From owner-chemistry@ccl.net Wed Oct 1 07:30:00 2008 From: "Seth Olsen s.olsen1_._uq.edu.au" To: CCL Subject: CCL: ADF Visualization Message-Id: <-37820-080930021538-29470-FwdrtLePqUReKlolx/TTcA++server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 30 Sep 2008 16:15:34 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1 ~ uq.edu.au] HI CCLers, A colleague and I are working with ADF for the first time, and we are curious about visualization options for the results. We know ADF has a GUI, but we are also curious if there are other 3rd party programs that can process the output, whether binary or ascii-converted. Any suggestions? Many Thanks, Seth From owner-chemistry@ccl.net Wed Oct 1 08:28:01 2008 From: "Mateusz Galuszka ccs * fqs.pl" To: CCL Subject: CCL: FUJITSU Seminar - Cambridge, UK, 30.10.2008 Message-Id: <-37821-081001054703-1158-jbfNAMLfSI56+91Euys0Aw!=!server.ccl.net> X-Original-From: "Mateusz Galuszka" Date: Wed, 1 Oct 2008 05:46:59 -0400 Sent to CCL by: "Mateusz Galuszka" [ccs[A]fqs.pl] Dear All, We are very proud to invite you to our 1st "Computational Chemistry and Molecular Modelling Solutions for Chemical and Materials Industry" Seminar in Cambridge, UK. The seminar will take place on 30th October, 2008 in The Trinity Centre - a conference centre of the Cambridge Science Park. The seminar will be devoted to general aspects of use of computational methods in chemical, materials and semiconductor industry. It will also be a great opportunity to present the latest computational solutions offered by FUJITSU company. Our invited speakers include Prof. Akira Takada from Asahi Glass Corporation, one of the largest glass and chemical companies in the World, and Dr. Chioko Kaneta, an expert in molecular simulations of semiconductor materials from Fujitsu Laboratories Japan. The participation in FUJITSU seminar is FREE OF CHARGE. In order to register to our seminar, please send us the filled registration form which can be downloaded, together with the information brochure, from our website: http://www.fqs.pl/seminars/2008-10-30 You can also simply send a message to ccs=-=fqs.pl. Please remember to register in advance as the order of registration will be important due to the limited number of seats. We hope that you find our proposition very interesting. If you would have any additional questions, please do not hesitate to contact us. I look forward to your reply. Best regards, Mateusz Galuszka -- ************************ Mateusz Galuszka FUJITSU ul. Starowislna 13-15 31-038 Krakow Poland Tel.: (+48) 12 429 43 45, Fax: (+48) 12 429 61 24 e-mail: ccs=-=fqs.pl URL: http://www.fqs.pl ************************ From owner-chemistry@ccl.net Wed Oct 1 09:12:00 2008 From: "Jinsong Zhao jszhao||mail.hzau.edu.cn" To: CCL Subject: CCL: Compile MOPAC7.1 under Linux using gfortran Message-Id: <-37822-081001090229-22941-zwxlylMK3b9sGGL1b1pDJA%x%server.ccl.net> X-Original-From: "Jinsong Zhao" Date: Wed, 1 Oct 2008 09:02:23 -0400 Sent to CCL by: "Jinsong Zhao" [jszhao]-[mail.hzau.edu.cn] Hi there, I am wondering if anyone here compile MOPAC7.1 (obtained here: http://openmopac.net/Downloads/Mopac_7.1source.zip) under Linux using gfortran. I have try my best to compile it, however, I am fail. After renaming all source to *.f90, I use the following command to compile it (I have get help from comp.lang.fortran newsgroup, because there is no a Makefile, even README on how to compile it.): cd src_modules gfortran -c vastkind.f90 gfortran -c *.f90 cp *.mod ../Modules ar -r libmodules.a *.o rm *.o rm *.mod cd ../src_interfaces gfortran -I ../Modules -c *.f90 cp *.mod ../Modules ar -r libinterfaces.a *.o rm *.o rm *.mod cd ../src_subroutines gfortran -I ../Modules -c *.f90 gfortran *.o ../src_modules/libmodules.a ../src_interfaces/libinterfaces.a -o mopac7.exe The last step give me many error message, like the following: analyt.o: In function `analyt_': analyt.F90:(.text+0x2ba): undefined reference to `__funcon_c__a0' analyt.F90:(.text+0x1875): undefined reference to `__funcon_c__fpc_9' When I change the line USE funcon_C, only : a0, fpc_9, ev to USE funcon_C After many such modification, I could compile it. However, when I run it on a example, I get error message: segmentation fault I try to trace the error, I find it in setup_mopac_arrays.F90 line 47, and I don't know how to fix it. I don't know how to do now, :-( Anyone could help me? Thanks in advance! Jinsong From owner-chemistry@ccl.net Wed Oct 1 09:43:00 2008 From: "Nuno A. G. Bandeira nuno.bandeira:ist.utl.pt" To: CCL Subject: CCL: ADF Visualization Message-Id: <-37823-081001091008-28713-uQQQypgINDId3jiHpJLVUw|server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Type: multipart/mixed; boundary="=======AVGMAIL-48E36DBD0000=======" Date: Wed, 01 Oct 2008 13:31:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira{:}ist.utl.pt] --=======AVGMAIL-48E36DBD0000======= Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Seth Olsen s.olsen1_._uq.edu.au wrote: > > A colleague and I are working with ADF for the first time, and we are > curious about visualization options for the results. We know ADF has a > GUI, but we are also curious if there are other 3rd party programs that > can process the output, whether binary or ascii-converted. Any > suggestions? Commercially you have Chemcraft that can do basis readout of outputs and tape41 text files. For free you can use Molekel and Gabedit that can read tape41s too. Regards, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ^ IST,Lisbon -- --=======AVGMAIL-48E36DBD0000======= Content-Type: multipart/alternative; boundary="=======AVGMAIL-48E36DBD0000=======" --=======AVGMAIL-48E36DBD0000======= Content-Type: text/plain; x-avg=cert; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Content-Description: "AVG certification" No virus found in this outgoing message. Checked by AVG - http://www.avg.com Version: 8.0.173 / Virus Database: 270.7.5/1701 - Release Date: 30-09-2008 1= 9:08 --=======AVGMAIL-48E36DBD0000=======-- --=======AVGMAIL-48E36DBD0000=======-- From owner-chemistry@ccl.net Wed Oct 1 11:02:00 2008 From: "Grigoriy Zhurko reg_zhurko[*]chemcraftprog.com" To: CCL Subject: CCL:G: Wavefunction stability Message-Id: <-37824-081001105548-10009-tz6Za7qc5/cjkIFR/eNj/A%x%server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 1 Oct 2008 18:54:48 -0700 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko_+_chemcraftprog.com] I know that for transition metal complexes, a quantum chemistry computation often finds unstable excited states instead of the ground state, thus making the result improper. With Gaussian, the Stable keyword can be used to check whether the computed molecule is in the ground state. How can this checking be performed with other QC programs, in particular PCGamess? Grigoriy Zhurko. From owner-chemistry@ccl.net Wed Oct 1 11:36:01 2008 From: "Anna Kuzak a.kuzak,fqs.pl" To: CCL Subject: CCL: ADF Visualization Message-Id: <-37825-081001093305-25000-kSKO6enKpedwKe585aHRQA:server.ccl.net> X-Original-From: Anna Kuzak Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Oct 2008 14:32:39 +0200 MIME-Version: 1.0 Sent to CCL by: Anna Kuzak [a.kuzak#,#fqs.pl] Dear Seth, Fujitsu is developing with the cooperation of SCM a version of Scigress/ (earlier known as CAChe) that will support ADF. It will not only visualize the results but also it will allow the simulations to be started from the software. The final release date has not been fixed yet, but the first version should be released soon. Wishes, Anna Seth Olsen s.olsen1_._uq.edu.au pisze: > > Sent to CCL by: Seth Olsen [s.olsen1 ~ uq.edu.au] > > > HI CCLers, > > A colleague and I are working with ADF for the first time, and we are > curious about visualization options for the results. We know ADF has > a GUI, but we are also curious if there are other 3rd party programs > that can process the output, whether binary or ascii-converted. Any > suggestions? > > Many Thanks, > > Sethhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > -- ================================================= Anna Kuzak Sales & Marketing FQS Poland Sp. z o.o. (Fujitsu Group) ul. Starowislna 13-15 31-038 Krakow, Poland Tel.: (+48 12) 429 43 45 Fax: (+48 12) 429 61 24 e-mail: ccs\a/fqs.pl e-mail: a.kuzak\a/fqs.pl URL: http://www.fqs.pl ================================================= KRS: 0000033524 Sad Rejonowy dla Krakowa Sródmiescia w Krakowie XI Wydzial Gospodarczy Kapital: 1 000 000 PLN NIP 676 20 43 548 REGON 351421847 ================================================ From owner-chemistry@ccl.net Wed Oct 1 13:08:00 2008 From: "Adam Tenderholt atenderholt/a\gmail.com" To: CCL Subject: CCL: ADF Visualization Message-Id: <-37826-081001130623-8146-JU78qJ+Oc2NfKQXR8nUM1Q]|[server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 1 Oct 2008 10:06:05 -0700 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt~~gmail.com] QMForge and GaussSum are other options. QMForge will let you visualize the geometry as it changes during an optimization and calculates Mulliken populations for a user-defined set of orbitals. There is also a very simple XYZ coordinate editor with tools for re-orienting a molecule. GaussSum will (I think) let you calculate IR/Raman spectra > from frequency calculations, UV/Vis from TD-DFT, and Density of States. It also provides tools to visualize the progress of SCF and Geometry convergences. Adam On Wed, Oct 1, 2008 at 5:32 AM, Anna Kuzak a.kuzak,fqs.pl wrote: > > Sent to CCL by: Anna Kuzak [a.kuzak#,#fqs.pl] > Dear Seth, > > Fujitsu is developing with the cooperation of SCM a version of Scigress/ > (earlier known as CAChe) that will support ADF. It will not only visualiz= e > the results but also it will allow the simulations to be started from the > software. The final release date has not been fixed yet, but the first > version should be released soon. > > Wishes, > Anna > > Seth Olsen s.olsen1_._uq.edu.au pisze: >> >> Sent to CCL by: Seth Olsen [s.olsen1 ~ uq.edu.au] >> >> >> HI CCLers, >> >> A colleague and I are working with ADF for the first time, and we are >> curious about visualization options for the results. We know ADF has a = GUI, >> but we are also curious if there are other 3rd party programs that can >> process the output, whether binary or ascii-converted. Any suggestions? >> >> Many Thanks, >> >> Sethhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> >> > > > -- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > Anna Kuzak > Sales & Marketing > > FQS Poland Sp. z o.o. > (Fujitsu Group) > ul. Starowislna 13-15 > 31-038 Krakow, Poland > Tel.: (+48 12) 429 43 45 Fax: (+48 12) 429 61 24 > e-mail: ccs###fqs.pl > e-mail: a.kuzak###fqs.pl > URL: http://www.fqs.pl > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > KRS: 0000033524 > Sad Rejonowy dla Krakowa Sr=F3dmiescia w Krakowie > XI Wydzial Gospodarczy > > Kapital: 1 000 000 PLN > NIP 676 20 43 548 > REGON 351421847 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Wed Oct 1 15:46:01 2008 From: "carlos simmerling carlos.simmerling|gmail.com" To: CCL Subject: CCL: Final call for ACS/CCG graduate student research excellence awards Message-Id: <-37827-081001153309-20296-cpVtY1nfkdK+w2bJutoBqw*|*server.ccl.net> X-Original-From: "carlos simmerling" Date: Wed, 1 Oct 2008 15:33:05 -0400 Sent to CCL by: "carlos simmerling" [carlos.simmerling() gmail.com] REMINDER: DEADLINE FOR APPLICATIONS IS OCTOBER 6 Five $1,150 ACS/CCG Excellence Student Travel Award Stipends Available for the Spring 2009 Salt Lake City ACS National Meeting The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. The awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas (North, South or Central) are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. To apply for an award for the ACS National Meeting in Salt Lake City, Utah, March 22-26, 2009, an extended abstract of the work (no more than 2 pages), a two page CV along with a letter of support from the research advisor, and a personal statement (no more than 1 page) should be sent as pdf or text files to carlos.simmerling-x-gmail.com IMPORTANT: APPLICATION MATERIALS MUST BE RECEIVED BY 9AM EASTERN TIME ON OCTOBER 6, 2008. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by October 8, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal poster abstract to the "Chemical Computing Group Excellence Award" symposium on the OASYS system (the COMP OASYS deadline is October 20, 2008 for the Salt Lake City ACS Meeting). More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling-x-gmail.com From owner-chemistry@ccl.net Wed Oct 1 16:20:00 2008 From: "carlos simmerling carlos.simmerling-*-gmail.com" To: CCL Subject: CCL: Thomas Kuhn Paradigm Shift Award symposium at Spring ACS meeting Message-Id: <-37828-081001154444-21694-I2y4EO06zp0fYAceLc81kg*server.ccl.net> X-Original-From: "carlos simmerling" Date: Wed, 1 Oct 2008 15:44:40 -0400 Sent to CCL by: "carlos simmerling" [carlos.simmerling:-:gmail.com] Please forward this announcement of an award symposium to be held in the COMP division at the Spring ACS national meeting in Salt lake City. The Thomas Kuhn Paradigm Shift Award is given each year to the talk that most captures the spirit of Kuhn's writings, exemplified in his landmark book, "The Structure of Scientific Revolutions". The symposium at each Spring ACS is open to all and attempts to attract those whose work has the potential to change the way we think about an aspect of science. Kuhn's words for this, a "Paradigm Shift", have been much over used and as such can be an intimidating standard to approach, but the intent is for talks that represent a fresh way of looking at an aspect of our field. As an example, the 2006 winner, Christopher Bayly of Merck-Frosst, proposed that focused screening was a more efficient path to drug discovery than high throughput screening and in 2008 Derek Debe of Abbott Laboratories presented the case for knowing confidence intervals in molecular modeling. Talks are usually within the computational sphere. They are judged on novelty, potential impact and quality of presentation by a panel of independent scientists with extensive computational experience. It is hoped the Award, which carries a stipend of one thousand dollars, can provide a platform to researchers extending a mirror to our field and questioning the scientific status quo. Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four will be selected for 40 minute presentations to take place during a half-day symposium at the national meeting. Abstracts not selected for the symposium competition can be moved into consideration for the general symposia (which are always well attended!) if desired. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html From owner-chemistry@ccl.net Wed Oct 1 16:55:01 2008 From: "carlos simmerling carlos.simmerling : gmail.com" To: CCL Subject: CCL: Final call for ACS/HP Junior Faculty Award Applications Message-Id: <-37829-081001153138-20091-MB2qhHBMN7i+opuXdNrUiQ||server.ccl.net> X-Original-From: "carlos simmerling" Date: Wed, 1 Oct 2008 15:31:34 -0400 Sent to CCL by: "carlos simmerling" [carlos.simmerling%%gmail.com] REMINDER: THE DEADLINE FOR APPLICATIONS IS OCTOBER 6 The HP Outstanding Junior Faculty Award program provides $1,000 to each of four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for HP Outstanding Junior Faculty Awards are invited from all current tenure-track junior faculty who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, as well as the level of Departmental support as indicated by a letter of support by the Chair or Chair designee. To apply for an award for the ACS National Meeting in Salt Lake City, Utah, March 22-26, 2009, an extended abstract of the work (no more than 2 pages), a CV and the letter of departmental support should be sent as pdf or text files to carlos.simmerling#%#gmail.com IMPORTANT: APPLICATION MATERIALS MUST BE RECEIVED BY 9AM EASTERN TIME ON OCTOBER 6, 2008. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by October 8, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the "HP Outstanding Junior Faculty Award" symposium on the OASYS system (the COMP OASYS deadline is October 20, 2008 for the Salt Lake City ACS Meeting). Note that this is an abstract for the poster presentation. We also suggest that HP award applicants submit a separate abstract to OASYS for an oral presentation, in addition to their poster abstract in the HP award section (note that acceptance into the oral sessions is not guaranteed). More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling#%#gmail.com From owner-chemistry@ccl.net Wed Oct 1 21:10:01 2008 From: "Berkholz, Donnie - dberkholz[#]gentoo.org" To: CCL Subject: CCL: Compile MOPAC7.1 under Linux using gfortran Message-Id: <-37830-081001144215-11194-VbnhnGc0j8wzZqoCpsrDvA#,#server.ccl.net> X-Original-From: "Berkholz, Donnie -" Content-Disposition: inline Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="IJpNTDwzlM2Ie8A6" Date: Wed, 1 Oct 2008 10:46:20 -0700 MIME-Version: 1.0 Sent to CCL by: "Berkholz, Donnie -" [dberkholz-#-gentoo.org] --IJpNTDwzlM2Ie8A6 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On 09:02 Wed 01 Oct , Jinsong Zhao jszhao||mail.hzau.edu.cn wrote: > I am wondering if anyone here compile MOPAC7.1 (obtained here:=20 > http://openmopac.net/Downloads/Mopac_7.1source.zip) under Linux using=20 > gfortran. >=20 > I have try my best to compile it, however, I am fail. After renaming=20 > all source to *.f90, I use the following command to compile it (I have=20 > get help from comp.lang.fortran newsgroup, because there is no a=20 > Makefile, even README on how to compile it.): I use the version from=20 http://www.bioinformatics.org/ghemical/download/current/ -- it's easier=20 to build because it just uses the standard autotools (./configure;=20 make). You end up with run_mopac7 and mopac7 in the build directory. --=20 Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com --IJpNTDwzlM2Ie8A6 Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.9 (GNU/Linux) iEYEABECAAYFAkjjt2sACgkQXVaO67S1rttXbQCg1QBAGSeOQ+aZjQB4ovpHEaQv UXAAn2yBdubPCddVbdsskYa71LCKQjkY =n/Fn -----END PGP SIGNATURE----- --IJpNTDwzlM2Ie8A6--