>> like to optimize the molecules in the crystal and the parameters of
the = >> unit cell, simultaneously. I don't think these features are really
i= >> mplemented in Turbomole or Orca (or maybe I am wrong?)

My question i= >> s still open for your suggestions!
>>
Best regards,
Mariusz Radon



On Sat, Nov 21, 2009 at 9= >> :27 AM, Adam Kubas adam.kubas]*[kit.edu
&= >> lt;owner-chemistry . ccl.net> wrote:
&= >> gt;
>> > Sent to CCL by: Adam Kubas [adam.kubas^kit.= >> edu]
> Dear Mariusz,
>
> My propositions are Turbomol= >> e and Orca - first is the fastest DFT code
> I've ever seen with = >> wide range of options to control spin state of
>> > optimized compound but you have to buy it (free demo is available).>> > The second program is a free package and is easily to use.
>>> > 2009/11/20 Mariusz Radon mariusz.radon(0)>> gmail.com <owner-chemistry,,ccl.net&= >> gt;:
>> >>
>> Sent to CCL by: Mariusz Radon [mariusz.radon]-[> =3D"http://gmail.com">gmail.com]
>> Dear Colleagues,
>&g= >> t;
>> I am looking for a program being able to optimize the crysta= >> l
>> >> structure of transition metal complex (molecular structure and uni= >> t
>> cell parameters) at DFT level. An important point is that I m= >> ust be
>> able to control the spin state of the complex, because I= >> would like to
>> >> perform such optimizations for different spin states in order to> r>>> capture the influence of the spin state on the molecular structu= >> re and
>> packing in the crystal.
>>
>> Could yo= >> u recommend me any program capable to achieve this goal
>> >> (preferably, but not necessarily free software)? Thank you in adva= >> nce
>> very much.
>>
>> Best regards,
>>= >> ; Mariusz Radon
>
>
> --
> Adam Kubas
> Karls= >> ruher Institut f=FCr Technologie (KIT)
>> > Institut f=FCr Physikalische Chemie
> Abteilung f=FCr Theoretisc= >> he Chemie
> Geb. 30.45, Kaiserstra=DFe 12, D-76131 Karlsruhe
> = >> http://www.ipc.uni-ka= >> rlsruhe.de/theochem/
>> > ----------------------------------------------------------------------= >>
> Office:
> Institut f=FCr Nanotechnologie
> Raum: 640/0= >> -333
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopold= >> shafen
>> > Tel.: +49 7247 82-8834
> http= >> ://www.int.kit.edu
>
> KIT - Universit=E4t des Landes Baden= >> -W=FCrttemberg und
> nationales Gro=DFforschungszentrum in der Helmho= >> ltz-Gemeinschaft
>> >
>
>
> - This is automatically added to each message = >> by the mailing script ->=A0=A0=A0=A0=A0=A0> cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= >> ge>=A0=A0=A0=A0=A0=A0> ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message>=A0=A0= >> =A0=A0=A0=A0http:/= >> /www.ccl.net/chemistry/sub_unsub.shtml>=A0=A0=A0=A0=A0=A0http://www.ccl.net/spammers.txt>> >
>



--
Mariusz Radon, PhD student
Department = >> of Theoretical Chemistry
Jagiellonian University
> w.chemia.uj.edu.pl/~mradon">http://www.chemia.uj.edu.pl/~mradon
mrad= >> on /at/ chemia.uj.edu.pl
>> (PGP public key available on the website)



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> ote>



--
AHMAD IRFAN
PhD Scholar
No= >> rtheast Normal University
>> Changchun, Jilin Province
P.R. China
13596043265=20 >> >> --0016e64f44f0cdce760478e520e5--> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Mon Nov 23 05:23:01 2009 From: "Jacco van de Streek vandestreek!^!avmatsim.de" To: CCL Subject: CCL: Which program to optimize the crystal structure of transition metal complex? Message-Id: <-40761-091123051801-25428-I8dEooJQW3EUaemJ9cfTrQ() server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Nov 2009 10:37:58 +0100 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek(!)avmatsim.de] Jose Alberto Fernandes jafernandes{}ua.pt wrote: > This subject is also interesting to me. Every possible program I find > presents MgO as an example, and this seems to me a limitation of > those programs (little asymetrical units). I want to do calculations > with 50 atoms in the asymetrical unit, at DFT level. Do those > programs work with that? We have been using VASP for years and it is able to optimise unit cells with volumes of 10,000 A^3, probably even 12,000 A^3 and perhaps higher. We regularly optimise crystal structures (organics only) with more than 100 atoms in the asymmetric unit (but that includes the hydrogens). The minimisation is not necessarily straightforward, requires decent hardware and may take several weeks for a single structure even on 32 cores, but VASP is capable of minimising such structures. Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Mon Nov 23 06:09:01 2009 From: "Frank Neese neese,,thch.uni-bonn.de" To: CCL Subject: CCL:G: ground states of open-shell atoms Message-Id: <-40762-091123060053-9383-AwYmHlWwywaDr900rWo5Hw|-|server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 23 Nov 2009 11:03:14 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese/./thch.uni-bonn.de] Dear Ulrike, in order to maintain the space and spin symmetry of the atom and calculate correct Russel Saunders multiplets you must average the CASSCF over the degenerate spatial components. For example, you need three roots of triplet multiplicity to describe the 3P state of the carbon atom correctly. If you only include one component of the 3P state or use a single reference method, the variational procedure will break the symmetry. For example, with the ORCA program the input ! tzvp tightscf conv %casscf nel 2 norb 3 nroots 3 orbstep diis end * xyz 0 3 C 0 0 0 * yields at the one-electron level: Orbital Occ. Energy(Eh) Energy(eV): 0: 2.000000 -11.325276 -308.1764 1: 2.000000 -0.705314 -19.1926 2: 0.666667 -0.057851 -1.5742 3: 0.666667 -0.057851 -1.5742 4: 0.666667 -0.057851 -1.5742 and at the many electron level: ROOT 0: E= -37.6874747895 Eh 0.94074 [ 2]: 011 0.05926 [ 1]: 101 ROOT 1: E= -37.6874747895 Eh 0.000 eV 0.0 cm**-1 1.00000 [ 0]: 110 ROOT 2: E= -37.6874747895 Eh 0.000 eV 0.0 cm**-1 0.94074 [ 1]: 101 0.05926 [ 2]: 011 So, things are happy; the three p-orbtials are on average all equally populated and the three components of the 3P state are degenerate. Of course, if one does a MRCI on top of this reference space one also obtains states that properly reflect the space and spin symmetry of the Born-Oppenheimer Hamiltonian. Best regards, Frank > Dear Collegues, > a couple days ago, I had a discussion with a theoretical physicist > about natural occupation numbers in atoms. He is investigating systems > with up to ten spin orbitals and checking all inequalities that should > hold. He also showed me results from "SDPA-GMP" calculations for the > triplet P1 and triplet P0 terms of carbon. The natural orbital > occupations for the former were 0.9999997, 0.9999994, 0.9763837, > 0.9763834,0.674538 (three times), and 0.007872 (three times). To me > this seems perfectly reasonable, if the first two spin orbitals are > the alpha and beta 1s electrons, the next two are 2s electrons, and > the two p-electrons are evenly distributed among the three p-orbitals, > considering the 15 microstates that can be formed for two p-electrons > in three orbitals for C. For the first excited state of beryllium, the > single p-electron was not distributed over the three p-orbitals but > resided in one of them. This seems strange to me.The physicist said > that distributing the electron evenly over three degenerate orbitals > will violate the inequalities, which must hold and he asked me what a > standard quantum chemical code would produce. So I tried CASSCF on > carbon with Gaussian03 with (4,4) and (6,9) active spaces. In both > cases, I got two singly occupied and one empty p-orbital. I did not > expect this and now I am at a loss. What is correct? How do I make a > proper calculations of open-shell atoms. When I search the internet, I > find only references to HF calculations. I am sure there must be > extensive literature on this. I would be very grateful for a good > reference to learn about such calculations. > Thanks, > Ulrike Salzner > > -- > Assoc. Prof. Ulrike Salzner > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara -- ----------------------------------------------------------------- Prof. Dr. Frank Neese Chair of Theoretical Chemistry Department of Chemistry University of Bonn Wegelerstr. 12 D-53115 Bonn Germany E-Mail: neese(!)thch.uni-bonn.de URL: http://www.thch.uni-bonn.de/tc/ Telephone: +49-228-732351 ----------------------------------------------------------------- From owner-chemistry@ccl.net Mon Nov 23 06:43:01 2009 From: "Dave.Winkler/./csiro.au" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40763-091123061959-25470-GNMRUcyRUaIRAk0WnAy9kw**server.ccl.net> X-Original-From: Content-Language: en-AU Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="Windows-1252" Date: Mon, 23 Nov 2009 21:38:23 +1100 MIME-Version: 1.0 Sent to CCL by: [Dave.Winkler[]csiro.au] You may also want to try some new methods based on modern mathematical algo= rithms developed specifically for grossly underdetermined systems that you = describe, and that are not difficult to implement. See=20 =95 Optimum QSAR Feature Selection using Sparse Bayesian Methods, Burden, = FR, Winkler DA, QSAR Comb Sci. 28, 645-653, (2009). =95 An optimal self-pruning neural network that performs nonlinear descrip= tor selection for QSAR, Frank R. Burden, David A. Winkler, QSAR Comb. Sci. = 28, 1092 =96 1097 (2009). Prof. Dave Winkler Senior Principal Research Scientist Biomaterials & Regenerative Medicine CSIRO Molecular & Health Technologies Clayton 3168, Australia ________________________________________ > From: owner-chemistry+dave.winkler=3D=3Dcsiro.au###ccl.net [owner-chemistry+d= ave.winkler=3D=3Dcsiro.au###ccl.net] On Behalf Of Yvonne Martin yvonnecmartin= _._gmail.com [owner-chemistry###ccl.net] Sent: Sunday, 22 November 2009 2:54 AM To: Winkler, Dave (CMHT, Clayton) Subject: CCL: PLS implementation? Joe, Try the SAMPLS program from QCPE. Yvonne Martin On Wed, Nov 18, 2009 at 6:01 PM, Joe Leonard jleonard42-$-gmail.com > wr= ote: Sent to CCL by: Joe Leonard [jleonard42|gmail.com] Folks, I would appreciate any pointers to PLS implementations that can hand= le much larger number of X variables as compared to Y (to-be-fit) variables= . I recall that PLS was used in 3D QSAR applications because of its stabil= ity in such cases, but it seems that individual implementations differ in h= ow this statement applies to them... 3D QSAR test sets w/ aligned compounds would also be of use - if people are= aware of such collections on-line. But the PLS engine(s) are my primary s= earch right now... Thanks in advance! Joe Leonard jleonard42]=3D[gmail.com -- I have fought a good fight, I have finished my course, I have kept the faith. EFL/11-6-09 -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY-#-ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/an= nouncements/conferences/http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Nov 23 09:04:01 2009 From: "Peter Khlyabich khlyabic|*|usc.edu" To: CCL Subject: CCL:G: PBC SCF information not saved Message-Id: <-40764-091122191556-12006-xwMcvbc3ko8VbWvc/WvZtQ++server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Sun, 22 Nov 2009 19:15:52 -0500 Sent to CCL by: "Peter Khlyabich" [khlyabic],[usc.edu] Hello, I'm trying to run TDDFT calculations on the optimized PBC calculations. My first step is PBC optimization and them TDDFT of the optimized structures. I'm trying to get excitation energies. My input file: %chk=/tmp/hjgfkhfhfklh7.chk %mem=800MW %NProcShared=8 %LindaWorkers=hpc2608 #T PBC-B3LYP/6-31G(d) PBC=(NCellMax=25) SCF=(Maxcyc=1000) 2 unit with hydrogens in cis and in iso 0 1 C -1.259203 5.172201 -0.015115 C -0.951911 4.703715 -1.344581 C -0.787520 6.288771 0.647209 H 5.143528 -0.508959 -11.908372 H 3.613244 -1.398020 -11.905393 S 0.222710 3.605109 -6.352413 H 1.639559 6.536553 -4.752515 H 2.367975 6.373882 -7.262330 Tv 5.079725 0.232684 -0.051935 --Link1-- %chk=/tmp/hjgfkhfhfklh7.chk %mem=800MW %NProcShared=8 %LindaWorkers=hpc2608 #T TD-B3LYP/6-31G(d) Geom=Check Guess=Read 2 unit with hydrogens in cis and in iso 0 1 The first step runs without problems and I can get optimized structures. But when I start TDDFF calculations I get this error message: SCF Done: E(RB+HF-LYP) = -5852.66267368 A.U. after 12 cycles Convg = 0.1818D-07 -V/T = 2.0064 S**2 = 0.0000 NROrb= 1184 NOA= 196 NOB= 196 NVA= 988 NVB= 988 PBC SCF information not saved. Error termination via Lnk1e in /usr/usc/gaussian/g03-E01/g03/l801.exe at Sun Nov 22 15:30:11 2009. Job cpu time: 0 days 0 hours 24 minutes 9.6 seconds. File lengths (MBytes): RWF= 17476 Int= 0 D2E= 0 Chk= 319 Scr= 1 How can I overcome this problem? I appreciate any help From owner-chemistry@ccl.net Mon Nov 23 09:39:01 2009 From: "Peter Khlyabich khlyabic:+:usc.edu" To: CCL Subject: CCL: CIS calculations Message-Id: <-40765-091122220858-28806-eKs0HrPPeKh2L1eJ1ZBKBA%x%server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Sun, 22 Nov 2009 22:08:54 -0500 Sent to CCL by: "Peter Khlyabich" [khlyabic:+:usc.edu] Hello, I'm trying to run CIS calculations. I'm getting the same mistake every time: My input file: %chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk %mem=800MW %NProcShared=1 %LindaWorkers=hpc2710 #T CIS/6-31G(d) Opt 1 units with hydrogens in cis and in iso 0 1 C -1.840437 0.706171 -0.354132 C -3.201699 0.281759 -0.135866 C -1.321092 1.985045 -0.388839 C 0.072243 2.030730 -0.631150 C 13.819777 0.997878 1.716103 C 14.002317 0.288677 0.370512 H 14.048836 2.065918 1.629273 C 13.729470 -1.230913 0.418112 C 14.045439 -1.906099 -0.928274 H 13.353905 0.756517 -0.384748 H 15.031246 0.436544 0.014990 H 14.375565 -1.670810 1.185830 C 12.308628 -1.545117 0.911608 O 12.102449 -2.080712 1.995263 N 11.294079 -1.170258 0.069898 Integral accuracy reduced to 1.0D-05 until final iterations. Initial convergence to 1.0D-05 achieved. Increase integral accuracy. SCF Done: E(RHF) = -2994.03487357 A.U. after 16 cycles Convg = 0.8573D-08 -V/T = 2.0012 S**2 = 0.0000 ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 NROrb= 632 NOA= 105 NOB= 105 NVA= 527 NVB= 527 Semi-Direct transformation. ModeAB= 4 MOrb= 105 LenV= 830431129 LASXX= 4135761315 LTotXX= 4135761315 LenRXX= 8310879360 LTotAB= 4175118045 MaxLAS= 5189219280 LenRXY= 0 NonZer= 12446640675 LenScr= 24990907392 LnRSAI= 5189219280 LnScr1= 10419141632 LExtra= 0 Total= 48910147664 MaxDsk= -1 SrtSym= T ITran= 3 Erroneous write. Write -1 instead of 12288. fd = 4 orig len = 12288 left = 12288 g_write How can I overcome this problem? I appreciate any help From owner-chemistry@ccl.net Mon Nov 23 10:13:00 2009 From: "andras.borosy(_)givaudan.com" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40766-091123085753-10804-uLKFsMDRELJaYPQRwkrGLA-x-server.ccl.net> X-Original-From: andras.borosy!^!givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004CB05BC1257677_=" Date: Mon, 23 Nov 2009 14:57:39 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy(a)givaudan.com This is a multipart message in MIME format. --=_alternative 004CB05BC1257677_= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: base64 RGVhciBDb2xsZWFndWUsDQoNClRoZXJlIGlzIGEgZnJlZSBtdWx0aXZhcmlhdGUgc3RhdC4gdG9v bGJveDoNCg0KaHR0cDovL3d3dy5iaXRqdW5nbGUuY29tL212YXJ0b29scy8NCg0KWW91IG1heSBu ZWVkIEtlcm5lbCBQTFMgKGlmIHlvdSBoYWQgbXVjaCBtb3JlIFgtdmFyaWFibGVzIHRoZW4gb2Jq ZWN0cywgDQphbHNvIFNBTVBMUyBpcyBzdWNoIGEgbWV0aG9kKToNCg0KaHR0cDovL3d3dy55b3Y0 MDguY29tL2h0bWwvY29kZXNwb3QucGhwP2dnPTU1DQoNCkJlc3Qgd2lzaGVzLA0KDQpBbmRyw6Fz IEJvcm9zeQ0KDQoNCg0KDQoiRGF2ZS5XaW5rbGVyLy4vY3Npcm8uYXUiIDxvd25lci1jaGVtaXN0 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ICZuYnNwOyAmbmJzcDsgJm5ic3A7aHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRf Y2NsX21lc3NhZ2U8YnI+DQo8YnI+DQpTdWJzY3JpYmUvVW5zdWJzY3JpYmU6IDxicj4NCiAmbmJz cDsgJm5ic3A7ICZuYnNwO2h0dHA6Ly93d3cuY2NsLm5ldC9jaGVtaXN0cnkvc3ViX3Vuc3ViLnNo dG1sPGJyPg0KPGJyPg0KQmVmb3JlIHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDogaHR0cDov L3d3dy5jY2wubmV0PGJyPg0KPGJyPg0KSm9iOiBodHRwOi8vd3d3LmNjbC5uZXQvam9icyA8YnI+ DQpDb25mZXJlbmNlczogaHR0cDovL3NlcnZlci5jY2wubmV0L2NoZW1pc3RyeS9hbm5vdW5jZW1l bnRzL2NvbmZlcmVuY2VzLzxicj4NCjxicj4NClNlYXJjaCBNZXNzYWdlczogaHR0cDovL3d3dy5j Y2wubmV0L2NoZW1pc3RyeS9zZWFyY2hjY2wvaW5kZXguc2h0bWw8YnI+DQo8YnI+DQpJZiB5b3Vy IG1haWwgYm91bmNlcyBmcm9tIENDTCB3aXRoIDUuNy4xIGVycm9yLCBjaGVjazo8YnI+DQogJm5i c3A7ICZuYnNwOyAmbmJzcDtodHRwOi8vd3d3LmNjbC5uZXQvc3BhbW1lcnMudHh0PGJyPg0KPGJy Pg0KUlRGSTogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlv bnMvPGJyPg0KPGJyPg0KPGJyPg0KPC9mb250PjwvdHQ+DQo8YnI+DQo= --=_alternative 004CB05BC1257677_=-- From owner-chemistry@ccl.net Mon Nov 23 11:39:01 2009 From: "Cleophas Muhavini Wawire muhavini(~)yahoo.com" To: CCL Subject: CCL:G: How does one apply the "GEN keyword" to a "Checkpoint file" geometry Message-Id: <-40767-091123113422-4935-KQWcb2bSA3UPZPxf8DVXmg * server.ccl.net> X-Original-From: "Cleophas Muhavini Wawire" Date: Mon, 23 Nov 2009 11:34:19 -0500 Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini-.-yahoo.com] Dear CCL Subscibers, Could someone kindly help me to know why the third step of this multi-step job fails. the first two steps were successful and had normal termination. The problem is with the third step. There is Unrecognized atomic symbol ****. Precisely I am doing an optimization in three steps and then carry out a tddft calculation in step four. The problem it seems is in using the GEN keyword where the read basis set and its ECP are applied to the geometry read from the checkpoint. How am I supposed to specify the Basis set and its ECP after the Charge and multiplicity line? The are two parts in this Question namely part (a) INPUT and Part (b) OUTPUT. (a)INPUT %chk=RUBPY1a %mem=2Gb %nproc=4 #P B3LYP/STO-3G gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) [Ru(bpy)3]2+ (part 1) 2 1 Ru 0.000000 0.000000 0.000000 N 1.637655 0.788035 1.046540 N 1.637655 -0.788035 -1.046540 C 2.859124 0.449484 0.571137 C 1.548271 1.609776 2.097857 C 2.662250 2.124769 2.727798 C 3.919291 1.790734 2.248252 C 4.014758 0.948118 1.158544 C 2.859124 -0.449484 -0.571137 C 1.548271 -1.609776 -2.097857 C 2.662250 -2.124769 -2.727798 C 3.919291 -1.790734 -2.248252 C 4.014758 -0.948118 -1.158544 H 0.535711 1.851838 2.435586 H 2.538391 2.789686 3.587166 H 4.821855 2.189017 2.721122 H 4.993359 0.671879 0.757350 H 0.535711 -1.851838 -2.435586 H 2.538391 -2.789686 -3.587166 H 4.821855 -2.189017 -2.721122 H 4.993359 -0.671879 -0.757350 N -0.136369 -1.812268 1.046540 N -1.501286 -1.024233 -1.046540 C -1.040298 -2.700816 0.571137 C 0.619971 -2.145730 2.097857 C 0.508979 -3.367961 2.727798 C -0.408825 -4.289573 2.248252 C -1.186285 -3.950941 1.158544 C -1.818826 -2.251332 -0.571137 C -2.168242 -0.535954 -2.097857 C -3.171229 -1.243192 -2.727798 C -3.510466 -2.498839 -2.248252 C -2.828473 -3.002823 -1.158544 H 1.335883 -1.389858 2.435586 H 1.146743 -3.593154 3.587166 H -0.515183 -5.270357 2.721122 H -1.914815 -4.660315 0.757350 H -1.871594 0.461980 -2.435586 H -3.685134 -0.803468 -3.587166 H -4.306672 -3.081340 -2.721122 H -3.078544 -3.988437 -0.757350 N -1.501286 1.024233 1.046540 N -0.136369 1.812268 -1.046540 C -1.818826 2.251332 0.571137 C -2.168242 0.535954 2.097857 C -3.171229 1.243192 2.727798 C -3.510466 2.498839 2.248252 C -2.828473 3.002823 1.158544 C -1.040298 2.700816 -0.571137 C 0.619971 2.145730 -2.097857 C 0.508979 3.367961 -2.727798 C -0.408825 4.289573 -2.248252 C -1.186285 3.950941 -1.158544 H -1.871594 -0.461980 2.435586 H -3.685134 0.803468 3.587166 H -4.306672 3.081340 2.721122 H -3.078544 3.988437 0.757350 H 1.335883 1.389858 -2.435586 H 1.146743 3.593154 -3.587166 H -0.515183 5.270357 -2.721122 H -1.914815 4.660315 -0.757350 --link1-- %chk=RUBPY1a %mem=2Gb %nproc=4 #P B3LYP/3-21G gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) Geom=Check Guess=Read [Ru(bpy)3]2+ (part 2) 2 1 --link1-- %chk=RUBPY1a %mem=2Gb %nproc=4 #P B3LYP/Gen pseudo=read gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) Geom=Check Guess=Read [Ru(bpy)3]2+ (part 3) 2 1 Ru 0 LANL2DZ **** C N H 0 6-31G **** Ru 0 LANL2DZ --link1-- %chk=RUBPY1a %Nosave %mem=2Gb %nproc=4 #P td=(singlet, Nstates=20 ) guess=read Geom=check [Ru(bpy)3]2+ (part 4) (b) OUTPUT----- =================================================================================================================================== Pseudopotential Parameters =================================================================================================================================== Center Atomic Valence Angular Power Coordinates Number Number Electrons Momentum of R Exponent Coefficient X Y Z =================================================================================================================================== Unrecognized atomic symbol **** Error termination via Lnk1e in /p5cecic/home/gaussian/g03/l301.exe at Fri Nov 20 21:22:18 2009. Job cpu time: 0 days 0 hours 0 minutes .9 seconds. File lengths (MBytes): RWF= 39 Int= 0 D2E= 0 Chk= 22 Scr= 2 From owner-chemistry@ccl.net Mon Nov 23 14:05:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim]~[compchem.net" To: CCL Subject: CCL: CIS calculations Message-Id: <-40768-091123103737-12447-oed03qRzXpEKAJbloTv9fg_-_server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=000e0cd5a01a3301a604790b840c Date: Mon, 23 Nov 2009 15:31:16 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim]|[compchem.net] --000e0cd5a01a3301a604790b840c Content-Type: text/plain; charset=ISO-8859-1 Sorry Peter another possiblity is that there is not free space on your disk. Check it. Sincerely; M. Ibrahim On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu < owner-chemistry/./ccl.net> wrote: > > Sent to CCL by: "Peter Khlyabich" [khlyabic:+:usc.edu] > Hello, > > I'm trying to run CIS calculations. I'm getting the same mistake every > time: > > My input file: > > %chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk > %mem=800MW > %NProcShared=1 > %LindaWorkers=hpc2710 > > #T CIS/6-31G(d) Opt > > 1 units with hydrogens in cis and in iso > > 0 1 > C -1.840437 0.706171 -0.354132 > C -3.201699 0.281759 -0.135866 > C -1.321092 1.985045 -0.388839 > C 0.072243 2.030730 -0.631150 > C 13.819777 0.997878 1.716103 > C 14.002317 0.288677 0.370512 > H 14.048836 2.065918 1.629273 > C 13.729470 -1.230913 0.418112 > C 14.045439 -1.906099 -0.928274 > H 13.353905 0.756517 -0.384748 > H 15.031246 0.436544 0.014990 > H 14.375565 -1.670810 1.185830 > C 12.308628 -1.545117 0.911608 > O 12.102449 -2.080712 1.995263 > N 11.294079 -1.170258 0.069898 > > > Integral accuracy reduced to 1.0D-05 until final iterations. > Initial convergence to 1.0D-05 achieved. Increase integral accuracy. > SCF Done: E(RHF) = -2994.03487357 A.U. after 16 cycles > Convg = 0.8573D-08 -V/T = 2.0012 > S**2 = 0.0000 > ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= > 1 AccDes= 1.00D-06 > HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > NROrb= 632 NOA= 105 NOB= 105 NVA= 527 NVB= 527 > Semi-Direct transformation. > ModeAB= 4 MOrb= 105 LenV= 830431129 > LASXX= 4135761315 LTotXX= 4135761315 LenRXX= 8310879360 > LTotAB= 4175118045 MaxLAS= 5189219280 LenRXY= 0 > NonZer= 12446640675 LenScr= 24990907392 LnRSAI= 5189219280 > LnScr1= 10419141632 LExtra= 0 Total= 48910147664 > MaxDsk= -1 SrtSym= T ITran= 3 > Erroneous write. Write -1 instead of 12288. > fd = 4 > orig len = 12288 left = 12288 > g_write > > > How can I overcome this problem? > > I appreciate any help> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim/./compchem.net Website: www.compchem.net Fax No.: +20862342601 --000e0cd5a01a3301a604790b840c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Sorry Peter
another possiblity is that there is not free space on your d= isk.
Check it.
Sincerely;
M. Ibrahim

On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu <owner-chemistry/./ccl.net> wrote:

Sent to CCL by: "Peter =A0Khlyabich" [khlyabic:+:usc.edu]
Hello,

I'm trying to run CIS calculations. I'm getting the same mistake ev= ery time:

My input file:

%chk=3D/tmp/khaddsrkl89sjfhdskjh30o697.chk
%mem=3D800MW
%NProcShared=3D1
%LindaWorkers=3Dhpc2710

#T CIS/6-31G(d) Opt

1 units with hydrogens in cis and in iso

0 1
=A0C =A0 =A0 =A0 -1.840437 =A0 =A00.706171 =A0 -0.354132
=A0C =A0 =A0 =A0 -3.201699 =A0 =A00.281759 =A0 -0.135866
=A0C =A0 =A0 =A0 -1.321092 =A0 =A01.985045 =A0 -0.388839
=A0C =A0 =A0 =A0 =A00.072243 =A0 =A02.030730 =A0 -0.631150
=A0C =A0 =A0 =A0 13.819777 =A0 =A00.997878 =A0 =A01.716103
=A0C =A0 =A0 =A0 14.002317 =A0 =A00.288677 =A0 =A00.370512
=A0H =A0 =A0 =A0 14.048836 =A0 =A02.065918 =A0 =A01.629273
=A0C =A0 =A0 =A0 13.729470 =A0 -1.230913 =A0 =A00.418112
=A0C =A0 =A0 =A0 14.045439 =A0 -1.906099 =A0 -0.928274
=A0H =A0 =A0 =A0 13.353905 =A0 =A00.756517 =A0 -0.384748
=A0H =A0 =A0 =A0 15.031246 =A0 =A00.436544 =A0 =A00.014990
=A0H =A0 =A0 =A0 14.375565 =A0 -1.670810 =A0 =A01.185830
=A0C =A0 =A0 =A0 12.308628 =A0 -1.545117 =A0 =A00.911608
=A0O =A0 =A0 =A0 12.102449 =A0 -2.080712 =A0 =A01.995263
=A0N =A0 =A0 =A0 11.294079 =A0 -1.170258 =A0 =A00.069898


=A0Integral accuracy reduced to 1.0D-05 until final iterations.
=A0Initial convergence to 1.0D-05 achieved. =A0Increase integral accuracy.<= br> =A0SCF Done: =A0E(RHF) =3D =A0-2994.03487357 =A0 =A0 A.U. after =A0 16 cycl= es
=A0 =A0 =A0 =A0 =A0 =A0 Convg =A0=3D =A0 =A00.8573D-08 =A0 =A0 =A0 =A0 =A0= =A0 -V/T =3D =A02.0012
=A0 =A0 =A0 =A0 =A0 =A0 S**2 =A0 =3D =A0 0.0000
=A0ExpMin=3D 1.17D-01 ExpMax=3D 2.19D+04 ExpMxC=3D 3.30D+03 IAcc=3D1 IRadAn= =3D =A0 =A0 =A0 =A0 1 AccDes=3D 1.00D-06
=A0HarFok: =A0IExCor=3D 205 AccDes=3D 1.00D-06 IRadAn=3D =A0 =A0 =A0 =A0 1 = IDoV=3D1
=A0ScaDFX=3D =A01.000000 =A01.000000 =A01.000000 =A01.000000
=A0NROrb=3D =A0 =A0632 NOA=3D =A0 105 NOB=3D =A0 105 NVA=3D =A0 527 NVB=3D = =A0 527
=A0Semi-Direct transformation.
=A0ModeAB=3D =A0 =A0 =A0 =A0 =A0 4 MOrb=3D =A0 =A0 =A0 =A0 =A0 105 LenV=3D = =A0 =A0 830431129
=A0LASXX=3D =A0 4135761315 LTotXX=3D =A04135761315 LenRXX=3D =A08310879360<= br> =A0LTotAB=3D =A04175118045 MaxLAS=3D =A05189219280 LenRXY=3D =A0 =A0 =A0 = =A0 =A0 0
=A0NonZer=3D 12446640675 LenScr=3D 24990907392 LnRSAI=3D =A05189219280
=A0LnScr1=3D 10419141632 LExtra=3D =A0 =A0 =A0 =A0 =A0 0 Total=3D =A0489101= 47664
=A0MaxDsk=3D =A0 =A0 =A0 =A0 =A0-1 SrtSym=3D =A0 =A0 =A0 =A0 =A0 T ITran=3D= =A0 =A0 =A0 =A0 =A0 =A03
Erroneous write. Write -1 instead of 12288.
fd =3D 4
orig len =3D 12288 left =3D 12288
g_write


How can I overcome this problem?

I appreciate any help



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=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
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=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

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=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim/./compche= m.net
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--000e0cd5a01a3301a604790b840c-- From owner-chemistry@ccl.net Mon Nov 23 14:40:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim\a/compchem.net" To: CCL Subject: CCL: CIS calculations Message-Id: <-40769-091123102250-445-/SMjwJ4CcEoJPte3bWUX3Q##server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=000e0cd5a01a24cc9104790b656a Date: Mon, 23 Nov 2009 15:22:35 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim[*]compchem.net] --000e0cd5a01a24cc9104790b656a Content-Type: text/plain; charset=ISO-8859-1 Dear Peter I am not sure about your error, but could you change the name of your chk point file, I think you are running two jobs with the same check file name. Have a go, if it didn't work, could you send your input and output files as attachment files? Sicnerely; M. Ibrahim On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu < owner-chemistry(a)ccl.net> wrote: > > Sent to CCL by: "Peter Khlyabich" [khlyabic:+:usc.edu] > Hello, > > I'm trying to run CIS calculations. I'm getting the same mistake every > time: > > My input file: > > %chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk > %mem=800MW > %NProcShared=1 > %LindaWorkers=hpc2710 > > #T CIS/6-31G(d) Opt > > 1 units with hydrogens in cis and in iso > > 0 1 > C -1.840437 0.706171 -0.354132 > C -3.201699 0.281759 -0.135866 > C -1.321092 1.985045 -0.388839 > C 0.072243 2.030730 -0.631150 > C 13.819777 0.997878 1.716103 > C 14.002317 0.288677 0.370512 > H 14.048836 2.065918 1.629273 > C 13.729470 -1.230913 0.418112 > C 14.045439 -1.906099 -0.928274 > H 13.353905 0.756517 -0.384748 > H 15.031246 0.436544 0.014990 > H 14.375565 -1.670810 1.185830 > C 12.308628 -1.545117 0.911608 > O 12.102449 -2.080712 1.995263 > N 11.294079 -1.170258 0.069898 > > > Integral accuracy reduced to 1.0D-05 until final iterations. > Initial convergence to 1.0D-05 achieved. Increase integral accuracy. > SCF Done: E(RHF) = -2994.03487357 A.U. after 16 cycles > Convg = 0.8573D-08 -V/T = 2.0012 > S**2 = 0.0000 > ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= > 1 AccDes= 1.00D-06 > HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > NROrb= 632 NOA= 105 NOB= 105 NVA= 527 NVB= 527 > Semi-Direct transformation. > ModeAB= 4 MOrb= 105 LenV= 830431129 > LASXX= 4135761315 LTotXX= 4135761315 LenRXX= 8310879360 > LTotAB= 4175118045 MaxLAS= 5189219280 LenRXY= 0 > NonZer= 12446640675 LenScr= 24990907392 LnRSAI= 5189219280 > LnScr1= 10419141632 LExtra= 0 Total= 48910147664 > MaxDsk= -1 SrtSym= T ITran= 3 > Erroneous write. Write -1 instead of 12288. > fd = 4 > orig len = 12288 left = 12288 > g_write > > > How can I overcome this problem? > > I appreciate any help> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim(a)compchem.net Website: www.compchem.net Fax No.: +20862342601 --000e0cd5a01a24cc9104790b656a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Peter
I am not sure about your error, but could you change the name= of your chk point file, I think you are running two jobs with the same che= ck file name.
Have a go, if it didn't work, could you send your inpu= t and output files as attachment files?
Sicnerely;
M. Ibrahim

On Mon, Nov 23, = 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.= edu <ow= ner-chemistry(a)ccl.net> wrote:

Sent to CCL by: "Peter =A0Khlyabich" [khlyabic:+:usc.edu]
Hello,

I'm trying to run CIS calculations. I'm getting the same mistake ev= ery time:

My input file:

%chk=3D/tmp/khaddsrkl89sjfhdskjh30o697.chk
%mem=3D800MW
%NProcShared=3D1
%LindaWorkers=3Dhpc2710

#T CIS/6-31G(d) Opt

1 units with hydrogens in cis and in iso

0 1
=A0C =A0 =A0 =A0 -1.840437 =A0 =A00.706171 =A0 -0.354132
=A0C =A0 =A0 =A0 -3.201699 =A0 =A00.281759 =A0 -0.135866
=A0C =A0 =A0 =A0 -1.321092 =A0 =A01.985045 =A0 -0.388839
=A0C =A0 =A0 =A0 =A00.072243 =A0 =A02.030730 =A0 -0.631150
=A0C =A0 =A0 =A0 13.819777 =A0 =A00.997878 =A0 =A01.716103
=A0C =A0 =A0 =A0 14.002317 =A0 =A00.288677 =A0 =A00.370512
=A0H =A0 =A0 =A0 14.048836 =A0 =A02.065918 =A0 =A01.629273
=A0C =A0 =A0 =A0 13.729470 =A0 -1.230913 =A0 =A00.418112
=A0C =A0 =A0 =A0 14.045439 =A0 -1.906099 =A0 -0.928274
=A0H =A0 =A0 =A0 13.353905 =A0 =A00.756517 =A0 -0.384748
=A0H =A0 =A0 =A0 15.031246 =A0 =A00.436544 =A0 =A00.014990
=A0H =A0 =A0 =A0 14.375565 =A0 -1.670810 =A0 =A01.185830
=A0C =A0 =A0 =A0 12.308628 =A0 -1.545117 =A0 =A00.911608
=A0O =A0 =A0 =A0 12.102449 =A0 -2.080712 =A0 =A01.995263
=A0N =A0 =A0 =A0 11.294079 =A0 -1.170258 =A0 =A00.069898


=A0Integral accuracy reduced to 1.0D-05 until final iterations.
=A0Initial convergence to 1.0D-05 achieved. =A0Increase integral accuracy.<= br> =A0SCF Done: =A0E(RHF) =3D =A0-2994.03487357 =A0 =A0 A.U. after =A0 16 cycl= es
=A0 =A0 =A0 =A0 =A0 =A0 Convg =A0=3D =A0 =A00.8573D-08 =A0 =A0 =A0 =A0 =A0= =A0 -V/T =3D =A02.0012
=A0 =A0 =A0 =A0 =A0 =A0 S**2 =A0 =3D =A0 0.0000
=A0ExpMin=3D 1.17D-01 ExpMax=3D 2.19D+04 ExpMxC=3D 3.30D+03 IAcc=3D1 IRadAn= =3D =A0 =A0 =A0 =A0 1 AccDes=3D 1.00D-06
=A0HarFok: =A0IExCor=3D 205 AccDes=3D 1.00D-06 IRadAn=3D =A0 =A0 =A0 =A0 1 = IDoV=3D1
=A0ScaDFX=3D =A01.000000 =A01.000000 =A01.000000 =A01.000000
=A0NROrb=3D =A0 =A0632 NOA=3D =A0 105 NOB=3D =A0 105 NVA=3D =A0 527 NVB=3D = =A0 527
=A0Semi-Direct transformation.
=A0ModeAB=3D =A0 =A0 =A0 =A0 =A0 4 MOrb=3D =A0 =A0 =A0 =A0 =A0 105 LenV=3D = =A0 =A0 830431129
=A0LASXX=3D =A0 4135761315 LTotXX=3D =A04135761315 LenRXX=3D =A08310879360<= br> =A0LTotAB=3D =A04175118045 MaxLAS=3D =A05189219280 LenRXY=3D =A0 =A0 =A0 = =A0 =A0 0
=A0NonZer=3D 12446640675 LenScr=3D 24990907392 LnRSAI=3D =A05189219280
=A0LnScr1=3D 10419141632 LExtra=3D =A0 =A0 =A0 =A0 =A0 0 Total=3D =A0489101= 47664
=A0MaxDsk=3D =A0 =A0 =A0 =A0 =A0-1 SrtSym=3D =A0 =A0 =A0 =A0 =A0 T ITran=3D= =A0 =A0 =A0 =A0 =A0 =A03
Erroneous write. Write -1 instead of 12288.
fd =3D 4
orig len =3D 12288 left =3D 12288
g_write


How can I overcome this problem?

I appreciate any help



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(a)ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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--
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim(a)compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--000e0cd5a01a24cc9104790b656a-- From owner-chemistry@ccl.net Mon Nov 23 15:15:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim{}compchem.net" To: CCL Subject: CCL: CIS calculations Message-Id: <-40770-091123120846-20284-qzFFuZun6ljxCMdoSjQp5w*server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=000e0cd668ec74e5ef04790bd415 Date: Mon, 23 Nov 2009 15:53:42 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim++compchem.net] --000e0cd668ec74e5ef04790bd415 Content-Type: text/plain; charset=ISO-8859-1 Dear Peter Sorry, your error may also return to no enoguh space on your disk. Check your quota. I am not sure, but these all are possibilities. Sincerely; M. Ibrahim On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu < owner-chemistry-,-ccl.net> wrote: > > Sent to CCL by: "Peter Khlyabich" [khlyabic:+:usc.edu] > Hello, > > I'm trying to run CIS calculations. I'm getting the same mistake every > time: > > My input file: > > %chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk > %mem=800MW > %NProcShared=1 > %LindaWorkers=hpc2710 > > #T CIS/6-31G(d) Opt > > 1 units with hydrogens in cis and in iso > > 0 1 > C -1.840437 0.706171 -0.354132 > C -3.201699 0.281759 -0.135866 > C -1.321092 1.985045 -0.388839 > C 0.072243 2.030730 -0.631150 > C 13.819777 0.997878 1.716103 > C 14.002317 0.288677 0.370512 > H 14.048836 2.065918 1.629273 > C 13.729470 -1.230913 0.418112 > C 14.045439 -1.906099 -0.928274 > H 13.353905 0.756517 -0.384748 > H 15.031246 0.436544 0.014990 > H 14.375565 -1.670810 1.185830 > C 12.308628 -1.545117 0.911608 > O 12.102449 -2.080712 1.995263 > N 11.294079 -1.170258 0.069898 > > > Integral accuracy reduced to 1.0D-05 until final iterations. > Initial convergence to 1.0D-05 achieved. Increase integral accuracy. > SCF Done: E(RHF) = -2994.03487357 A.U. after 16 cycles > Convg = 0.8573D-08 -V/T = 2.0012 > S**2 = 0.0000 > ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= > 1 AccDes= 1.00D-06 > HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > NROrb= 632 NOA= 105 NOB= 105 NVA= 527 NVB= 527 > Semi-Direct transformation. > ModeAB= 4 MOrb= 105 LenV= 830431129 > LASXX= 4135761315 LTotXX= 4135761315 LenRXX= 8310879360 > LTotAB= 4175118045 MaxLAS= 5189219280 LenRXY= 0 > NonZer= 12446640675 LenScr= 24990907392 LnRSAI= 5189219280 > LnScr1= 10419141632 LExtra= 0 Total= 48910147664 > MaxDsk= -1 SrtSym= T ITran= 3 > Erroneous write. Write -1 instead of 12288. > fd = 4 > orig len = 12288 left = 12288 > g_write > > > How can I overcome this problem? > > I appreciate any help> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim-,-compchem.net Website: www.compchem.net Fax No.: +20862342601 --000e0cd668ec74e5ef04790bd415 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Peter
Sorry, your error may also return to no enoguh space on your = disk. Check your quota.
I am not sure, but these all are possibilities.<= br>Sincerely;
M. Ibrahim

On Mon, Nov 2= 3, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:u= sc.edu <owner-chemistry-,-ccl.net> wrote:

Sent to CCL by: "Peter =A0Khlyabich" [khlyabic:+:usc.edu]
Hello,

I'm trying to run CIS calculations. I'm getting the same mistake ev= ery time:

My input file:

%chk=3D/tmp/khaddsrkl89sjfhdskjh30o697.chk
%mem=3D800MW
%NProcShared=3D1
%LindaWorkers=3Dhpc2710

#T CIS/6-31G(d) Opt

1 units with hydrogens in cis and in iso

0 1
=A0C =A0 =A0 =A0 -1.840437 =A0 =A00.706171 =A0 -0.354132
=A0C =A0 =A0 =A0 -3.201699 =A0 =A00.281759 =A0 -0.135866
=A0C =A0 =A0 =A0 -1.321092 =A0 =A01.985045 =A0 -0.388839
=A0C =A0 =A0 =A0 =A00.072243 =A0 =A02.030730 =A0 -0.631150
=A0C =A0 =A0 =A0 13.819777 =A0 =A00.997878 =A0 =A01.716103
=A0C =A0 =A0 =A0 14.002317 =A0 =A00.288677 =A0 =A00.370512
=A0H =A0 =A0 =A0 14.048836 =A0 =A02.065918 =A0 =A01.629273
=A0C =A0 =A0 =A0 13.729470 =A0 -1.230913 =A0 =A00.418112
=A0C =A0 =A0 =A0 14.045439 =A0 -1.906099 =A0 -0.928274
=A0H =A0 =A0 =A0 13.353905 =A0 =A00.756517 =A0 -0.384748
=A0H =A0 =A0 =A0 15.031246 =A0 =A00.436544 =A0 =A00.014990
=A0H =A0 =A0 =A0 14.375565 =A0 -1.670810 =A0 =A01.185830
=A0C =A0 =A0 =A0 12.308628 =A0 -1.545117 =A0 =A00.911608
=A0O =A0 =A0 =A0 12.102449 =A0 -2.080712 =A0 =A01.995263
=A0N =A0 =A0 =A0 11.294079 =A0 -1.170258 =A0 =A00.069898


=A0Integral accuracy reduced to 1.0D-05 until final iterations.
=A0Initial convergence to 1.0D-05 achieved. =A0Increase integral accuracy.<= br> =A0SCF Done: =A0E(RHF) =3D =A0-2994.03487357 =A0 =A0 A.U. after =A0 16 cycl= es
=A0 =A0 =A0 =A0 =A0 =A0 Convg =A0=3D =A0 =A00.8573D-08 =A0 =A0 =A0 =A0 =A0= =A0 -V/T =3D =A02.0012
=A0 =A0 =A0 =A0 =A0 =A0 S**2 =A0 =3D =A0 0.0000
=A0ExpMin=3D 1.17D-01 ExpMax=3D 2.19D+04 ExpMxC=3D 3.30D+03 IAcc=3D1 IRadAn= =3D =A0 =A0 =A0 =A0 1 AccDes=3D 1.00D-06
=A0HarFok: =A0IExCor=3D 205 AccDes=3D 1.00D-06 IRadAn=3D =A0 =A0 =A0 =A0 1 = IDoV=3D1
=A0ScaDFX=3D =A01.000000 =A01.000000 =A01.000000 =A01.000000
=A0NROrb=3D =A0 =A0632 NOA=3D =A0 105 NOB=3D =A0 105 NVA=3D =A0 527 NVB=3D = =A0 527
=A0Semi-Direct transformation.
=A0ModeAB=3D =A0 =A0 =A0 =A0 =A0 4 MOrb=3D =A0 =A0 =A0 =A0 =A0 105 LenV=3D = =A0 =A0 830431129
=A0LASXX=3D =A0 4135761315 LTotXX=3D =A04135761315 LenRXX=3D =A08310879360<= br> =A0LTotAB=3D =A04175118045 MaxLAS=3D =A05189219280 LenRXY=3D =A0 =A0 =A0 = =A0 =A0 0
=A0NonZer=3D 12446640675 LenScr=3D 24990907392 LnRSAI=3D =A05189219280
=A0LnScr1=3D 10419141632 LExtra=3D =A0 =A0 =A0 =A0 =A0 0 Total=3D =A0489101= 47664
=A0MaxDsk=3D =A0 =A0 =A0 =A0 =A0-1 SrtSym=3D =A0 =A0 =A0 =A0 =A0 T ITran=3D= =A0 =A0 =A0 =A0 =A0 =A03
Erroneous write. Write -1 instead of 12288.
fd =3D 4
orig len =3D 12288 left =3D 12288
g_write


How can I overcome this problem?

I appreciate any help



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--000e0cd668ec74e5ef04790bd415-- From owner-chemistry@ccl.net Mon Nov 23 15:49:01 2009 From: "tuhin*o*iitk.ac.in" To: CCL Subject: CCL:G: Optimization completed: Basis of negligible forces. Message-Id: <-40771-091123140110-12565-Nls8E6YQvCyos4L8WG9zDA|-|server.ccl.net> X-Original-From: tuhin__iitk.ac.in Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 23 Nov 2009 23:55:46 +0530 MIME-Version: 1.0 Sent to CCL by: tuhin__iitk.ac.in Dear All, I'm running "full geometry optimization" on some molecules using Gaussian-03 suit. These are the arguments/terms at the router: #B3LYP/6-31++G** Opt(Z-matrix,CalcAll,Tight,MaxCycle=132) Int=Ultrafine The program terminates normally. But looking into the "output" file, it appears the optimization is yet to be over as I have not observed all "4 YES". I'm a bit skeptical!! Item Value Threshold Converged? Maximum Force 0.000000 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.001365 0.000060 NO RMS Displacement 0.000324 0.000040 NO Predicted change in Energy=-2.522311D-09 Optimization completed on the basis of negligible forces. -- Stationary point found. Am I doing something wrong? I want to be very careful as I would like to carryout “frequency calculations” on the optimized geometries of the molecules. I would much appreciate if anybody could come up with some suggestions. Thanks and kind regards, Tuhin From owner-chemistry@ccl.net Mon Nov 23 16:24:00 2009 From: "Stephen.Garrison#,#srnl.doe.gov" To: CCL Subject: CCL:G: CIS calculations Message-Id: <-40772-091123153729-12031-yaS/2tjI1lIOl7hYGCP5Qg : server.ccl.net> X-Original-From: Stephen.Garrison]~[srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 007144B985257677_=" Date: Mon, 23 Nov 2009 15:37:10 -0500 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison,srnl.doe.gov This is a multipart message in MIME format. --=_alternative 007144B985257677_= Content-Type: text/plain; charset="US-ASCII" The problem is probably indicated by the following line: LnScr1= 10419141632 LExtra= 0 Total= 48910147664 This "Total" is the disk space used in units of words (bytes / 8) and represents a value of about 364GB. Since you did not set a MaxDisk value (as indicated by MaxDisk=-1 in the output), G03/G09 is trying to write a scratch file of about 350GB. The "Erroneous write" line indicates a failed write, probably because you are out of space on the disk. Assuming CIS calculations in G03/G09 honor MaxDisk, set this value in your route line to the amount of scratch space you want the calculation to be able to use. Gaussian will choose a calculation routine (indicated by ITran=X where X is a number between 1 and 5) to try to remain within the MaxDisk limitation you specify. Good luck, Stephen -- Stephen L. Garrison, Ph.D. Senior Engineer A Process Modeling & Computational Chemistry Group Computational Sciences Directorate Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison++SRNL.doe.gov "Mahmoud A. A. Ibrahim m.ibrahim\a/compchem.net" Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov++ccl.net 11/23/2009 10:22 AM Please respond to "CCL Subscribers" To "Garrison, Stephen " cc Subject CCL: CIS calculations Dear Peter I am not sure about your error, but could you change the name of your chk point file, I think you are running two jobs with the same check file name. Have a go, if it didn't work, could you send your input and output files as attachment files? Sicnerely; M. Ibrahim On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu < owner-chemistry(-)ccl.net> wrote: Sent to CCL by: "Peter Khlyabich" [khlyabic:+:usc.edu] Hello, I'm trying to run CIS calculations. I'm getting the same mistake every time: My input file: %chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk %mem=800MW %NProcShared=1 %LindaWorkers=hpc2710 #T CIS/6-31G(d) Opt 1 units with hydrogens in cis and in iso 0 1 C -1.840437 0.706171 -0.354132 C -3.201699 0.281759 -0.135866 C -1.321092 1.985045 -0.388839 C 0.072243 2.030730 -0.631150 C 13.819777 0.997878 1.716103 C 14.002317 0.288677 0.370512 H 14.048836 2.065918 1.629273 C 13.729470 -1.230913 0.418112 C 14.045439 -1.906099 -0.928274 H 13.353905 0.756517 -0.384748 H 15.031246 0.436544 0.014990 H 14.375565 -1.670810 1.185830 C 12.308628 -1.545117 0.911608 O 12.102449 -2.080712 1.995263 N 11.294079 -1.170258 0.069898 Integral accuracy reduced to 1.0D-05 until final iterations. Initial convergence to 1.0D-05 achieved. Increase integral accuracy. SCF Done: E(RHF) = -2994.03487357 A.U. after 16 cycles Convg = 0.8573D-08 -V/T = 2.0012 S**2 = 0.0000 ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 NROrb= 632 NOA= 105 NOB= 105 NVA= 527 NVB= 527 Semi-Direct transformation. ModeAB= 4 MOrb= 105 LenV= 830431129 LASXX= 4135761315 LTotXX= 4135761315 LenRXX= 8310879360 LTotAB= 4175118045 MaxLAS= 5189219280 LenRXY= 0 NonZer= 12446640675 LenScr= 24990907392 LnRSAI= 5189219280 LnScr1= 10419141632 LExtra= 0 Total= 48910147664 MaxDsk= -1 SrtSym= T ITran= 3 Erroneous write. Write -1 instead of 12288. fd = 4 orig len = 12288 left = 12288 g_write How can I overcome this problem? I appreciate any helpE-mail to subscribers: CHEMISTRY(-)ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST(-)ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim(-)compchem.net Website: www.compchem.net Fax No.: +20862342601 --=_alternative 007144B985257677_= Content-Type: text/html; charset="US-ASCII"
The problem is probably indicated by the following line:

 LnScr1= 10419141632 LExtra=           0 Total=  48910147664

This "Total" is the disk space used in units of words (bytes / 8) and represents a value of about 364GB. Since you did not set a MaxDisk value (as indicated by MaxDisk=-1 in the output), G03/G09 is trying to write a scratch file of about 350GB. The "Erroneous write" line indicates a failed write, probably because you are out of space on the disk. Assuming CIS calculations in G03/G09 honor MaxDisk, set this value in your route line to the amount of scratch space you want the calculation to be able to use. Gaussian will choose a calculation routine (indicated by ITran=X where X is a number between 1 and 5) to try to remain within the MaxDisk limitation you specify.

Good luck,
Stephen

--
Stephen L. Garrison, Ph.D.
Senior Engineer A
Process Modeling & Computational Chemistry Group
Computational Sciences Directorate
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison++SRNL.doe.gov


"Mahmoud A. A. Ibrahim m.ibrahim\a/compchem.net" <owner-chemistry++ccl.net>
Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov++ccl.net

11/23/2009 10:22 AM
Please respond to
"CCL Subscribers" <chemistry++ccl.net>
To
"Garrison, Stephen " <stephen.garrison++srnl.doe.gov>
cc
Subject
CCL: CIS calculations





Dear Peter
I am not sure about your error, but could you change the name of your chk point file, I think you are running two jobs with the same check file name.
Have a go, if it didn't work, could you send your input and output files as attachment files?
Sicnerely;
M. Ibrahim
On Mon, Nov 23, 2009 at 3:08 AM, Peter Khlyabich khlyabic:+:usc.edu <owner-chemistry(-)ccl.net> wrote:

Sent to CCL by: "Peter  Khlyabich" [khlyabic:+:usc.edu]
Hello,

I'm trying to run CIS calculations. I'm getting the same mistake every time:

My input file:

%chk=/tmp/khaddsrkl89sjfhdskjh30o697.chk
%mem=800MW
%NProcShared=1
%LindaWorkers=hpc2710

#T CIS/6-31G(d) Opt

1 units with hydrogens in cis and in iso

0 1
 C       -1.840437    0.706171   -0.354132
 C       -3.201699    0.281759   -0.135866
 C       -1.321092    1.985045   -0.388839
 C        0.072243    2.030730   -0.631150
 C       13.819777    0.997878    1.716103
 C       14.002317    0.288677    0.370512
 H       14.048836    2.065918    1.629273
 C       13.729470   -1.230913    0.418112
 C       14.045439   -1.906099   -0.928274
 H       13.353905    0.756517   -0.384748
 H       15.031246    0.436544    0.014990
 H       14.375565   -1.670810    1.185830
 C       12.308628   -1.545117    0.911608
 O       12.102449   -2.080712    1.995263
 N       11.294079   -1.170258    0.069898


 Integral accuracy reduced to 1.0D-05 until final iterations.
 Initial convergence to 1.0D-05 achieved.  Increase integral accuracy.
 SCF Done:  E(RHF) =  -2994.03487357     A.U. after   16 cycles
            Convg  =    0.8573D-08             -V/T =  2.0012
            S**2   =   0.0000
 ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn=         1 AccDes= 1.00D-06
 HarFok:  IExCor= 205 AccDes= 1.00D-06 IRadAn=         1 IDoV=1
 ScaDFX=  1.000000  1.000000  1.000000  1.000000
 NROrb=    632 NOA=   105 NOB=   105 NVA=   527 NVB=   527
 Semi-Direct transformation.
 ModeAB=           4 MOrb=           105 LenV=     830431129
 LASXX=   4135761315 LTotXX=  4135761315 LenRXX=  8310879360
 LTotAB=  4175118045 MaxLAS=  5189219280 LenRXY=           0
 NonZer= 12446640675 LenScr= 24990907392 LnRSAI=  5189219280
 LnScr1= 10419141632 LExtra=           0 Total=  48910147664
 MaxDsk=          -1 SrtSym=           T ITran=            3
Erroneous write. Write -1 instead of 12288.
fd = 4
orig len = 12288 left = 12288
g_write


How can I overcome this problem?

I appreciate any help


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--
                 Mahmoud A. A. Ibrahim        
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim(-)compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601
--=_alternative 007144B985257677_=-- From owner-chemistry@ccl.net Mon Nov 23 17:04:01 2009 From: "Jeff Woodford jwoodfor+/-eou.edu" To: CCL Subject: CCL:G: PCM solvation Message-Id: <-40773-091123150531-18168-rXia8BH+rVdq9qlwJXAGtQ(0)server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Nov 2009 11:25:47 -0800 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor!A!eou.edu] All: I am a bit confused about how PCM solvation models are supposed to work in, e.g., Gaussian. I have a molecule optimized at the B3LYP-D/cc-pVTZ level (gas phase) and I would like to compute its solvation free energy, taking into account both electrostatic and nonelectrostatic contributions. The Gaussian 03 manual suggests that the recommended method to do this is to use the SCFVAC keyword and the UAHF radii model, which are optimized at the HF/6-31G(d) level. Does this mean that I ought to use the HF/6-31G(d) method in to compute the solvation free energy in order to be consistent with the parameterization of the radii? And if so, would it also be consistent with the properties I compute at the B3LYP-D/cc-pVTZ level? Thanks for your time, -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 From owner-chemistry@ccl.net Mon Nov 23 17:34:01 2009 From: "Patrick McCarren patrick.mccarren^gmail.com" To: CCL Subject: CCL:G: How does one apply the "GEN keyword" to a "Checkpoint file" geometry Message-Id: <-40774-091123130906-7639-rzrP7fV738CrcikYzZXUPg(_)server.ccl.net> X-Original-From: Patrick McCarren Content-Type: multipart/alternative; boundary=000e0cd3acf0d8602c04790db766 Date: Mon, 23 Nov 2009 13:08:52 -0500 MIME-Version: 1.0 Sent to CCL by: Patrick McCarren [patrick.mccarren,gmail.com] --000e0cd3acf0d8602c04790db766 Content-Type: text/plain; charset=ISO-8859-1 It looks like there is an extra line in the third step. There are two blank lines after the charge and multiplicity but there should be one. You may also have to change that route section to integral=(grid=ultrafine). Patrick --link1-- %chk=RUBPY1a %mem=2Gb %nproc=4 #P B3LYP/Gen pseudo=read gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) Geom=Check Guess=Read [Ru(bpy)3]2+ (part 3) 2 1 * *Ru 0 LANL2DZ **** C N H 0 6-31G **** Ru 0 LANL2DZ On Mon, Nov 23, 2009 at 11:34 AM, Cleophas Muhavini Wawire muhavini(~) yahoo.com wrote: > > Sent to CCL by: "Cleophas Muhavini Wawire" [muhavini-.-yahoo.com] > Dear CCL Subscibers, > Could someone kindly help me to know why the third step of this multi-step > job fails. the first two steps were successful and had normal termination. > The problem is with the third step. There is Unrecognized atomic symbol > ****. > Precisely I am doing an optimization in three steps and then carry out a > tddft calculation in step four. The problem it seems is in using the GEN > keyword where the read basis set and its ECP are applied to the geometry > read from the checkpoint. How am I supposed to specify the Basis set and its > ECP after the Charge and multiplicity line? The are two parts in this > Question namely part (a) INPUT and Part (b) OUTPUT. > > (a)INPUT > %chk=RUBPY1a > %mem=2Gb > %nproc=4 > #P B3LYP/STO-3G gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) > > [Ru(bpy)3]2+ (part 1) > > 2 1 > Ru 0.000000 0.000000 0.000000 > N 1.637655 0.788035 1.046540 > N 1.637655 -0.788035 -1.046540 > C 2.859124 0.449484 0.571137 > C 1.548271 1.609776 2.097857 > C 2.662250 2.124769 2.727798 > C 3.919291 1.790734 2.248252 > C 4.014758 0.948118 1.158544 > C 2.859124 -0.449484 -0.571137 > C 1.548271 -1.609776 -2.097857 > C 2.662250 -2.124769 -2.727798 > C 3.919291 -1.790734 -2.248252 > C 4.014758 -0.948118 -1.158544 > H 0.535711 1.851838 2.435586 > H 2.538391 2.789686 3.587166 > H 4.821855 2.189017 2.721122 > H 4.993359 0.671879 0.757350 > H 0.535711 -1.851838 -2.435586 > H 2.538391 -2.789686 -3.587166 > H 4.821855 -2.189017 -2.721122 > H 4.993359 -0.671879 -0.757350 > N -0.136369 -1.812268 1.046540 > N -1.501286 -1.024233 -1.046540 > C -1.040298 -2.700816 0.571137 > C 0.619971 -2.145730 2.097857 > C 0.508979 -3.367961 2.727798 > C -0.408825 -4.289573 2.248252 > C -1.186285 -3.950941 1.158544 > C -1.818826 -2.251332 -0.571137 > C -2.168242 -0.535954 -2.097857 > C -3.171229 -1.243192 -2.727798 > C -3.510466 -2.498839 -2.248252 > C -2.828473 -3.002823 -1.158544 > H 1.335883 -1.389858 2.435586 > H 1.146743 -3.593154 3.587166 > H -0.515183 -5.270357 2.721122 > H -1.914815 -4.660315 0.757350 > H -1.871594 0.461980 -2.435586 > H -3.685134 -0.803468 -3.587166 > H -4.306672 -3.081340 -2.721122 > H -3.078544 -3.988437 -0.757350 > N -1.501286 1.024233 1.046540 > N -0.136369 1.812268 -1.046540 > C -1.818826 2.251332 0.571137 > C -2.168242 0.535954 2.097857 > C -3.171229 1.243192 2.727798 > C -3.510466 2.498839 2.248252 > C -2.828473 3.002823 1.158544 > C -1.040298 2.700816 -0.571137 > C 0.619971 2.145730 -2.097857 > C 0.508979 3.367961 -2.727798 > C -0.408825 4.289573 -2.248252 > C -1.186285 3.950941 -1.158544 > H -1.871594 -0.461980 2.435586 > H -3.685134 0.803468 3.587166 > H -4.306672 3.081340 2.721122 > H -3.078544 3.988437 0.757350 > H 1.335883 1.389858 -2.435586 > H 1.146743 3.593154 -3.587166 > H -0.515183 5.270357 -2.721122 > H -1.914815 4.660315 -0.757350 > > --link1-- > %chk=RUBPY1a > %mem=2Gb > %nproc=4 > #P B3LYP/3-21G gfinput iop(6/7=3) scf=tight opt integral(grid=ultrafine) > Geom=Check Guess=Read > > [Ru(bpy)3]2+ (part 2) > > 2 1 > > --link1-- > %chk=RUBPY1a > %mem=2Gb > %nproc=4 > #P B3LYP/Gen pseudo=read gfinput iop(6/7=3) scf=tight opt > integral(grid=ultrafine) Geom=Check Guess=Read > > [Ru(bpy)3]2+ (part 3) > > 2 1 > > > Ru 0 > LANL2DZ > **** > C N H 0 > 6-31G > **** > > Ru 0 > LANL2DZ > > --link1-- > %chk=RUBPY1a > %Nosave > %mem=2Gb > %nproc=4 > #P td=(singlet, Nstates=20 ) guess=read Geom=check > > [Ru(bpy)3]2+ (part 4) > > > > (b) OUTPUT----- > > > =================================================================================================================================== > Pseudopotential Parameters > > =================================================================================================================================== > Center Atomic Valence Angular Power > Coordinates > Number Number Electrons Momentum of R Exponent > Coefficient X Y Z > > =================================================================================================================================== > Unrecognized atomic symbol **** > Error termination via Lnk1e in /p5cecic/home/gaussian/g03/l301.exe at Fri > Nov 20 21:22:18 2009. > Job cpu time: 0 days 0 hours 0 minutes .9 seconds. > File lengths (MBytes): RWF= 39 Int= 0 D2E= 0 Chk= 22 > Scr= 2> > > --000e0cd3acf0d8602c04790db766 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
It looks like there is an extra line in the third step.=A0 There are t= wo blank lines=A0after the charge and multiplicity but there should be one.= =A0 You may also have to change that route section to integral=3D(grid=3Dul= trafine).
=A0
Patrick
=A0
--link1--
%chk=3DRUBPY1a
%mem=3D2Gb
%nproc=3D4
#P =A0B3LYP= /Gen pseudo=3Dread =A0gfinput iop(6/7=3D3) scf=3Dtight =A0opt =A0integral(g= rid=3Dultrafine) =A0Geom=3DCheck Guess=3DRead

[Ru(bpy)3]2+ =A0(part = 3)

2 1
<line>
<line>
Ru 0
LANL2DZ
****
C N H 0
6-31G
***= *

Ru 0
LANL2DZ



On Mon, Nov 23, 2009 at 11:34 AM, Cleophas Muhav= ini Wawire muhavini(~)yahoo.com <owner-chemistry:_:ccl= .net> wrote:

Sent to CCL by: "Cleoph= as Muhavini Wawire" [muhavini-.-yahoo.com]
Dear CCL Subscibers,
Could someone kindly help me to know why the third = step of this multi-step job fails. the first two steps were successful and = had normal termination.
The problem is with the third step. There is Unr= ecognized atomic symbol ****.
Precisely I am doing an optimization in three steps and then carry out a td= dft calculation in step four. The problem it seems is in using the GEN keyw= ord where the read basis set and its ECP are applied to the geometry read f= rom the checkpoint. How am I supposed to specify the Basis set and its ECP = after the Charge and multiplicity line? The are two parts in this Question = namely part (a) INPUT and Part (b) OUTPUT.

(a)INPUT
%chk=3DRUBPY1a
%mem=3D2Gb
%nproc=3D4
#P B3LYP/STO-= 3G gfinput iop(6/7=3D3) scf=3Dtight =A0opt integral(grid=3Dultrafine)
[Ru(bpy)3]2+ =A0(part 1)

2 1
=A0 Ru =A0 =A00.000000 =A0 =A00.00= 0000 =A0 =A00.000000
=A0 =A0N =A0 =A01.637655 =A0 =A00.788035 =A0 =A01.0= 46540
=A0 =A0N =A0 =A01.637655 =A0 -0.788035 =A0 -1.046540
=A0 =A0C =A0 =A02.8= 59124 =A0 =A00.449484 =A0 =A00.571137
=A0 =A0C =A0 =A01.548271 =A0 =A01.= 609776 =A0 =A02.097857
=A0 =A0C =A0 =A02.662250 =A0 =A02.124769 =A0 =A02= .727798
=A0 =A0C =A0 =A03.919291 =A0 =A01.790734 =A0 =A02.248252
=A0 = =A0C =A0 =A04.014758 =A0 =A00.948118 =A0 =A01.158544
=A0 =A0C =A0 =A02.859124 =A0 -0.449484 =A0 -0.571137
=A0 =A0C =A0 =A01.5= 48271 =A0 -1.609776 =A0 -2.097857
=A0 =A0C =A0 =A02.662250 =A0 -2.124769= =A0 -2.727798
=A0 =A0C =A0 =A03.919291 =A0 -1.790734 =A0 -2.248252
= =A0 =A0C =A0 =A04.014758 =A0 -0.948118 =A0 -1.158544
=A0 =A0H =A0 =A00.5= 35711 =A0 =A01.851838 =A0 =A02.435586
=A0 =A0H =A0 =A02.538391 =A0 =A02.789686 =A0 =A03.587166
=A0 =A0H =A0 = =A04.821855 =A0 =A02.189017 =A0 =A02.721122
=A0 =A0H =A0 =A04.993359 =A0= =A00.671879 =A0 =A00.757350
=A0 =A0H =A0 =A00.535711 =A0 -1.851838 =A0 = -2.435586
=A0 =A0H =A0 =A02.538391 =A0 -2.789686 =A0 -3.587166
=A0 = =A0H =A0 =A04.821855 =A0 -2.189017 =A0 -2.721122
=A0 =A0H =A0 =A04.993359 =A0 -0.671879 =A0 -0.757350
=A0 =A0N =A0 -0.136= 369 =A0 -1.812268 =A0 =A01.046540
=A0 =A0N =A0 -1.501286 =A0 -1.024233 = =A0 -1.046540
=A0 =A0C =A0 -1.040298 =A0 -2.700816 =A0 =A00.571137
= =A0 =A0C =A0 =A00.619971 =A0 -2.145730 =A0 =A02.097857
=A0 =A0C =A0 =A00= .508979 =A0 -3.367961 =A0 =A02.727798
=A0 =A0C =A0 -0.408825 =A0 -4.289573 =A0 =A02.248252
=A0 =A0C =A0 -1.186= 285 =A0 -3.950941 =A0 =A01.158544
=A0 =A0C =A0 -1.818826 =A0 -2.251332 = =A0 -0.571137
=A0 =A0C =A0 -2.168242 =A0 -0.535954 =A0 -2.097857
=A0 = =A0C =A0 -3.171229 =A0 -1.243192 =A0 -2.727798
=A0 =A0C =A0 -3.510466 = =A0 -2.498839 =A0 -2.248252
=A0 =A0C =A0 -2.828473 =A0 -3.002823 =A0 -1.158544
=A0 =A0H =A0 =A01.335= 883 =A0 -1.389858 =A0 =A02.435586
=A0 =A0H =A0 =A01.146743 =A0 -3.593154= =A0 =A03.587166
=A0 =A0H =A0 -0.515183 =A0 -5.270357 =A0 =A02.721122=A0 =A0H =A0 -1.914815 =A0 -4.660315 =A0 =A00.757350
=A0 =A0H =A0 -1.87= 1594 =A0 =A00.461980 =A0 -2.435586
=A0 =A0H =A0 -3.685134 =A0 -0.803468 =A0 -3.587166
=A0 =A0H =A0 -4.30667= 2 =A0 -3.081340 =A0 -2.721122
=A0 =A0H =A0 -3.078544 =A0 -3.988437 =A0 -= 0.757350
=A0 =A0N =A0 -1.501286 =A0 =A01.024233 =A0 =A01.046540
=A0 = =A0N =A0 -0.136369 =A0 =A01.812268 =A0 -1.046540
=A0 =A0C =A0 -1.818826 = =A0 =A02.251332 =A0 =A00.571137
=A0 =A0C =A0 -2.168242 =A0 =A00.535954 =A0 =A02.097857
=A0 =A0C =A0 -3.1= 71229 =A0 =A01.243192 =A0 =A02.727798
=A0 =A0C =A0 -3.510466 =A0 =A02.49= 8839 =A0 =A02.248252
=A0 =A0C =A0 -2.828473 =A0 =A03.002823 =A0 =A01.158= 544
=A0 =A0C =A0 -1.040298 =A0 =A02.700816 =A0 -0.571137
=A0 =A0C =A0= =A00.619971 =A0 =A02.145730 =A0 -2.097857
=A0 =A0C =A0 =A00.508979 =A0 =A03.367961 =A0 -2.727798
=A0 =A0C =A0 -0.4= 08825 =A0 =A04.289573 =A0 -2.248252
=A0 =A0C =A0 -1.186285 =A0 =A03.9509= 41 =A0 -1.158544
=A0 =A0H =A0 -1.871594 =A0 -0.461980 =A0 =A02.435586=A0 =A0H =A0 -3.685134 =A0 =A00.803468 =A0 =A03.587166
=A0 =A0H =A0 -4.= 306672 =A0 =A03.081340 =A0 =A02.721122
=A0 =A0H =A0 -3.078544 =A0 =A03.988437 =A0 =A00.757350
=A0 =A0H =A0 =A01= .335883 =A0 =A01.389858 =A0 -2.435586
=A0 =A0H =A0 =A01.146743 =A0 =A03.= 593154 =A0 -3.587166
=A0 =A0H =A0 -0.515183 =A0 =A05.270357 =A0 -2.72112= 2
=A0 =A0H =A0 -1.914815 =A0 =A04.660315 =A0 -0.757350

--link1--
%chk=3DRUBPY1a
%mem=3D2Gb
%nproc=3D4
#P B3LYP/3-21G = =A0gfinput iop(6/7=3D3) scf=3Dtight =A0opt integral(grid=3Dultrafine) =A0Ge= om=3DCheck Guess=3DRead

[Ru(bpy)3]2+ =A0(part 2)

2 1

-= -link1--
%chk=3DRUBPY1a
%mem=3D2Gb
%nproc=3D4
#P =A0B3LYP/Gen pseudo=3Dread =A0gfinput iop(6/= 7=3D3) scf=3Dtight =A0opt =A0integral(grid=3Dultrafine) =A0Geom=3DCheck Gue= ss=3DRead

[Ru(bpy)3]2+ =A0(part 3)

2 1


Ru 0
LAN= L2DZ
****
C N H 0
6-31G
****

Ru 0
LANL2DZ

--link1--
%chk=3DRUBPY1a
= %Nosave
%mem=3D2Gb
%nproc=3D4
#P td=3D(singlet, Nstates=3D20 ) gue= ss=3Dread Geom=3Dcheck

[Ru(bpy)3]2+ =A0(part 4)



(b) O= UTPUT-----

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D
=A0Pseudopotential Parameters
=A0=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D
=A0Center =A0 =A0 Atomic =A0 =A0 =A0Valence =A0 =A0 =A0Angular =A0 =A0 =A0P= ower =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Coordinates
=A0Number =A0 =A0 Nu= mber =A0 =A0 Electrons =A0 =A0 Momentum =A0 =A0 of R =A0 =A0 =A0Exponent = =A0 =A0 =A0 =A0Coefficient =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0X =A0 =A0 =A0 =A0= =A0 Y =A0 =A0 =A0 =A0 =A0 Z
=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D
=A0Unrecognized atomic symbol ****
=A0Error ter= mination via Lnk1e in /p5cecic/home/gaussian/g03/l301.exe at Fri Nov 20 21:= 22:18 2009.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A0 .9 seconds.
=A0Fi= le lengths (MBytes): =A0RWF=3D =A0 =A0 39 Int=3D =A0 =A0 =A00 D2E=3D =A0 = =A0 =A00 Chk=3D =A0 =A0 22 Scr=3D =A0 =A0 =A02



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--000e0cd3acf0d8602c04790db766-- From owner-chemistry@ccl.net Mon Nov 23 23:58:01 2009 From: "Thomas A. Manz thomasamanz(a)gmail.com" To: CCL Subject: CCL: dimensionless reaction coordinate Message-Id: <-40775-091123193203-28149-cjurB8JNzss1Ykx9cqOyPg*server.ccl.net> X-Original-From: "Thomas A. Manz" Date: Mon, 23 Nov 2009 19:32:00 -0500 Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com] An early transition state resembles the reactants more than the products, while a late transition state resembles the products more than the reactants. Several postulates in chemistry and catalysis require a quantitative measure of transition state lateness for their application. These include the Hammond-Leffler postulate, the structure sensitivity postulate, and the reactant sensitivity postulate. The Hammond-Leffler postulate is taught in several college textbooks, and Hammonds 1955 article describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has received more than three thousand citations. However, until now there was no universal method for quantifying transition state lateness from geometries along a minimum energy reaction pathway. A new method published in the Journal of Computational Chemistry describes a dimensionless reaction coordinate, W, that can be used to quantify the relative lateness of transition states. W varies monotonically from 0 (reactant) to 1 (product) along a minimum energy reaction pathway. Let WTS denote the dimensionless reaction coordinate of the transition state. When WTS < 0.5, the transition state is early. When WTS > 0.5, the transition state is late. When WTS = 0.5, the transition state is equidistant between reactants and products. This descriptor can be computed using only a series of optimized geometries (aka images) along the minimum energy reaction pathway. A minimum of three images (reactant, transition state, and product) is required, and there is no maximum in the number of images that can be used. Once optimized geometries along the minimum energy reaction pathway are known, the time for computing W is a small fraction of a second. (The equations for computing W of each image are simple algebraic equations.) A free program implementing the method is available at http://sourceforge.net/projects/drcs/ This type of analysis should be useful to those performing nudged elastic band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction coordinate (IRC) calculations. The method is applicable to both periodic and nonperiodic systems and can be used for reactions occuring in the gas-phase, in liquid-phase, in solids, or on surfaces. Link to the published abstract: http://www3.interscience.wiley.com/journal/122682417/abstract The article describes both the quantification of transition state lateness and its application to several postulates in chemistry and catalysis. Tom Manz thomasamanz [at] gmail.com