From owner-chemistry@ccl.net Mon Apr 30 05:24:01 2018 From: "Mark Andrew Blitz m.blitz!A!leeds.ac.uk" To: CCL Subject: CCL: MESMER 5.1 Message-Id: <-53288-180430052038-11818-ZbFjKskF3MIb5GxKtfxoPg{=}server.ccl.net> X-Original-From: "Mark Andrew Blitz" Date: Mon, 30 Apr 2018 05:20:34 -0400 Sent to CCL by: "Mark Andrew Blitz" [m.blitz!^!leeds.ac.uk] Dear Colleague, On behalf of the MESMER team, we are delighted to announce that MESMER 5.1 (Master Equation Solver for Multi Energy-well Reactions) is now available for download. MESMER is designed to analyze and simulate reactions in the gas phase that take place on a potential energy surface that is characterized by having one or more potential wells, and which are typically described by rate coefficients that depend on pressure (or concentration) as well as temperature. MESMER allows you to simulate systems over a wide range of pressures and temperatures, extract rate coefficients, analyze experimental data, fit model parameters and represent rate coefficients in formats that can be used directly in large scale simulations (e.g. Cantera or Chemkin). The Windows installer and Linux tar file are located at: http://sourceforge.net/projects/mesmer/ The source can also be viewed and downloaded from this site. There are also bug and feature request tracking facilities which we encourage you to use. The following new features have been implemented: New features: Direct analysis of trace data. Addition of Canonical Rate Calculator for use in conjunction with irreversible exchange reactions. Addition of full classical coupled internal-external rotor density of states calculator. Extension of the analytic representation facility to include the Plog representation. Bug fixes, Input Format and Other Changes: An issue that caused MESMER 5.0 to crash on some Linux platforms when run in parallel has been addressed. An issue with the derivedFrom key word that allowed certain variables to be related during a fitting exercise has been addressed. The keyword RRKM replaces the deprecated keyword SimpleRRKM for the specification of an RRKM based microcanonical rate calculator, though the latter keyword will continue to function. Further to user feedback, the keyword me:ForceMacroDetailedBalance has been set to apply at all times, that is detailed balance will be enforced when macroscopic rate coefficients are calculated. Previous behavior can be restored if required. The MesmerILT method for determining microcanonical rate coefficients has been altered so as to observe the limits on n parameter of the modified Arrhenius form. The conversion factor used to convert inertia tensor elements into rotational constants has been altered so that it is consistent with the other fundamental constants used within MESMER. This may mean small changes in partition functions and densities of states. For users compiling MESMER for parallel execution on Windows using Visual Studio, a new configuration MPIRelease has been added to simplify the procedure. If you have any comments or suggestions, please do not hesitate to let us know, either through the above site or by email (Mark Blitz(M.Blitz{:}leeds.ac.uk) and Struan Robertson (struanhrobertson{:}gmail.com) would be very happy to receive feedback). More information is available at the MESMER website: http://www.chem.leeds.ac.uk/mesmer.html Also some of the implementation details of MESMER are described in Journal of Physical Chemistry A, 95459560, 116 (2012). A web based graphical user interface for creating MESMER input files, develop by Dr. Xiaoqing You and colleagues of the University of Tsinghua, in collaboration with the MESMER team, is available for testing and can be found at the following address: http://www.cce.tsinghua.edu.cn:8000/ Dr. You and the MESMER team would welcome feedback on this interface. We would like to acknowledge useful discussion and feedback from Prof. Timo Pekkanen of the University of Helsinki and Charles McGill of NCSU. Regards, Mark Blitz and Struan Robertson Mark Blitz School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT. U.K. Tel 0113 343 6594 Email: M.Blitz{:}leeds.ac.uk From owner-chemistry@ccl.net Mon Apr 30 10:44:01 2018 From: "Murat Kilic muratmkilic/a\gmail.com" To: CCL Subject: CCL: Reminder: CC2AI abstract submission deadline is TODAY Message-Id: <-53289-180430053654-1744-Q2tcrz3pCUY/eKyiHjIwVw]*[server.ccl.net> X-Original-From: "Murat Kilic" Date: Mon, 30 Apr 2018 05:36:53 -0400 Sent to CCL by: "Murat Kilic" [muratmkilic,,gmail.com] Dear colleagues, Please notice that the abstract submission deadline of CC2AI is today. Computational Chemistry meets Artificial Intelligence 13-15 June 2018 EPFL, Lausanne - Switzerland https://cc2ai.epfl.ch/ The main goal of this conference is to bring together research groups from biomolecular simulations and ab-initio computations with those from machine learning and evolutionary/stochastic optimisation to further encourage the development of these fields. Confirmed invited speakers include Paul Ayers (Canada) Albert P. Bartok (United Kingdom) Kieron Burke (United States) Pablo Campomanes (Switzerland) Roberto Car (United States) Michele Ceriotti (Switzerland) Clemence Corminboeuf (Switzerland) Martin Head-Gordon (United States) Heather Kulik (United States) Anatole von Lilienfeld (Switzerland) Nicola Marzari (Switzerland) Markus Meuwly (Switzerland) Michele Parrinello (Switzerland) Sereina Riniker (Switzerland) Didier Rognan (France) Alessandro De Vita (United Kingdom) To attend this conference, please fill in our registration form: https://goo.gl/5NJFqy On behalf of the organizing committee, we look forward to welcoming you at CC2AI! Cordially, the organizers Ursula Roethlisberger Nicholas Browning Murat Kilic Justin Villard Karin Pasche From owner-chemistry@ccl.net Mon Apr 30 19:12:01 2018 From: "Igors Mihailovs igorsm(!)cfi.lu.lv" To: CCL Subject: CCL:G: Magnitude of static field used for calculation ofpolarizability Message-Id: <-53290-180430133530-21631-IgzElM1t6Os9rKOFNPuiWw(_)server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: lv-LV Content-Type: multipart/alternative; boundary="------------24CD07C5FD29298B5B50F4AF" Date: Mon, 30 Apr 2018 20:35:10 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm() cfi.lu.lv] This is a multi-part message in MIME format. --------------24CD07C5FD29298B5B50F4AF Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear all, Thank You very, very much for Your suggestions! I hope these will help me to get some understanding on the matter. The math is quite tough for me, since I never actually used calculus since the second undergraduate year. But I understand I cannot do QM without math <:-/ With deep gratitude, Igors Mihailovs ISSP UL On 29/04/18 09:14, Heribert Reis Hreis%x%eie.gr wrote: > There is a nice chapter 'Introduction to Response Theory' by Thomas > Pedersen in the Handbook of Computational Chemistry, written by an > expert for the non-expert. > > https://link.springer.com/referenceworkentry/10.1007%2F978-94-007-0711-5_5 > > Heribert > > Disclosure: I'm a co-editor of the Handbook. > > On Sat, Apr 28, 2018 at 9:21 PM, Steve Williams willsd,appstate.edu > > wrote: > > Yes....fat fingers,  small on-screen keyboard, aggressive > autocorrect, and poor proofreading is not a good combination. I > have given copies of this book to half a dozen or so undergraduate > research students as graduation presents over the past several > years. Sorry for mangling your name Chris Cramers....your book is > a nice, quite readable introduction to our broad field. > Steve > > On Sat, Apr 28, 2018, 1:53 PM John Keller jwkeller**alaska.edu > > wrote: > > Hi, > > Actually, Chris Cramer is the author of “Essentials..”. > > Errol Lewars’ “Computational Chemistry” is another good intro > to the mathematics of Hartree-Fock MO method and basis > functions. It has exercises for the student, with answers in > the back of the book. > > John Keller > > *From: *Steve Williams willsd:-:appstate.edu > > *Sent: *Saturday, April 28, 2018 2:58 AM > *To: *Keller, John W > *Subject: *CCL:G: Magnitude of static field used for > calculation ofpolarizability > > I think Chris Farmer's book "Essentials of Computational > Chemistry" would be a good place to start. It have quite a bit > on how various methods work and does not have a great deal of > mathematical details. > > Steve Williams > > On Sat, Apr 28, 2018, 2:58 AM Igors Mihailovs > igorsm{=}cfi.lu.lv > > wrote: > > Dear Dr. Lehtola, > > Can You please suggest something good to read about the > theory of CPHF and response functions? I have performed > some literature search but it was quite hard to me to sum > it up to get at least some understanding of "how it > works": I have never attended any serious course on > quantum mechanics or chemistry, and I didn't find much > literature for laymen like me either. Most books I have > read contain either the essential basics or deep > discussion, being quite sparse in between. > > With deep gratitude, > Igors Mihailovs > ISSP UL > > On 26/04/18 20:54, Susi Lehtola susi.lehtola- > -alumni.helsinki.fi wrote: > > > Sent to CCL by: Susi Lehtola > [susi.lehtola^alumni.helsinki.fi > ] > On 04/26/2018 03:46 PM, Igors Mihailovs igorsm : > cfi.lu.lv wrote: > > Dear Suresh, > > By default, Gaussian uses CPHF for > polarizabilities (quite different from the > response formalism, as far as I can judge – /can > anyone comment on that?/) > > CPHF *is* linear response. > --------------24CD07C5FD29298B5B50F4AF Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear all,

Thank You very, very much for Your suggestions! I hope these will help me to get some understanding on the matter. The math is quite tough for me, since I never actually used calculus since the second undergraduate year. But I understand I cannot do QM without math <:-/

With deep gratitude,
Igors Mihailovs
ISSP UL

On 29/04/18 09:14, Heribert Reis Hreis%x%eie.gr wrote:
There is a nice chapter 'Introduction to Response Theory' by Thomas Pedersen in the Handbook of Computational Chemistry, written by an expert for the non-expert. 


Heribert

Disclosure: I'm a co-editor of the Handbook.

On Sat, Apr 28, 2018 at 9:21 PM, Steve Williams willsd,appstate.edu <owner-chemistry()ccl.net> wrote:
Yes....fat fingers,  small on-screen keyboard, aggressive autocorrect, and poor proofreading is not a good combination. I have given copies of this book to half a dozen or so undergraduate research students as graduation presents over the past several years. Sorry for mangling your name Chris Cramers....your book is a nice, quite readable introduction to our broad field.
Steve

On Sat, Apr 28, 2018, 1:53 PM John Keller jwkeller**alaska.edu <owner-chemistryÌl.net> wrote:

Hi,

Actually, Chris Cramer is the author of “Essentials..”.

Errol Lewars’  “Computational Chemistry” is another good intro to the mathematics of Hartree-Fock MO method and basis functions. It has exercises for the student, with answers in the back of the book.

John Keller

 

From: Steve Williams willsd:-:appstate.edu
Sent: Saturday, April 28, 2018 2:58 AM
To: Keller, John W
Subject: CCL:G: Magnitude of static field used for calculation ofpolarizability

 

I think Chris Farmer's book "Essentials of Computational Chemistry" would be a good place to start. It have quite a bit on how various methods work and does not have a great deal of mathematical details. 

Steve Williams 

 

On Sat, Apr 28, 2018, 2:58 AM Igors Mihailovs igorsm{=}cfi.lu.lv <owner-chemistry^^ccl.net> wrote:

Dear Dr. Lehtola,

Can You please suggest something good to read about the theory of CPHF and response functions? I have performed some literature search but it was quite hard to me to sum it up to get at least some understanding of "how it works": I have never attended any serious course on quantum mechanics or chemistry, and I didn't find much literature for laymen like me either. Most books I have read contain either the essential basics or deep discussion, being quite sparse in between.

With deep gratitude,
Igors Mihailovs
ISSP UL

On 26/04/18 20:54, Susi Lehtola susi.lehtola- -alumni.helsinki.fi wrote:


Sent to CCL by: Susi Lehtola [susi.lehtola^alumni.helsinki.fi]
On 04/26/2018 03:46 PM, Igors Mihailovs igorsm : cfi.lu.lv wrote:

Dear Suresh,

By default, Gaussian uses CPHF for polarizabilities (quite different from the response formalism, as far as I can judge – /can anyone comment on that?/)

CPHF *is* linear response. 

 


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