From owner-chemistry@ccl.net Fri Mar 16 09:33:00 2018 From: "Emilio Mart nez Martinez-Nunez emilio.nunez-$-usc.es" To: CCL Subject: CCL: tsscds-2018 computer program Message-Id: <-53223-180316034102-26263-78Oaq1Brrno49z4xyhxwuA]-[server.ccl.net> X-Original-From: "Emilio Mart nez Martinez-Nunez" Date: Fri, 16 Mar 2018 03:40:57 -0400 Sent to CCL by: "Emilio Mart nez Martinez-Nunez" [emilio.nunez:+:usc.es] Dear CCL members, I'd like to announce the release of tsscds-2018, a computer program to discover reaction mechanisms in an automated fashion. The transition states guess structures are obtained from accelerated trajectory simulations, and minima/products from the IRC. Finally, the kinetics is solver using KMC. http://forge.cesga.es/wiki/g/tsscds/HomePage All the best, Emilio Martnez Nez Departamento de Qumica Fsica Facultade de Qumica Avda. das Ciencas s/n 15782 Santiago de Compostela SPAIN Phone: +34 881 814216 e-mail address: emilio.nunez:_:usc.es http://webspersoais.usc.es/persoais/emilio.nunez/index.html tsscds-2018 program Download code: http://forge.cesga.es/projects/tsscds Wiki: http://forge.cesga.es/wiki/g/tsscds/HomePage From owner-chemistry@ccl.net Fri Mar 16 10:08:00 2018 From: "Marcel Swart marcel.swart,icrea.cat" To: CCL Subject: CCL: TS search algorithm code Message-Id: <-53224-180316042402-15625-MIm+GacTAQtbcqK5SQJpfQ-x-server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 16 Mar 2018 09:23:49 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart^^icrea.cat] For algorithms you could have a look at Zerner’s Linear-Then-Plane or Mopac’s Saddle approach, or the QUILD approach (J. Comput. Chem. 2008, 29, 724, http://www.dx.doi.org/10.1002/jcc.20834) which is based on quasi-Newton, model Hessian, and TSRC mode following, and can be used (through a general input script) with any program: https://www.scm.com/doc/Quild/index.html Numerical gradients are possible there as well. Marcel On 15 Mar 2018, at 19:28, Anja Muzdalo muzdalo!^!gmail.com wrote: Sent to CCL by: "Anja Muzdalo" [muzdalo=-=gmail.com] Dear CCL Subscribers, does anyone have tips on a generic transition state/structure search algorithm one could use, by means of "feeding it" single point energy evaluations from an external QM package? (an existing open-access code perhaps) Any type of a TS algorithm would do the job (e.g. Newton-Rhapson local), since we have a good idea of the geometry but have not implemented it for the QM method we are using at the moment. Thanks for any suggestions! Best, AM From owner-chemistry@ccl.net Fri Mar 16 10:43:00 2018 From: "Jan Halborg Jensen jhjensen=-=chem.ku.dk" To: CCL Subject: CCL: TS search algorithm code Message-Id: <-53225-180316043242-15988-1UUDijLvccfrVJX/Tu2A2Q]|[server.ccl.net> X-Original-From: Jan Halborg Jensen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_ADE00B5565D143E1A87F7007C6B85DA0kudk_" Date: Fri, 16 Mar 2018 08:32:31 +0000 MIME-Version: 1.0 Sent to CCL by: Jan Halborg Jensen [jhjensen _ chem.ku.dk] --_000_ADE00B5565D143E1A87F7007C6B85DA0kudk_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Here are some options, but they both require energy + gradient. https://github.com/azag0/pyberny https://github.com/ZimmermanGroup/molecularGSM Best regards, Jan On 15 Mar 2018, at 19:28, Anja Muzdalo muzdalo!^!gmail.com > wrote: Sent to CCL by: "Anja Muzdalo" [muzdalo=3D-=3Dgmail.com] Dear CCL Subscribers, does anyone have tips on a generic transition state/structure search algori= thm one could use, by means of "feeding it" single point energy evaluations= from an external QM package? (an existing open-access code perhaps) Any type of a TS algorithm would do the job (e.g. Newton-Rhapson local), si= nce we have a good idea of the geometry but have not implemented it for the= QM method we are using at the moment. Thanks for any suggestions! Best, AM -=3D This is automatically added to each message by the mailing script =3D-E-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--_000_ADE00B5565D143E1A87F7007C6B85DA0kudk_ Content-Type: text/html; charset="us-ascii" Content-ID: <9A6B6F300D35074D97C5908FAF98D78C]=[alumni.ku.dk> Content-Transfer-Encoding: quoted-printable
Here are some options, but they both require energy + g= radient.

https://github.com/= azag0/pyberny

https://github.com/ZimmermanGroup/molecularGSM

Best regards, Jan

On 15 Mar 2018, at 19:28, Anja Muzdalo muzdalo!^!gmail.com <owner-chemistry]=[ccl.net> wrote:


Sent to CCL by: "Anja  Muzdalo" [muzdalo=3D-=3Dgmail.com]
Dear CCL Subscribers,

does anyone have tips on a generic transition state/structure search algori= thm one could use, by means of "feeding it" single point energy e= valuations from an external QM package? (an existing open-access code perha= ps)

Any type of a TS algorithm would do the job (e.g. Newton-Rhapson local), si= nce we have a good idea of the geometry but have not implemented it for the= QM method we are using at the moment.

Thanks for any suggestions!

Best,
AM



-=3D This is automatically added to each message by the mailing script =3D-=

E-mail to subscribers: CHEM= ISTRY]=[ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]=[ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs=
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--_000_ADE00B5565D143E1A87F7007C6B85DA0kudk_-- From owner-chemistry@ccl.net Fri Mar 16 11:18:00 2018 From: "Keith Refson krefson^-^gmail.com" To: CCL Subject: CCL: TS search algorithm code Message-Id: <-53226-180316071633-27411-2/seb8LrI7I1vdV4ipGQNQ**server.ccl.net> X-Original-From: Keith Refson Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 16 Mar 2018 11:16:24 +0000 MIME-Version: 1.0 Sent to CCL by: Keith Refson [krefson^_^gmail.com] The "atomic simulation environment", ASE https://wiki.fysik.dtu.dk/ase/ does exactly that and already has interfaces to a large number of QC codes but should be extensible for your own. Keith Refson On 15/03/18 21:54, Fedor Goumans goumans^scm.com wrote: > Dear AM, > You could check out Johannes Kaestner's DL-FIND code for instance: > http://www.theochem.uni-stuttgart.de/kaestner/dlfind.html > Which has several TS optimizer, either Hessian- or gradient-based > Although if you only have energies and no gradients, you will probably > need to teach it how to get numerical gradients. > To do Hessian-based TS search methods with only energies, you would have > then to do another numerical derivation of the gradients, which I guess > would become both costly and noisy … > > Best wishes, > Fedor > >> On Mar 15, 2018, at 19:28, Anja Muzdalo muzdalo!^!gmail.com >> > ~ ccl.net>> wrote: >> >> >> Sent to CCL by: "Anja  Muzdalo" [muzdalo=-=gmail.com ] >> Dear CCL Subscribers, >> >> does anyone have tips on a generic transition state/structure search >> algorithm one could use, by means of "feeding it" single point energy >> evaluations from an external QM package? (an existing open-access code >> perhaps) >> >> Any type of a TS algorithm would do the job (e.g. Newton-Rhapson >> local), since we have a good idea of the geometry but have not >> implemented it for the QM method we are using at the moment. >> >> Thanks for any suggestions! >> >> Best, >> AM>> the strange characters on the top line to the ~ sign. You can also >> >> E-mail to subscribers: CHEMISTRY ~ ccl.net > ccl.net> or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST ~ ccl.net >> or use> > Dr. T. P. M. (Fedor) Goumans > Business Developer > Software for Chemistry & Materials BV > De Boelelaan 1083 > 1081 HV Amsterdam, The Netherlands > T +31 20 598 7625 > https://www.scm.com > https://twitter.com/SCM_Amsterdam > https://www.linkedin.com/company/software-for-chemistry-&-materials > > > >