From owner-chemistry@ccl.net Wed Jun 25 02:05:00 2008 From: "Ralf Tonner ralf.tonner : googlemail.com" To: CCL Subject: CCL: WATOC 2008, Satellite Meeting in Auckland/New Zealand Message-Id: <-37249-080624195202-30960-p6aXGvYBHq/1KgFeroNVtA(-)server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 25 Jun 2008 11:51:36 +1200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [ralf.tonner ~ googlemail.com] Dear CCL'ers, there will be a satellite meeting to the WATOC 2008 titled "Beyond the non-relativistic Schroedinger equation - from the Dirac-equation to electroweak theory" It brings together the experts in the field of relativistic quantum chemistry, quantum electrodynamic effects and electroweak interactions in molecules and the solid state with particular applications to heavy and superheavy element chemistry. The meeting will be held in Auckland/New Zealand from September 10 - September 13 2008 enabling a smooth connection to the main conference starting in Sydney at September 14 (www.watoc2008.com). Registration is now open with prices ranging from 500NZ$ (~380 US$) for the conference package to 1100NZ$ (~830 US$) including accomodation and conference dinner. Several internationally renowned speakers confirmed their participation already and there are a few slots left for short talks. Additionally a poster session is scheduled. The deadline for the submission of contributions is July 11 2008. For further details please refer to our website: http://ctcp.massey.ac.nz/satellite.html Please direct all enquiries about the programme, application for talks/posters or registration to Peter Schwerdtfeger (P.A.Schwerdtfeger[-]massey.ac.nz), Matthias Lein (m.lein[-]massey.ac.nz) or Ralf Tonner (r.e.tonner[-]massey.ac.nz). Hope to see you in Auckland soon! In behalf of the organisation team Ralf. -- Dr. Ralf Tonner Centre of Theoretical Chemistry and Physics New Zealand Institute for Advanced Study Massey University Auckland NEW ZEALAND Phone (64) 09 414 0800 extn 9894 Fax (64) 09 443 9779 ---- From owner-chemistry@ccl.net Wed Jun 25 04:24:01 2008 From: "Ol Ga eurisco1=-=pochta.ru" To: CCL Subject: CCL:G: error in CCSD calculation Message-Id: <-37250-080625040854-12569-/e5e4SZzl+iOtqjkKKcycA*o*server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 25 Jun 2008 04:08:50 -0400 Sent to CCL by: "Ol Ga" [eurisco1],[pochta.ru] Hello All, I get very tenacious error in Gaussian (C02) calculation optimization CCSD/6-311+G(2d). If the level is CCSD/6-311G*, the calculation is successfully terminated. input (route section): #P uccsd(T1diag)/6-311+G(2d) NoSymm opt=(maxcycle=300,Tight,gDIIS) # scf=(xqc,tight,maxcycle=512) output (end) ------------.. Coupled Cluster theory with single and double substitutions =========================================================== Iterations= 50 Convergence= 0.100D-07 Iteration Nr. 1 ********************** Erroneous write. write -1 instead of -1472711800. <- There are different values.Its one example. fd = 8 writwa If it is needed, You can see additional output below. Would You help me to treat or bypass the bug (error)? I get similar bug in MP2 calculation if it is bigger than other on different PC, OS and different releases of Gaussian 03. Comments are highly appreciated. Thank you very much in advance. Sincerely, Ol Ga Open-shell transformation, MDV= 353894400 ITran=7 ISComp=1. Estimate disk for full transformation 627907874 words. Compute canonical integrals, LenV= 121927117. 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. Compute canonical integrals, LenV= 121927117. Spin components of T(2) and E(2): alpha-alpha T2 = 0.5239031443D-01 E2= -0.1729961232D+00 alpha-beta T2 = 0.2728778731D+00 E2= -0.9124275297D+00 beta-beta T2 = 0.5239031443D-01 E2= -0.1729961232D+00 ANorm= 0.1173736982D+01 E2= -0.1258419776D+01 EUMP2= -0.40938885429741D+03 (S**2,0)= 0.00000D+00 (S**2,1)= 0.00000D+00 E(PUHF)= -0.40813043452D+03 E(PMP2)= -0.40938885430D+03 Leave Link 804 at Tue Jun 24 17:54:45 2008, MaxMem= 353894400 cpu: 550.5 (Enter /bin/g03/l913.exe) CIDS: MDV= 353894400. Using original routines for 1st iteration, S=T. Using DD4UQ or CC4UQ for 2nd and later iterations. Coupled Cluster theory with single and double substitutions =========================================================== Iterations= 50 Convergence= 0.100D-07 Iteration Nr. 1 ********************** Erroneous write. write -1 instead of -1472711800. fd = 8 writwa From owner-chemistry@ccl.net Wed Jun 25 06:13:00 2008 From: "Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37251-080625061047-19087-g5ekSJORNpPB41zw5oZ2EA%x%server.ccl.net> X-Original-From: Alberto Sergio Garay Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 25 Jun 2008 07:10:33 -0300 MIME-Version: 1.0 Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar] Hi Don That's the problem. There is not any defined variable with these names =20 (rsolv, asolv) in any ".i" files. I have downloaded the source tinker's files many times to check their =20 number and sizes and I have not found any problem with this yet. If you have any idea to try please let me know. Sergio --=20 Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol=F3gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 Mensaje escrito por: "Don Steiger sd00_2002=3D=3D=3Dyahoo.com" =20 : > It sounds like a problem with a ".i" file. Use grep (or egrep) to =20 > find where these variable are defined and allocated. E.g. egrep =20 > "variable name" *.i > > --- On Tue, 6/24/08, Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar =20 > wrote: >> From: Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar =20 >> > Subject: CCL: Problem compiling tinker binaries.... > To: "Steiger, Don " > Date: Tuesday, June 24, 2008, 5:06 AM > > Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar] > Hi > > My name is Sergio Garay and I've been trying to compile the tinkers > binaries without success. I'm working in a linux system (redhat 9.0) > with ifort compiler. I run firstly the script debug.make in order to > find some trouble and I got many errors like these: (Am I doing > something wrong? > > > fortcom: Error: analyze.f, line 1581: This name does not have a type, > and must have an explicit type. [RSOLV] > write (iout,480) k,i,rsolv(i),asolv(i) > .....................................^ > fortcom: Error: analyze.f, line 1581: This name does not have a type, > and must have an explicit type. [ASOLV] > write (iout,480) k,i,rsolv(i),asolv(i) > ..............................................^ > compilation aborted for analyze.f (code 1) > fortcom: Error: born.f, line 74: This name does not have a type, and > must have an explicit type. [RSOLV] > roff(i) =3D rsolv(i) + doffset > ...................^ > fortcom: Error: born.f, line 74: This name does not have a type, and > must have an explicit type. [DOFFSET] > roff(i) =3D rsolv(i) + doffset > ..............................^ > fortcom: Error: born.f, line 79: This name does not have a type, and > must have an explicit type. [SOLVTYP] > if (solvtyp .eq. 'ONION') then > ..........^ > fortcom: Error: born.f, line 104: This name has not been declared as > an array or a function. [RBORN] > rborn(i) =3D 1.0d0 / total > ............^ > fortcom: Error: born.f, line 115: This name does not have a type, and > must have an explicit type. [P5] > p5inv =3D 1.0d0 / p5 > .........................^ > > Any help will be appreciated. > > > -- > Dr. Sergio Garay > Facultad de Bioquimica y Cs. Biol=F3gicas > Universidad Nacional del Litoral > Santa Fe - Argentina > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA > Argentina > Ph. +54 (342) 4575-213 > Fax. +54 (342) 4575-221 > > > > -=3D This is automatically added to each message by the mailing script =20 > =20 > =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem= istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > From owner-chemistry@ccl.net Wed Jun 25 08:15:00 2008 From: "Cenk Selcuki cselcuki+*+yahoo.com" To: CCL Subject: CCL:G: error in CCSD calculation Message-Id: <-37252-080625065152-6058-y0D4BI40JjXGfxSJOgfOcA===server.ccl.net> X-Original-From: Cenk Selcuki Content-Type: text/plain; charset=us-ascii Date: Wed, 25 Jun 2008 02:51:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Cenk Selcuki [cselcuki||yahoo.com] Hi, This error usually indicates that disk space is full and not sufficient for your calculation. Cheers, Cenk --- On Wed, 6/25/08, Ol Ga eurisco1=-=pochta.ru wrote: > From: Ol Ga eurisco1=-=pochta.ru > Subject: CCL:G: error in CCSD calculation > To: "Selcuki, Cenk " > Date: Wednesday, June 25, 2008, 1:08 AM > Sent to CCL by: "Ol Ga" [eurisco1],[pochta.ru] > Hello All, > > I get very tenacious error in Gaussian (C02) calculation > optimization CCSD/6-311+G(2d). If the level is > CCSD/6-311G*, the calculation is successfully terminated. > > input (route section): > #P uccsd(T1diag)/6-311+G(2d) NoSymm > opt=(maxcycle=300,Tight,gDIIS) > # scf=(xqc,tight,maxcycle=512) > > output (end) > ------------.. > Coupled Cluster theory with single and double substitutions > > =========================================================== > Iterations= 50 Convergence= 0.100D-07 > Iteration Nr. 1 > ********************** > Erroneous write. write -1 instead of -1472711800. <- > There are different values.Its one example. > fd = 8 > writwa > > If it is needed, You can see additional output below. > Would You help me to treat or bypass the bug (error)? I get > similar bug in MP2 calculation if it is bigger than other on > different PC, OS and different releases of Gaussian 03. > > Comments are highly appreciated. Thank you very much in > advance. > Sincerely, > Ol Ga > > > Open-shell transformation, MDV= 353894400 ITran=7 > ISComp=1. > Estimate disk for full transformation 627907874 words. > Compute canonical integrals, LenV= 121927117. > 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. > Compute canonical integrals, LenV= 121927117. > Spin components of T(2) and E(2): > alpha-alpha T2 = 0.5239031443D-01 E2= > -0.1729961232D+00 > alpha-beta T2 = 0.2728778731D+00 E2= > -0.9124275297D+00 > beta-beta T2 = 0.5239031443D-01 E2= > -0.1729961232D+00 > ANorm= 0.1173736982D+01 > E2= -0.1258419776D+01 EUMP2= > -0.40938885429741D+03 > (S**2,0)= 0.00000D+00 (S**2,1)= 0.00000D+00 > E(PUHF)= -0.40813043452D+03 E(PMP2)= > -0.40938885430D+03 > Leave Link 804 at Tue Jun 24 17:54:45 2008, MaxMem= > 353894400 cpu: 550.5 > (Enter /bin/g03/l913.exe) > CIDS: MDV= 353894400. > Using original routines for 1st iteration, S=T. > Using DD4UQ or CC4UQ for 2nd and later iterations. > Coupled Cluster theory with single and double > substitutions > > =========================================================== > Iterations= 50 Convergence= 0.100D-07 > Iteration Nr. 1 > ********************** > Erroneous write. write -1 instead of -1472711800. > fd = 8 > writwa > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the ,, sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search) From owner-chemistry@ccl.net Wed Jun 25 08:49:01 2008 From: "Antonio G De Crisci antonio.decrisci###utoronto.ca" To: CCL Subject: CCL:G: Fluorescence: determination of Quantum Yield/efficiency Message-Id: <-37253-080625081334-25942-i9OKTMeMop7+Q38KC5/xaA ~~ server.ccl.net> X-Original-From: "Antonio G De Crisci" Date: Wed, 25 Jun 2008 08:13:30 -0400 Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci(!)utoronto.ca] Hello All, I would like to be able to calculate the quantum yield or quantum efficiency of molecules. Would it be possible to do this using Gaussian 03W or PC GAMESS? I presume it may have involve a TD-DFT (or TDHF) calculation but im not exactly sure. Thanks for time, Anthony From owner-chemistry@ccl.net Wed Jun 25 09:25:02 2008 From: "Breton, Gary gbreton ~ berry.edu" To: CCL Subject: CCL:G: [SPAM] - CCL:G: error in CCSD calculation - Bayesian Filter detected spam Message-Id: <-37254-080625090233-21917-UZ1Z/jtBPM1r/gwErsUHWQ===server.ccl.net> X-Original-From: "Breton, Gary" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 25 Jun 2008 08:58:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Breton, Gary" [gbreton . berry.edu] This suggests the scratch directory is full. I had the same problem = after a few of my calculations terminated prematurely, in which case = Gaussian does not eliminate the temp files. Each of these temp files = can take up many GB of space easily and quickly fill a directory. I'd = check to make sure that's not the problem (and if running in parallel, = make sure you check each slave). Good luck, Gary Breton -----Original Message----- > From: Ol Ga eurisco1=3D-=3Dpochta.ru [mailto:owner-chemistry]_[ccl.net] Sent: Wed 6/25/2008 4:08 AM To: Breton, Gary Subject: [SPAM] - CCL:G: error in CCSD calculation - Bayesian Filter = detected spam =20 Sent to CCL by: "Ol Ga" [eurisco1],[pochta.ru] Hello All, I get very tenacious error in Gaussian (C02) calculation optimization = CCSD/6-311+G(2d). If the level is CCSD/6-311G*, the calculation is = successfully terminated. input (route section): #P uccsd(T1diag)/6-311+G(2d) NoSymm opt=3D(maxcycle=3D300,Tight,gDIIS)=20 # scf=3D(xqc,tight,maxcycle=3D512) output (end) ------------.. Coupled Cluster theory with single and double substitutions = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D Iterations=3D 50 Convergence=3D 0.100D-07 Iteration Nr. 1 ********************** Erroneous write. write -1 instead of -1472711800. <- There are different = values.Its one example. fd =3D 8 writwa If it is needed, You can see additional output below. Would You help me to treat or bypass the bug (error)? I get similar bug = in MP2 calculation if it is bigger than other on different PC, OS and = different releases of Gaussian 03. Comments are highly appreciated. Thank you very much in advance.=20 Sincerely, Ol Ga Open-shell transformation, MDV=3D 353894400 ITran=3D7 ISComp=3D1. Estimate disk for full transformation 627907874 words. Compute canonical integrals, LenV=3D 121927117. Symmetry not used in FoFDir. MinBra=3D 0 MaxBra=3D 2 Meth=3D 1. IRaf=3D 0 NMat=3D 1 IRICut=3D 1 DoRegI=3DT DoRafI=3DF = ISym2E=3D 0 JSym2E=3D0. Compute canonical integrals, LenV=3D 121927117. Spin components of T(2) and E(2): alpha-alpha T2 =3D 0.5239031443D-01 E2=3D = -0.1729961232D+00 alpha-beta T2 =3D 0.2728778731D+00 E2=3D = -0.9124275297D+00 beta-beta T2 =3D 0.5239031443D-01 E2=3D = -0.1729961232D+00 ANorm=3D 0.1173736982D+01 E2=3D -0.1258419776D+01 EUMP2=3D -0.40938885429741D+03 (S**2,0)=3D 0.00000D+00 (S**2,1)=3D 0.00000D+00 E(PUHF)=3D -0.40813043452D+03 E(PMP2)=3D = -0.40938885430D+03 Leave Link 804 at Tue Jun 24 17:54:45 2008, MaxMem=3D 353894400 cpu: = 550.5 (Enter /bin/g03/l913.exe) CIDS: MDV=3D 353894400. Using original routines for 1st iteration, S=3DT. Using DD4UQ or CC4UQ for 2nd and later iterations. Coupled Cluster theory with single and double substitutions = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D Iterations=3D 50 Convergence=3D 0.100D-07 Iteration Nr. 1 ********************** Erroneous write. write -1 instead of -1472711800. fd =3D 8 writwa -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jun 25 10:14:01 2008 From: "Wolfram Altenhofen wolfram]|[chemcomp.com" To: CCL Subject: CCL: CCG Announces MOE Training Courses Message-Id: <-37255-080625100728-2557-gNa1hYU4jITGcxJu+zslug-.-server.ccl.net> X-Original-From: "Wolfram Altenhofen" Date: Wed, 25 Jun 2008 10:07:24 -0400 Sent to CCL by: "Wolfram Altenhofen" [wolfram.:.chemcomp.com] Chemical Computing Group is pleased to annouce two 2-day MOE training courses offered during July 2008 and one 3-day course in August 2008: July 10th & 11th 2008 hosted by the University of Torino, Italy July 17th & 18th 2008 hosted by the University of Wrzburg, Germany, and August 5th - 7th 2008 hosted by the University of Braunschweig, Germany. The courses will cover * Basic Introduction to MOE * Applications: QSAR / Library Design * Applications: Protein Modeling * Applications: Structure Based Design & PH4 Modeling * Basic Introduction to the Scientific Vector Language (SVL) The course in Braunschweig will also cover advanced SVL topics including interfacing with pipelining tools on the third day. The courses are free of charge, refreshments are included; food and accommodation have to be organized and covered individually. Please note that there will also be an extended option for training for existing customers following the upcoming UGM in Cambridge in October. Should you feel that someone else in your group would be more interested but may not have received this mail, please feel free to forward. For further questions and to register please contact Tracey Nixon (tnixon|*|chemcomp.com or +44 1223 422319) at the Cambridge office. We look forward to welcoming you, Dr. Wolfram Altenhofen Director of Scientific Services Chemical Computing Group AG Kaiser-Wilhelm-Ring 11 50672 Kln Germany From owner-chemistry@ccl.net Wed Jun 25 10:48:00 2008 From: "Sahan Thanthiriwatte sahanchem%%gmail.com" To: CCL Subject: CCL: Generation of grid points for ESP calculations Message-Id: <-37256-080625101651-7776-36J60Oh/S1tPiepZrCIv0Q##server.ccl.net> X-Original-From: "Sahan Thanthiriwatte" Date: Wed, 25 Jun 2008 10:16:48 -0400 Sent to CCL by: "Sahan Thanthiriwatte" [sahanchem-$-gmail.com] Dear CCL'ers I am calculating class III type molecular electrostatic potentials (MEP). How do you generate coordinates (grid) in order to calculate these point charges? How do we assign coordinates around each atom in the molecule without overlapping each other? As I read, in order to eliminate conformational errors you need to have 1000 2000 point per atom. I am looking forward to hearing from you. Thank you. Regards, -Sahan- From owner-chemistry@ccl.net Wed Jun 25 11:24:01 2008 From: "Rodrigo Casasnovas rodrigo.casasnovas|*|gmail.com" To: CCL Subject: CCL:G: error in CCSD calculation Message-Id: <-37257-080625063323-28641-aQUa0IikKpJmmXOjpmUtZw/./server.ccl.net> X-Original-From: "Rodrigo Casasnovas" Date: Wed, 25 Jun 2008 06:33:19 -0400 Sent to CCL by: "Rodrigo Casasnovas" [rodrigo.casasnovas~!~gmail.com] Hello Ol Ga, Coupled Cluster calculations in G03 require a lot of physic (hard disk) memory, when you get an error like "Erroneous write. write -1 instead of -1472711800" you should clean up your scratch directory. If it isn't the solution and you are calculating on a supercomputer with a queue system, try to launch the job on a queue with more hard disk resources. In MP2 calculations wit G03, the default algorithm for producing integrals on disk is in-core or semi-direct, most of the times the program decides wrong and takes up the full hard disk memory, in order to avoid this, you can use de keyword MaxDisk. For example: MP2(MaxDisk=150GB)/6-311+G(2d) I hope you to be successful, Rodrigo Casasnovas > "Ol Ga eurisco1=-=pochta.ru" wrote: > > Sent to CCL by: "Ol Ga" [eurisco1],[pochta.ru] > Hello All, > > I get very tenacious error in Gaussian (C02) calculation optimization CCSD/6-311+G(2d). If the level is CCSD/6-311G*, the calculation is successfully terminated. > > input (route section): > #P uccsd(T1diag)/6-311+G(2d) NoSymm opt=(maxcycle=300,Tight,gDIIS) > # scf=(xqc,tight,maxcycle=512) > > output (end) > ------------.. > Coupled Cluster theory with single and double substitutions > =========================================================== > Iterations= 50 Convergence= 0.100D-07 > Iteration Nr. 1 > ********************** > Erroneous write. write -1 instead of -1472711800. <- There are different values.Its one example. > fd = 8 > writwa > > If it is needed, You can see additional output below. > Would You help me to treat or bypass the bug (error)? I get similar bug in MP2 calculation if it is bigger than other on different PC, OS and different releases of Gaussian 03. > > Comments are highly appreciated. Thank you very much in advance. > Sincerely, > Ol Ga > > > Open-shell transformation, MDV= 353894400 ITran=7 ISComp=1. > Estimate disk for full transformation 627907874 words. > Compute canonical integrals, LenV= 121927117. > 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. > Compute canonical integrals, LenV= 121927117. > Spin components of T(2) and E(2): > alpha-alpha T2 = 0.5239031443D-01 E2= -0.1729961232D+00 > alpha-beta T2 = 0.2728778731D+00 E2= -0.9124275297D+00 > beta-beta T2 = 0.5239031443D-01 E2= -0.1729961232D+00 > ANorm= 0.1173736982D+01 > E2= -0.1258419776D+01 EUMP2= -0.40938885429741D+03 > (S**2,0)= 0.00000D+00 (S**2,1)= 0.00000D+00 > E(PUHF)= -0.40813043452D+03 E(PMP2)= -0.40938885430D+03 > Leave Link 804 at Tue Jun 24 17:54:45 2008, MaxMem= 353894400 cpu: 550.5 > (Enter /bin/g03/l913.exe) > CIDS: MDV= 353894400. > Using original routines for 1st iteration, S=T. > Using DD4UQ or CC4UQ for 2nd and later iterations. > Coupled Cluster theory with single and double substitutions > =========================================================== > Iterations= 50 Convergence= 0.100D-07 > Iteration Nr. 1 > ********************** > Erroneous write. write -1 instead of -1472711800. > fd = 8 > writwa > > From owner-chemistry@ccl.net Wed Jun 25 12:06:01 2008 From: "Alcides Simao alsimao[#]gmail.com" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37258-080625101822-9601-Lge8lSrXj4NA/Gnw9Ft6Vw a server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_10397_29472059.1214403485988" Date: Wed, 25 Jun 2008 15:18:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao++gmail.com] ------=_Part_10397_29472059.1214403485988 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Alberto, The TINKER project has been frozen for about 4 years. There hasn't been any news, binaries, patches, whatsoever, from TINKER. I recommend you to switch to on of this: - Vega ZZ ( http://www.ddl.unimi.it/vega/index_noanim.htm ) -GROMACS ( http://www.gromacs.org/ ) There are some other software, but this two are very good programs, and still evolving! Best, Alcides 2008/6/25 Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar < owner-chemistry-.-ccl.net>: > > Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar] > Hi Don > > That's the problem. There is not any defined variable with these names > (rsolv, asolv) in any ".i" files. > > I have downloaded the source tinker's files many times to check their > number and sizes and I have not found any problem with this yet. > > If you have any idea to try please let me know. > > Sergio > > -- > Dr. Sergio Garay > Facultad de Bioquimica y Cs. Biol=F3gicas > Universidad Nacional del Litoral > Santa Fe - Argentina > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA > Argentina > Ph. +54 (342) 4575-213 > Fax. +54 (342) 4575-221 > > > Mensaje escrito por: "Don Steiger sd00_2002=3D=3D=3Dyahoo.com" > : > > It sounds like a problem with a ".i" file. Use grep (or egrep) to find >> where these variable are defined and allocated. E.g. egrep "variable n= ame" >> *.i >> >> --- On Tue, 6/24/08, Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar > ccl.net> wrote: >> >>> From: Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar >> ccl.net> >>> >> Subject: CCL: Problem compiling tinker binaries.... >> To: "Steiger, Don " >> Date: Tuesday, June 24, 2008, 5:06 AM >> >> Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar] >> Hi >> >> My name is Sergio Garay and I've been trying to compile the tinkers >> binaries without success. I'm working in a linux system (redhat 9.0) >> with ifort compiler. I run firstly the script debug.make in order to >> find some trouble and I got many errors like these: (Am I doing >> something wrong? >> >> >> fortcom: Error: analyze.f, line 1581: This name does not have a type, >> and must have an explicit type. [RSOLV] >> write (iout,480) k,i,rsolv(i),asolv(i) >> .....................................^ >> fortcom: Error: analyze.f, line 1581: This name does not have a type, >> and must have an explicit type. [ASOLV] >> write (iout,480) k,i,rsolv(i),asolv(i) >> ..............................................^ >> compilation aborted for analyze.f (code 1) >> fortcom: Error: born.f, line 74: This name does not have a type, and >> must have an explicit type. [RSOLV] >> roff(i) =3D rsolv(i) + doffset >> ...................^ >> fortcom: Error: born.f, line 74: This name does not have a type, and >> must have an explicit type. [DOFFSET] >> roff(i) =3D rsolv(i) + doffset >> ..............................^ >> fortcom: Error: born.f, line 79: This name does not have a type, and >> must have an explicit type. [SOLVTYP] >> if (solvtyp .eq. 'ONION') then >> ..........^ >> fortcom: Error: born.f, line 104: This name has not been declared as >> an array or a function. [RBORN] >> rborn(i) =3D 1.0d0 / total >> ............^ >> fortcom: Error: born.f, line 115: This name does not have a type, and >> must have an explicit type. [P5] >> p5inv =3D 1.0d0 / p5 >> .........................^ >> >> Any help will be appreciated. >> >> >> -- >> Dr. Sergio Garay >> Facultad de Bioquimica y Cs. Biol=F3gicas >> Universidad Nacional del Litoral >> Santa Fe - Argentina >> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA >> Argentina >> Ph. +54 (342) 4575-213 >> Fax. +54 (342) 4575-221 >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemis= try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >> >> >> >> > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_10397_29472059.1214403485988 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Alberto,

The TINKER project has been frozen for about 4 years. = There hasn't been any news, binaries, patches, whatsoever, from TINKER.=

I recommend you to switch to on of this:

- Vega ZZ ( http://www.ddl.unimi.it/= vega/index_noanim.htm )
-GROMACS ( http://www.gromacs.org/ = )

There are some other software, but this two are very good programs= , and still evolving!

Best,

Alcides

2008/6/25 Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar <owner-c= hemistry-.-ccl.net>:

Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar]
Hi Don

That's the problem. There is not any defined variable with these names = (rsolv, asolv) in any ".i" files.

I have downloaded the source tinker's files many times to check their n= umber and sizes and I have not found any problem with this yet.

If you have any idea to try please let me know.

Sergio

--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biol=F3gicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221


Mensaje escrito por:  "Don Steiger sd00_2002=3D=3D=3Dyahoo.com" <owner-chemistry*= _*ccl.net>:

It sounds like a problem with a ".i" file.  Use grep (or egr= ep) to  find where these variable are defined and allocated.  E.g= . egrep  "variable name" *.i

--- On Tue, 6/24/08, Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar  <owner-chemistry*= o*ccl.net> wrote:
> From: Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar  <owner-chemistry*o*ccl.net>
Subject: CCL: Problem compiling tinker binaries....
To: "Steiger, Don " <dsteiger*o*bioeng.ucsd.edu>
Date: Tuesday, June 24, 2008, 5:06 AM

Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar]
Hi

My name is Sergio Garay and I've been trying to compile the tinkers
binaries without success. I'm working in a linux system (redhat 9.0) with ifort compiler. I run firstly the script debug.make in order to
find some trouble and I got many errors like these: (Am I doing
something wrong?


fortcom: Error: analyze.f, line 1581: This name does not have a type,
and must have an explicit type.   [RSOLV]
                write (iout,480) &= nbsp;k,i,rsolv(i),asolv(i)
.....................................^
fortcom: Error: analyze.f, line 1581: This name does not have a type,
and must have an explicit type.   [ASOLV]
                write (iout,480) &= nbsp;k,i,rsolv(i),asolv(i)
..............................................^
compilation aborted for analyze.f (code 1)
fortcom: Error: born.f, line 74: This name does not have a type, and
must have an explicit type.   [RSOLV]
          roff(i) =3D rsolv(i) + doffset
...................^
fortcom: Error: born.f, line 74: This name does not have a type, and
must have an explicit type.   [DOFFSET]
          roff(i) =3D rsolv(i) + doffset
..............................^
fortcom: Error: born.f, line 79: This name does not have a type, and
must have an explicit type.   [SOLVTYP]
       if (solvtyp .eq. 'ONION') then
..........^
fortcom: Error: born.f, line 104: This name has not been declared as
an array or a function.   [RBORN]
             rborn(i) =3D 1.0d0 / total=
............^
fortcom: Error: born.f, line 115: This name does not have a type, and
must have an explicit type.   [P5]
          p5inv =3D 1.0d0 / p5
.........................^

Any help will be appreciated.


--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biol=F3gicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221



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------=_Part_10397_29472059.1214403485988-- From owner-chemistry@ccl.net Wed Jun 25 13:27:00 2008 From: "N. Sukumar nagams^^^rpi.edu" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37259-080625125307-22527-oiVVbgUq5mRy/5YzCcHa4g*server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Wed, 25 Jun 2008 11:38:28 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams/./rpi.edu] I don't know what you folks are talking about ".i" files. i here is an array index and the compiler is complaining that the variables RSOLV, ASOLV and RBORN have not been explicitly declared as arrays. N. Sukumar Associate Research Professor of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Wed, 25 Jun 2008 6:10:33 EDT "Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar" wrote: Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar] Hi Don That's the problem. There is not any defined variable with these names (rsolv, asolv) in any ".i" files. I have downloaded the source tinker's files many times to check their number and sizes and I have not found any problem with this yet. If you have any idea to try please let me know. Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 Mensaje escrito por: "Don Steiger sd00_2002===yahoo.com" : > It sounds like a problem with a ".i" file. Use grep (or egrep) to > find where these variable are defined and allocated. E.g. egrep > "variable name" *.i > > --- On Tue, 6/24/08, Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar > wrote: >> From: Alberto Sergio Garay sgaray(_)fbcb.unl.edu.ar >> > Subject: CCL: Problem compiling tinker binaries.... > To: "Steiger, Don " > Date: Tuesday, June 24, 2008, 5:06 AM > > Sent to CCL by: Alberto Sergio Garay [sgaray~~fbcb.unl.edu.ar] > Hi > > My name is Sergio Garay and I've been trying to compile the tinkers > binaries without success. I'm working in a linux system (redhat 9.0) > with ifort compiler. I run firstly the script debug.make in order to > find some trouble and I got many errors like these: (Am I doing > something wrong? > > > fortcom: Error: analyze.f, line 1581: This name does not have a type, > and must have an explicit type. [RSOLV] > write (iout,480) k,i,rsolv(i),asolv(i) > .....................................^ > fortcom: Error: analyze.f, line 1581: This name does not have a type, > and must have an explicit type. [ASOLV] > write (iout,480) k,i,rsolv(i),asolv(i) > ..............................................^ > compilation aborted for analyze.f (code 1) > fortcom: Error: born.f, line 74: This name does not have a type, and > must have an explicit type. [RSOLV] > roff(i) = rsolv(i) + doffset > ...................^ > fortcom: Error: born.f, line 74: This name does not have a type, and > must have an explicit type. [DOFFSET] > roff(i) = rsolv(i) + doffset > ..............................^ > fortcom: Error: born.f, line 79: This name does not have a type, and > must have an explicit type. [SOLVTYP] > if (solvtyp .eq. 'ONION') then > ..........^ > fortcom: Error: born.f, line 104: This name has not been declared as > an array or a function. [RBORN] > rborn(i) = 1.0d0 / total > ............^ > fortcom: Error: born.f, line 115: This name does not have a type, and > must have an explicit type. [P5] > p5inv = 1.0d0 / p5 > .........................^ > > Any help will be appreciated. > > > -- > Dr. Sergio Garay > Facultad de Bioquimica y Cs. Biológicas > Universidad Nacional del Litoral > Santa Fe - Argentina > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA > Argentina > Ph. +54 (342) 4575-213 > Fax. +54 (342) 4575-221 > > > > -= This is automatically added to each message by the mailing script > > =-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob: http://www.ccl.net/jobshttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Wed Jun 25 14:54:01 2008 From: "Germain Vallverdu germain.vallverdu%%lcp.u-psud.fr" To: CCL Subject: CCL:G: Fluorescence: determination of Quantum Yield/efficiency Message-Id: <-37260-080625104243-23958-+OoiMN6fSgbzGqkl1RuueA+/-server.ccl.net> X-Original-From: Germain Vallverdu Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 25 Jun 2008 15:51:19 +0200 MIME-Version: 1.0 Sent to CCL by: Germain Vallverdu [germain.vallverdu * lcp.u-psud.fr] Hello Antonio

I think you cannot do that just by quantum chemical calculation. In a simple way you can write the quantum yield as :

QY = kr / (kr + kq)

where kr is the rate constant of fluorescence and kq is the rate constant of the quenching processes. In order to compute the QY you need to evaluate kr AND kq. Thus you need to know which quenching processes may occur and their efficiency (this is quite hard). I think that a quantum calculation (TDDFT, CIS or other) can only give you information on kr from transition dipole moment calculation or oscillatory strength. In order to evaluate kq you need a model for your quenching process.

sincerely

Germain


Antonio G De Crisci antonio.decrisci###utoronto.ca a écrit : 
Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci(!)utoronto.ca]
Hello All,

I would like to be able to calculate the quantum yield or quantum efficiency of molecules. Would it be possible to do this using Gaussian 03W or PC GAMESS? I presume it may have involve a TD-DFT (or TDHF) calculation but im not exactly sure.

Thanks for time,
AnthonyE-mail to subscribers: CHEMISTRY],[ccl.net or use:
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--
Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
germain.vallverdu],[lcp.u-psud.fr
01 69 15 30 38 / 06 88 59 08 87
Chacun de nous a son étoile. Suivons la en nous félicitant de la voir chaque jour un peu plus loin ! (V. Grignard)
From owner-chemistry@ccl.net Wed Jun 25 18:29:00 2008 From: "Don Steiger sd00_2002]|[yahoo.com" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37261-080625181611-31025-FWjdbGifqUiGdJ3XTbRuVA]-[server.ccl.net> X-Original-From: Don Steiger Content-Type: multipart/alternative; boundary="0-1903267795-1214432140=:83996" Date: Wed, 25 Jun 2008 15:15:40 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Don Steiger [sd00_2002[*]yahoo.com] --0-1903267795-1214432140=:83996 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I checked my copy of Tinker, and rsolv, asolv are defined in "solute.i". = =A0=A0 "solute.i" is included in both "analyze.f" and "born.f". --- On Wed, 6/25/08, Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar wrote: > From: Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar Subject: CCL: Problem compiling tinker binaries.... To: "Steiger, Don " Date: Wednesday, June 25, 2008, 3:10 AM Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar] Hi Don That's the problem. There is not any defined variable with these names =20 (rsolv, asolv) in any ".i" files. I have downloaded the source tinker's files many times to check their =20 number and sizes and I have not found any problem with this yet. =0A=0A=0A --0-1903267795-1214432140=:83996 Content-Type: text/html; charset=us-ascii
I checked my copy of Tinker, and rsolv, asolv are defined in "solute.i".    "solute.i" is included in both "analyze.f" and "born.f".

--- On Wed, 6/25/08, Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar <owner-chemistry*ccl.net> wrote:
From: Alberto Sergio Garay sgaray .. fbcb.unl.edu.ar <owner-chemistry*ccl.net>
Subject: CCL: Problem compiling tinker binaries....
To: "Steiger, Don " <dsteiger*bioeng.ucsd.edu>
Date: Wednesday, June 25, 2008, 3:10 AM

Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar]
Hi
 Don

That's the problem. There is not any defined variable with these names  
(rsolv, asolv) in any ".i" files.

I have downloaded the source tinker's files many times to check
 their  
number and sizes and I have not found any problem with this yet.


--0-1903267795-1214432140=:83996-- From owner-chemistry@ccl.net Wed Jun 25 19:42:00 2008 From: "Christian =?iso-8859-1?q?M=FCck-Lichtenfeld?= cml**uni-muenster.de" To: CCL Subject: CCL: Problem compiling tinker binaries.... Message-Id: <-37262-080625073837-22203-n4bCnJaStMmo681Ftu9Naw!A!server.ccl.net> X-Original-From: Christian =?iso-8859-1?q?M=FCck-Lichtenfeld?= Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 25 Jun 2008 12:41:23 +0200 MIME-Version: 1.0 Sent to CCL by: Christian =?iso-8859-1?q?M=FCck-Lichtenfeld?= [cml-.-uni-muenster.de] Dear Sergio, rsolv and asolv are defined in "solute.i" (which also includes a common block with these variables). We have the 4.2 version of the code. Regards, Christian On Wednesday 25 June 2008 12:10, Alberto Sergio Garay sgaray ..=20 fbcb.unl.edu.ar wrote: > Sent to CCL by: Alberto Sergio Garay [sgaray : fbcb.unl.edu.ar] > Hi Don > > That's the problem. There is not any defined variable with these names > (rsolv, asolv) in any ".i" files. > > I have downloaded the source tinker's files many times to check their > number and sizes and I have not found any problem with this yet. > > If you have any idea to try please let me know. > > Sergio =2D-=20 =2D------------------------------------------------------------------ Dr. Christian M=FCck-Lichtenfeld Westfaelische Wilhelms-Universit=E4t Organisch-Chemisches Institut Corrensstrasse 40 D-48149 M=FCnster, Germany cml_-_uni-muenster.de Tel +49 251 83 33301 Fax +49 251 83 36506 http://www.uni-muenster.de/Chemie/OC/research/grimme/group/cml.html =2D------------------------------------------------------------------ support the progress of Quantum Chemistry with your PC http://qah.uni-muenster.de=20 =2D------------------------------------------------------------------ From owner-chemistry@ccl.net Wed Jun 25 21:16:00 2008 From: "Thet Lin Thu tiddwaylll#,#gmail.com" To: CCL Subject: CCL: GULP force field tweaking Message-Id: <-37263-080625152047-28893-wkALTZx1620obpeaWUDH8Q*server.ccl.net> X-Original-From: "Thet Lin Thu" Content-Type: multipart/alternative; boundary="----=_Part_25910_21258739.1214414709961" Date: Thu, 26 Jun 2008 01:25:09 +0800 MIME-Version: 1.0 Sent to CCL by: "Thet Lin Thu" [tiddwaylll|,|gmail.com] ------=_Part_25910_21258739.1214414709961 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, Does anyone where the force field segments are in the gulp source and how do I tweak them to my liking? Thanks, Thet ------=_Part_25910_21258739.1214414709961 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi,

Does anyone where the force field segments are in the gulp source and how do I tweak them to my liking?



Thanks,
Thet

------=_Part_25910_21258739.1214414709961--