From owner-chemistry@ccl.net Sun Oct 16 03:19:01 2011 From: "Ol Ga eurisco1^^pochta.ru" To: CCL Subject: CCL:G: problem with IRC on G09 Message-Id: <-45648-111015174427-27193-Pw2N6q4E+lZQRme0ftyf7w[A]server.ccl.net> X-Original-From: "Ol Ga" Date: Sat, 15 Oct 2011 17:44:24 -0400 Sent to CCL by: "Ol Ga" [eurisco1===pochta.ru] Dear Sir/Madam, I tried to preforme IRC calculations with energy calculation by CASSCF method by means G09 A and B suite of programms. I have tried (sure after hessian calculation): irc(forward,rcfc,DVV,maxcycle=100,stepsize=30,maxpoints=50) irc(forward,rcfc,Euler,maxcycle=100,stepsize=30,maxpoints=50) irc(forward,rcfc,EulerPC,maxcycle=100,stepsize=30,maxpoints=50) irc(forward,rcfc,GradientOnly,maxcycle=100,stepsize=30,maxpoints=50) irc(forward,rcfc,LQA,maxcycle=100,stepsize=30,maxpoints=50) The error message is clear "GetSCM: Allocation for REFSC failed: Core=1015201808 Need=37033585213 GauSpace=1015201808 MaxMem=1966080000 Avail=1966080000." The same calculation passed on G03 D very smoothly. I would ask you please to suggest how to performe such calculation on G09? I don't see now what was missed. Sincerely, Ol Ga PS: Several lines before and with error message are below Number of configurations 157080 SME calculated on fly RWF file will be 16 Words long Len28= 16 LenMCI= 30. Enter MCSCF program. NO. OF ORBITALS =108 NO. OF CORE-ORBITALS = 10 NO. OF VALENCE-ORBITALS = 16 NO. OF VIRTUAL-ORBITALS = 82 USED ACCURACY IN CHECKING CONVERGENCE = 1.00D-05 Memory needed for Incore Integrals: 49823586 Memory needed for direct integral evaluation: 23324976 Integrals KEPT IN MEMORY IBUJAK length= 9169761 Integral file not found: evaluate integrals Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. First order MCSCF but last itn is Quadratic GetSCM: Allocation for REFSC failed: Core=1015201808 Need=37033585213 GauSpace=1015201808 MaxMem=1966080000 Avail=1966080000. Error termination via Lnk1e in /gpfs/CLUSTERUSERS/neilparker2/soft/g09/l510.exe at Fri Sep 9 08:31:26 2011. Job cpu time: 0 days 0 hours 2 minutes 5.7 seconds. File lengths (MBytes): RWF= 153 Int= 0 D2E= 0 Chk= 77 Scr= 1 From owner-chemistry@ccl.net Sun Oct 16 05:36:00 2011 From: "Sebastian Kozuch kozuchs^_^yahoo.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45649-111016050644-9691-7hp5WbYxH/MyEMAnEtHjsw%%server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="-1080416818-798398627-1318755958=:51864" Date: Sun, 16 Oct 2011 02:05:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs^^yahoo.com] ---1080416818-798398627-1318755958=:51864 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I like the idea of open software, and in principle I support=0Athe proposal= of having access to the software code for the possibility of full=0Areview= of a theoretical work. However, I feel that this is more wishful=0Athinkin= g than real scientific life.=0A=C2=A0=0ALet=E2=80=99s say that I receive a = manuscript for review that uses=0Aprogram X, which I may have access to its= code now (since I=E2=80=99m the reviewer). Do=0AI have to spend a week try= ing to understand its algorithms to check if the=0Afrequencies are correctl= y calculated? For me, most (if not all) the programs are=0Ain practice blac= k boxes, as I=E2=80=99m hardly a programmer. Therefore, open or closed=0Aso= ftware (usually) doesn=E2=80=99t make me any difference, except from a phil= osophical perspective.=0A=0A=C2=A0=0ANow, let me consider an analogy from e= xperimental chemistry.=0AI have to review a manuscript where the authors te= sted some compound with a 600=0AMHz NMR. My lab is much more humble, and I = only have access to a 400 MHz NMR.=0AId est, I cannot reproduce the results= of the paper that I=E2=80=99m reviewing. Is here=0Aany difference compared= to the theoretical case?=0A=C2=A0=0AI had in a couple of cases problems to= reproduce the results=0Aof papers, mostly because the authors didn=E2=80= =99t provide enough information.=0AHowever, for 100% reproducibility I need= 100% the same conditions (and a lot of=0Aresources and time). This makes t= he selection of the software just a small=0Aissue.=0A=C2=A0=0AI would like = to hear the thoughts of other people about this=0Aissue, as I consider the = peer reviewing process a very complex and far from=0Aperfect system.=0A=C2= =A0=0A=0A=0A=0A=0ASebastian=0A=0A=0A=0A________________________________=0AF= rom: Brian.James.Duke{:}gmail.com =0ATo: "Kozuch, = Sebastian " =0ASent: Friday, October 14, 2011 11= :18 PM=0ASubject: CCL: Science code manifesto=0A=0A=0AI just encountered th= e Science Code Manifesto, which essentially states=0Athat all computer code= used for scientific analysis and modeling should=0Abe available for review= . It appears to have started with the Climate=0ACode Foundation. I encour= age you to visit the web site and consider=0Aendorsing the Manifesto.=0A=0A= http://sciencecodemanifesto.org/=0A=0ANote that this is not specifying open= source code, so GAMESS(US),=0AGAMESS(UK), DALTON etc., as well as open sou= rce codes such as PSI3 amd=0AMPQC satisfies the points of the manifesto. Of= course some other quantum=0Achemistry codes do not. I think we should be p= utting pressure on the=0Aauthors of such codes to meet the criteria in this= manifesto.=0A=0ABrian. ---1080416818-798398627-1318755958=:51864 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A=0A
I like the idea of open software, and in principle I support=0Athe= proposal of having access to the software code for the possibility of full= =0Areview of a theoretical work. However, I feel that this is more wishful= =0Athinking than real scientific life.
=0A=0A
=  
=0A=0A
Let=E2=80=99s say that I receive= a manuscript for review that uses=0Aprogram X, which I may have access to = its code now (since I=E2=80=99m the reviewer). Do=0AI have to spend a week = trying to understand its algorithms to check if the=0Afrequencies are corre= ctly calculated? For me, most (if not all) the programs are=0Ain practice b= lack boxes, as I=E2=80=99m hardly a programmer. Therefore, open or closed= =0Asoftware (usually) doesn=E2=80=99t make me any difference, except from a= philosophical perspective.
=0A=0A
 <= /div>=0A=0A
Now, let me consider an analogy from ex= perimental chemistry.=0AI have to review a manuscript where the authors tes= ted some compound with a 600=0AMHz NMR. My lab is much more humble, and I o= nly have access to a 400 MHz NMR.=0AId est, I cannot reproduce the results = of the paper that I=E2=80=99m reviewing. Is here=0Aany difference compared = to the theoretical case?
=0A=0A
 
= =0A=0A
I had in a couple of cases problems to repro= duce the results=0Aof papers, mostly because the authors didn=E2=80=99t pro= vide enough information.=0AHowever, for 100% reproducibility I need 100% th= e same conditions (and a lot of=0Aresources and time). This makes the selec= tion of the software just a small=0Aissue.
=0A=0A
 
=0A=0A
I would like to hear the tho= ughts of other people about this=0Aissue, as I consider the peer reviewing = process a very complex and far from=0Aperfect system.
=0A=0A
 = ;



Sebastian

From: Brian.James.Du= ke{:}gmail.com <owner-chemistry(a)ccl.net>
To: "Kozuch, Sebastian " <kozuchs(a)yahoo.= com>
Sent: Friday, O= ctober 14, 2011 11:18 PM
Subject:<= /span> CCL: Science code manifesto

=0A
I just encountered the Science Code Manifesto, which essentially sta= tes
that all computer code used for scientific analysis and modeling sho= uld
be available for review. It appears to have started with the Climat= e
Code Foundation. I encourage you to visit the web site and considerendorsing the Manifesto.

http://sciencecodemanifesto.org/

N= ote that this is not specifying open source code, so GAMESS(US),
GAMESS(= UK), DALTON etc., as well as open source codes such as PSI3 amd
MPQC sat= isfies the points of the manifesto. Of course some other quantum
chemist= ry codes do not. I think we should be putting pressure on the
authors of= such codes to meet the criteria in this manifesto.

Brian.

=
---1080416818-798398627-1318755958=:51864-- From owner-chemistry@ccl.net Sun Oct 16 13:00:01 2011 From: "George B Fitzgerald gfitzgerald[-]accelrys.com" To: CCL Subject: CCL:G: opt=Z-matrix convergence problems in Gaussian Message-Id: <-45650-111016125858-23564-995VNH2IwKtpkFCtZ9G9Zw-.-server.ccl.net> X-Original-From: "George B Fitzgerald" Date: Sun, 16 Oct 2011 12:58:55 -0400 Sent to CCL by: "George B Fitzgerald" [gfitzgerald : accelrys.com] I dont know specifically about Gaussian, but I've seen energy bouncing between 2 values in other applications. In the cases I've seen, it was oscillating between 2 nearly degenerate states. It sounds like you were ok when you started the optimization, and then the geometry found a spot on the potential energy surface where these 2 states are near degenerate. I solved my problem by going to an open-shell calculation, which resulted in a lower energy and no more oscillation. If you're currently running closed shell, you might try that. -george -----Original Message----- Sent to CCL by: Tanja van Mourik [tanja.vanmourik]=[st-andrews.ac.uk] Hi All, We are trying to optimise a cluster consisting of ~50 molecules with M06-L with Gaussian 09. We are using Opt=Z-matrix, as optimisation in redundant internal coordinates does not work ("Error in internal coordinate system"). With Opt=Z-matrix, the energy appears to converge nicely up to 100 cycles, but after that the energy starts to oscillate wildly. This happens always after 100 cycles. Does anyone know why this is, and how to solve this problem? Currently we restrict MaxCycle to 100, and restart the calculation repeatedly (it needs many hundreds of optimisation cycles to converge, particularly with Opt=Z-matrix), but I am hoping for a better solution. Any ideas? Best wishes, Tanja From owner-chemistry@ccl.net Sun Oct 16 13:53:01 2011 From: "Sergio Manzetti sergio.manzetti * gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45651-111016135234-11552-SCGD2TGrDVTtUWtLMgZpKg:server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=bcaec501c1042a7d7604af6e2732 Date: Sun, 16 Oct 2011 19:52:25 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti|a|gmail.com] --bcaec501c1042a7d7604af6e2732 Content-Type: text/plain; charset=ISO-8859-1 I agree with Sebastian, what is so "open" about closing open source into a manifesto? Sergio On Fri, Oct 14, 2011 at 11:18 PM, Brian.James.Duke{:}gmail.com < owner-chemistry---ccl.net> wrote: > I just encountered the Science Code Manifesto, which essentially states > that all computer code used for scientific analysis and modeling should > be available for review. It appears to have started with the Climate > Code Foundation. I encourage you to visit the web site and consider > endorsing the Manifesto. > > http://sciencecodemanifesto.org/ > > Note that this is not specifying open source code, so GAMESS(US), > GAMESS(UK), DALTON etc., as well as open source codes such as PSI3 amd > MPQC satisfies the points of the manifesto. Of course some other quantum > chemistry codes do not. I think we should be putting pressure on the > authors of such codes to meet the criteria in this manifesto. > > Brian. --bcaec501c1042a7d7604af6e2732 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I agree with Sebastian, what is so "open&qu= ot; about closing open source into a manifesto?

Sergio




On Fri, Oct 14, 2011 at 11:18 PM, Brian.James.Duke{:}gmail.com <owner-che= mistry---ccl.net> wrote:
I just encountered the Science Code Manifest= o, which essentially states
that all computer code used for scientific a= nalysis and modeling should
be available for review. It appears to have started with the Climate
Co= de Foundation. I encourage you to visit the web site and consider
endor= sing the Manifesto.

http://sciencecodemanifesto.org/

Note that this is not specifying open source code, so GAMESS(US),
GA= MESS(UK), DALTON etc., as well as open source codes such as PSI3 amd
MPQ= C satisfies the points of the manifesto. Of course some other quantum
chemistry codes do not. I think we should be putting pressure on the
aut= hors of such codes to meet the criteria in this manifesto.

Brian.


--bcaec501c1042a7d7604af6e2732-- From owner-chemistry@ccl.net Sun Oct 16 17:46:00 2011 From: "Brian Salter-Duke brian.james.duke.:.gmail.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45652-111016173325-5959-RVlRAt0zcyeFo2uBfJ3XHQ###server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 17 Oct 2011 08:33:15 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke(~)gmail.com] The review of manuscripts by referees prior to publication is just a small part of what this is all about. The main point is about proper review by the scientific community after publication. There, while not everyone has access to a 600MHz NMR or has paid to get Gaussian, some people in the community will have. The guys who paid for Gaussian however, may not have bought the code and in some cases, it is impossible to buy the code, as they are commercial secrets. This manifesto is saying that commercial secrets are not compatible with good science. Of course the need to this kind of review is not common, but if there are real concerns about the work, it is necessary that the scientific community can look seriously at the code to see exactly what the program is doing. Brian. On Sun, Oct 16, 2011 at 8:05 PM, Sebastian Kozuch kozuchs^_^yahoo.com wrote: > I like the idea of open software, and in principle I support the proposal of > having access to the software code for the possibility of full review of a > theoretical work. However, I feel that this is more wishful thinking than > real scientific life. > > Let’s say that I receive a manuscript for review that uses program X, which > I may have access to its code now (since I’m the reviewer). Do I have to > spend a week trying to understand its algorithms to check if the frequencies > are correctly calculated? For me, most (if not all) the programs are in > practice black boxes, as I’m hardly a programmer. Therefore, open or closed > software (usually) doesn’t make me any difference, except from a > philosophical perspective. > > Now, let me consider an analogy from experimental chemistry. I have to > review a manuscript where the authors tested some compound with a 600 MHz > NMR. My lab is much more humble, and I only have access to a 400 MHz NMR. Id > est, I cannot reproduce the results of the paper that I’m reviewing. Is here > any difference compared to the theoretical case? > > I had in a couple of cases problems to reproduce the results of papers, > mostly because the authors didn’t provide enough information. However, for > 100% reproducibility I need 100% the same conditions (and a lot of resources > and time). This makes the selection of the software just a small issue. > > I would like to hear the thoughts of other people about this issue, as I > consider the peer reviewing process a very complex and far from perfect > system. > > > > > Sebastian > > ________________________________ > From: Brian.James.Duke{:}gmail.com > To: "Kozuch, Sebastian " > Sent: Friday, October 14, 2011 11:18 PM > Subject: CCL: Science code manifesto > > I just encountered the Science Code Manifesto, which essentially states > that all computer code used for scientific analysis and modeling should > be available for review. It appears to have started with the Climate > Code Foundation. I encourage you to visit the web site and consider > endorsing the Manifesto. > > http://sciencecodemanifesto.org/ > > Note that this is not specifying open source code, so GAMESS(US), > GAMESS(UK), DALTON etc., as well as open source codes such as PSI3 amd > MPQC satisfies the points of the manifesto. Of course some other quantum > chemistry codes do not. I think we should be putting pressure on the > authors of such codes to meet the criteria in this manifesto. > > Brian. > > -- Brian Salter-Duke (aka Brian Duke) Brian.James.Duke-x-gmail.com From owner-chemistry@ccl.net Sun Oct 16 18:20:01 2011 From: "Sergio Manzetti sergio.manzetti(_)gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45653-111016134949-3629-OenTPwSdQbDjvZ4Tm3BsSQ,server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf307c9b2666555604af6e1da0 Date: Sun, 16 Oct 2011 19:49:41 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti++gmail.com] --20cf307c9b2666555604af6e1da0 Content-Type: text/plain; charset=ISO-8859-1 I agree with Sebastian, what is so "open" about closing open source into a manifesto? I was even more surprised that Google put their signature on that manifesto, a company who endorses free openness in information flow. Sergio On Fri, Oct 14, 2011 at 11:18 PM, Brian.James.Duke{:}gmail.com < owner-chemistry~~ccl.net> wrote: > I just encountered the Science Code Manifesto, which essentially states > that all computer code used for scientific analysis and modeling should > be available for review. It appears to have started with the Climate > Code Foundation. I encourage you to visit the web site and consider > endorsing the Manifesto. > > http://sciencecodemanifesto.org/ > > Note that this is not specifying open source code, so GAMESS(US), > GAMESS(UK), DALTON etc., as well as open source codes such as PSI3 amd > MPQC satisfies the points of the manifesto. Of course some other quantum > chemistry codes do not. I think we should be putting pressure on the > authors of such codes to meet the criteria in this manifesto. > > Brian. --20cf307c9b2666555604af6e1da0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I agree with Sebastian, what is so "ope= n" about closing open source into a manifesto? I was=A0 even more surp= rised that Google put their signature on that manifesto, a company who endo= rses free openness in information flow.

Sergio




On Fri, Oct 14, 2011 at 11:18 PM, Brian.James.Duke{:}gmail.com <owner-che= mistry~~ccl.net> wrote:
I just encountered the Science Code Manifest= o, which essentially states
that all computer code used for scientific a= nalysis and modeling should
be available for review. It appears to have started with the Climate
Co= de Foundation. I encourage you to visit the web site and consider
endor= sing the Manifesto.

http://sciencecodemanifesto.org/

Note that this is not specifying open source code, so GAMESS(US),
GA= MESS(UK), DALTON etc., as well as open source codes such as PSI3 amd
MPQ= C satisfies the points of the manifesto. Of course some other quantum
chemistry codes do not. I think we should be putting pressure on the
aut= hors of such codes to meet the criteria in this manifesto.

Brian.




--20cf307c9b2666555604af6e1da0-- From owner-chemistry@ccl.net Sun Oct 16 18:55:00 2011 From: "Sergio Manzetti sergio.manzetti++gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45654-111016134550-30046-iXH4V+QaTDAONuI3Y3NDpw,server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf3079bc9e21f10104af6e0f75 Date: Sun, 16 Oct 2011 19:45:41 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti,gmail.com] --20cf3079bc9e21f10104af6e0f75 Content-Type: text/plain; charset=ISO-8859-1 I agree with Sebastian, what is so "open" about closing open source into a manifesto? I was even more surprised that Google put their signature on that manifesto, a company who endorses free openness in information flow. Sergio On Fri, Oct 14, 2011 at 11:18 PM, Brian.James.Duke{:}gmail.com < owner-chemistry:-:ccl.net> wrote: > I just encountered the Science Code Manifesto, which essentially states > that all computer code used for scientific analysis and modeling should > be available for review. It appears to have started with the Climate > Code Foundation. I encourage you to visit the web site and consider > endorsing the Manifesto. > > http://sciencecodemanifesto.org/ > > Note that this is not specifying open source code, so GAMESS(US), > GAMESS(UK), DALTON etc., as well as open source codes such as PSI3 amd > MPQC satisfies the points of the manifesto. Of course some other quantum > chemistry codes do not. I think we should be putting pressure on the > authors of such codes to meet the criteria in this manifesto. > > Brian. --20cf3079bc9e21f10104af6e0f75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I agree with Sebastian, what is so "open" about closing open sour= ce into a manifesto? I was=A0 even more surprised that Google put their sig= nature on that manifesto, a company who endorses free openness in informati= on flow.

Sergio



On Fri, Oct 14, 2011 a= t 11:18 PM, Brian.James.Duke{:}gmail.com <= span dir=3D"ltr"><owner-chemi= stry:-:ccl.net> wrote:
I just encountered the Science Code Manifes= to, which essentially states
that all computer code used for scientific = analysis and modeling should
be available for review. It appears to have started with the Climate
Co= de Foundation. I encourage you to visit the web site and consider
endor= sing the Manifesto.

http://sciencecodemanifesto.org/

Note that this is not specifying open source code, so GAMESS(US),
GA= MESS(UK), DALTON etc., as well as open source codes such as PSI3 amd
MPQ= C satisfies the points of the manifesto. Of course some other quantum
chemistry codes do not. I think we should be putting pressure on the
aut= hors of such codes to meet the criteria in this manifesto.

Brian.


--20cf3079bc9e21f10104af6e0f75--