From owner-chemistry@ccl.net Sat Jan 11 07:31:01 2020 From: "Guzman, Francisco fg58-,-njit.edu" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53944-200111072939-14412-YwoKRVoPewwqq8X0nP5tjw%server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="000000000000e2ee24059bdc64f5" Date: Sat, 11 Jan 2020 07:29:20 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58]=[njit.edu] --000000000000e2ee24059bdc64f5 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable If needed, here is the link to Ikura's thermo.pl script itself. Just copy/pasta and run using "perl thermo.pl" https://www.nist.gov/system/files/documents/2017/03/01/thermo.txt On Fri, Jan 10, 2020 at 4:00 PM John Keller jwkeller:alaska.edu < owner-chemistry#%#ccl.net> wrote: > Sent to CCL by: John Keller [jwkeller++alaska.edu] > > HI, > > I tried the NIST website as suggested, but I got the following message: > > =E2=80=9CThe requested URL "https://www.nist.gov/cgi-bin/thermo_cgi.pl" w= as not > found on this server.=E2=80=9D > > One can also upload Gaussian (and several other program) .log files to th= e > free WebMO demo site, which will parse them completely, including a table > of frequencies that can be animated. > > > > https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi > > > > Best, > > John Keller > > University of Alaska Fairbanks > > > > > > Sent from Mail for > Windows 10 > > > > *From: *Grant Hill grant.hill _ sheffield.ac.uk > > *Sent: *Friday, January 10, 2020 9:07 AM > *To: *Keller, John W > *Subject: *CCL:G: Recomputing Free energy at different temperature from > Gaussian output > > > > > > Sent to CCL by: Grant Hill [grant.hill]-[sheffield.ac.uk] > > If I understand what you want correctly, this can be done on the NIST > website: > https://www.nist.gov/mml/csd/chemical-informatics-research-group/thermody= namics-functions-gaussian-output-files > > > > You can also download the underlying perl script for command line > automation. > > > > Hope this helps, > > Grant > > > > > > > > > On 10 Jan 2020, at 13:54, Fleurat-Lessard Paul Paul.Fleurat-Lessard^ > u-bourgogne.fr wrote: > > > > > > > > > Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^ > u-bourgogne.fr] > > > Dear colleagues, > > > > > > In one project using Gaussian09, one student computed the free energies > at room > > > temperature instead of T=3D110C. I usually use a small script based on > Freqchk > > > to correct for this.. but, to save some disk space in archiving, the > student > > > has deleted many CheckPoint files. > > > I am thus looking for some codes/scripts that would parse the Gaussian > output > > > file to compute the thermochemical functions from it and not from the > chk file. > > > I have tens of files so I need something that can be used in command > line with > > > no graphical user interface. > > > > > > Could you help me in finding such a tool? > > > > > > Best regards, > > > Paul.> > > > > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > the strange characters on the top line to the _+_ sign. You can also > > > > E-mail to subscribers: CHEMISTRY_+_ccl.net or use: > > > > > > E-mail to administrators: CHEMISTRY-REQUEST_+_ccl.net or use> > > > > > > > - 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 look up th= e > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY#%#ccl.net or use:Before posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail > bounces from CCL with 5.7.1 error, check:--=20 Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58#%#njit.edu, guzman.research#%#gmail.com --000000000000e2ee24059bdc64f5 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
If needed, here is the link to Ikura's thermo.pl script itself. Just copy/pasta and run usi= ng "perl thermo.pl"



On Fri, Jan 10, 2020 at 4:00 PM John Kel= ler jwkeller:alaska.edu <owner-chemistry#%#ccl.net> wrote:
Sent to CCL by: John Keller [jwkeller++alaska.edu]

HI,

I tried the NIST webs= ite as suggested, but I got the following message:

=E2=80=9CThe requ= ested URL "https://www.nist.gov/cgi-bin/thermo_cgi.pl" was not = found on this server.=E2=80=9D

One can also upl= oad Gaussian (and several other program) .log files to the free WebMO demo = site, which will parse them completely, including a table of frequencies th= at can be animated.

=C2=A0=

https://www.webmo.net/demoserver/cgi-bin/webmo/login.cg= i

=C2=A0

Best,

John Keller

University of Alaska Fairbanks

= =C2=A0

=C2=A0

Sent from Mail for Windows 10

=C2=A0

From: Grant Hill grant.hill _ sheffield.ac.uk
Sent: Friday, January 10, 2020 9:07 AM
To: Keller, John W
Subject: CCL:= G: Recomputing Free energy at different temperature from Gaussian output

=C2=A0

=C2=A0

Sent to CCL by: Grant Hill= [grant.hill]-[sheffie= ld.ac.uk]

If I understand what you want corre= ctly, this can be done on the NIST website: https://www.nist.gov/mml/csd/chemical-i= nformatics-research-group/thermodynamics-functions-gaussian-output-files

=C2=A0

= You can also download the underlying perl script for command line automatio= n.

=C2=A0

Hope this helps,

Grant

=C2=A0

=C2=A0

=C2=A0

> On = 10 Jan 2020, at 13:54, Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr <owner-chemistry__ccl.ne= t> wrote:

>

= >

> Sent to CCL by: "Fleurat-Lessard= =C2=A0 Paul" [Paul.Fleurat-Lessard^u-bourgogne.fr]

> Dear co= lleagues,

>

> In= one project using Gaussian09, one student computed the free energies at ro= om

> temperature instead of T=3D110C. I usual= ly use a small script based on Freqchk

> to c= orrect for this.. but, to save some disk space in archiving, the student

> has deleted many CheckPoint files.

> I am thus looking for some codes/scripts that would pa= rse the Gaussian output

> file to compute the= thermochemical functions from it and not from the chk file.

> I have tens of files so I need something that can be used = in command line with

> no graphical user inte= rface.

>

> Could= you help me in finding such a tool?

>

> Best regards,

> Paul.= >

>=C2=A0

=C2=A0

=C2=A0=

=C2=A0

-= =3D This is automatically added to each message by the mailing script =3D-<= /p>

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

=C2=A0

E-mail to subscribers: CHE= MISTRY_+_ccl.net or use:

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

=C2=A0

E-mail to administrat= ors: CHEMISTRY-REQUEST_+_ccl.n= et or use

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0

<= p class=3D"MsoNormal">=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.net/chemistry/sub_unsub= .shtml

=C2=A0

=C2=A0

Job: http://www.ccl.net/jobs =

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

= =C2=A0

Search Messages: http://www.c= cl.net/chemistry/searchccl/index.shtml

=C2=A0

=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 http://ww= w.ccl.net/spammers.txt

=C2=A0

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

=C2=A0

=C2=A0

=C2= =A0

- This is automatically added to each message by the mailing script -E-mail to subscribers: CHEMISTRY#%#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 Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.n= et/jobs=20 Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://= www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--
Francisco Guzman
PhD Candidate
Otto= H. York Department of Chemical, Biological and Pharmaceutical Engineering<= br>New Jersey Institute of Technology
--000000000000e2ee24059bdc64f5-- From owner-chemistry@ccl.net Sat Jan 11 12:40:00 2020 From: "achintya:chem.iitb.ac.in" To: CCL Subject: CCL: The best method to calculate the ionization potential of organic mol. Message-Id: <-53945-200111072317-13851-NqPyuqn85rCmCMGVaK7BbQ%x%server.ccl.net> X-Original-From: achintya.:.chem.iitb.ac.in Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 11 Jan 2020 18:01:32 +0530 MIME-Version: 1.0 Sent to CCL by: achintya^^chem.iitb.ac.in Dear All, As the original message as about global reactivity parameters, let me add that the electronegativity and hardness have been defined by Pearson and Parr in terms of derivatives of the energy as a function of the number of electrons (https://pubs.acs.org/doi/abs/10.1021/ja00364a005); A that a finite difference approach for those ultimately leads to these redefinitions in terms of IP and EA. Here one needs to calculate the vertical IP and EA since the derivatives in principle should be taken at the reference geometry. A good reference in the topic can be found in chapter 5 of the book "Density-Functional Theory of Atoms and Molecules." By Parr and Yang. For IP calculation my favorite(of course I am biassed!!) is IP-EOM-CCSD. The EOMCCSD method calculates the IP in a single calculation starting from the neutral state. The method is spin adapted, includes a balanced description of the correlation and relaxation effects and provides consistently superior accuracy across a variety of molecules. There is an EA version as well (EA-EOM-CCSD). With the recent DLPNO implementation in ORCA, the computation cost has become almost comparable to DFT methods. So, you can give a try if you are interested in going beyond DFT. With best regards, Achintya > Dear Robert, > > > "adiabatic" does indeed mean many things in many fields, and the > double-negative "non-adaiabatic" adds to the confusion about this term. > But, as Igors wrote, in the context of ionization potentials (and > excitation energies), I've only ever seen the use of "vertical" and > "adiabatic" to mean "fixed-geometry" and "relaxed-geometry", respectively. > This is also the meaning of these terms in the NIST webbook and other > databases. > > > Best regards, > > > Hannes > > ________________________________ >> From: owner-chemistry+johannes.margraf==tum.de[-]ccl.net >> on behalf of Robert >> Molt r.molt.chemical.physics{}gmail.com > Sent: Tuesday, January 7, 2020 8:30:48 PM > To: Margraf, Johannes > Subject: CCL: The best method to calculate the ionization potential of > organic mol. > > I am perhaps confused on the convention of “adiabatic.” A smart man once > advised me to never use the term, since its meaning can be ambiguous ;) I > think I am using the term properly, but conventions are useful only in so > much as they make things clearer rather than less clear. > > Regardless, my meaning is as I wrote in the paragraph or as Dr. Mihailovs > wrote: the geometry-relaxed ionization state corresponds to a different > ionization energy than the geometry-not-relaxed state. Different > experiments measure one or the other, but it is not correct to say that > they are different “methods” to describe the ionization energy; they are > different physical quantities, no more the same than the Gibbs energy is > the same as a spin-orbit correction. > > On Jan 7, 2020, at 11:19 AM, Igors Mihailovs igorsm,cfi.lu.lv > > wrote: > > Dear Dr. Molt, > > I was somewhat sure that "adiabatic" ionization correspond to the relaxed > geometries. You probably intended to compare "vertical" and "adiabatic" > (or "relaxed-geometry"). Or am I wrong? As far as I know the term > "adiabatic" is because there is no further energy exchange with the > environment expected because the geometry has already been relaxed. > > I also would like to add my bit to the discussion with the following > points. > > Adiabatic ionization energies and electron affinities are the quantities > needed to compare with experimental electrochemistry, for example (see the > Marcus equation), because the adiabatic difference is the driving force, > but the reorganization energies (difference between the adiabatic and > vertical quantities) are also involved because the transition is > vibrationally-assisted. > > Also, unoccupied levels for the pure (non-hybrid) Kohn—Sham roughly > correspond to excitation energies rather than to electron affinities (see, > e.g., Baerends, E. J.; Gritsenko, O. V; van Meer, R. Phys. Chem. Chem. > Phys. 2013, 15 (39), 16408). This is lost when HF admixture is introduced > (as in hybrid functionals). > > Also, I presume that optimally tuned range-separated hybrids are a more or > less viable alternative for the costly methods because, even if they are > tuned for every particular molecule, said generalized Koopmans' theorem is > the basis for tuning. I cannot find the article right now, though, so I am > not totally sure. For TD-DFT though, they are very good > (https://pubs.acs.org/doi/abs/10.1021/ct5000617). > > With hope this is not rubbish, > Igors Mihailovs > > On 1/7/20 2:45 PM, Robert Molt > r.molt.chemical.physics{:}gmail.com wrote: > 1.) Dr. Lehtola’s suggestion is correct. A distinction should be made when > saying that “Koopmans’s theorem does not hold for DFT.” Whether or not > “the true” DFT should have Koopmans’s theorem is a subject of some > scholarly debate. Dr. Bartlett’s work is intended to be proof that a > well-formulated DFT, with emphasis on enforcing physical constraints, can > do this. This is meant to be in contrast to the zoo of highly > parameterized KS-DFT functionals, which do badly poorly outside their > parameterization range (the Minnesota functionals being an example which > are stupendous at many, many things, then bizarrely terrible in certain > circumstances outside the standard comp chem goals). > > 2.) None of this is intended to argue that Dr. Bartlett’s work is or is > not the best you can do, accuracy -wise, right here right now. > > 3.) The original question has a false dichotomy. The original question > compared adiabatic vs. relaxed excitations (re-optimizing the structure of > the cation or not) asking which was “more accurate.” This is wrong; my > emphasis is intended for clarity, not to be pejorative. These correspond > to two totally different experimental situations. If you are trying to > model ionization energies, you should re-optimize the geometries iff you > are comparing to experimental ionization energies where the system’s > molecular geometry does have time to relax. The same is true that an > adiabatic ionization energy must be compared to an adiabatic ionization > experiment. Usually, people mean the adiabatic ionization energy if they > do not qualify what they mean (but one should specify). It would be > inconsistent to use relaxed structures to compute adiabatic ionization > energies. > > One could argue to do this anyway, on the grounds of judicious > cancellation of error; I am ignorant, personally, of how errors cancel, > assuming a systematic error exists in the first place. However, in so much > as the goal of our field is to compute the right answer for the right > reasons, it is inconsistent. > > On Jan 7, 2020, at 4:08 AM, Susi Lehtola > susi.lehtola[*]helsinki.fi > > wrote: > > > Sent to CCL by: Susi Lehtola [susi.lehtola a > helsinki.fi] > On 1/7/20 12:26 AM, Daniel Glossman-Mitnik dglossman _ > gmail.com wrote: > The Koopmans' theorem (note that it is Koopmans, not Koopman) does not > (theoretically) hold within DFT and it has been always used as > approximation. However, there is another theorem that it is valid within > Generalized Kohn-Sham model (GKS) that validates the use of E(HOMO as -I. > This does not hold for A and the LUMO, but it can be said that A is equal > to -E(HOMO) of the anion. From a practical point of view, if the E(HOMO) > of the anion is equal to the E(LUMO) of the neutral, then this counterpart > of Koopmans' theorem will hold within DFT. Indeed this is an > approximation, and its accuracy will be depending on the model chemistry > chosen for your calculations. In our research group, we have been doing > investigations to find the best model chemistry that satisfies this > approximation and our published results show that the MN12SX/Def2TZVP/H20 > reproduce the values with great accuracy. Of course, there could be > another combinations that could help (including tuned density functionals > to get the desired Koopmans behavior) but most of the usually recommended > density functionals are not useful in this regard. > > Bartlett's "consistent DFT" should also be mentioned in this context; > their QTP functionals are obtained by enforcing correct excitation > spectra. See dois 10.1016/j.cplett.2016.12.017 and 10.1063/1.5116338. > -- > ------------------------------------------------------------------ > Mr. Susi Lehtola, PhD Junior Fellow, Adjunct Professor > susi.lehtola() alumni.helsinki.fi University > of Helsinki > http://susilehtola.github.io/ Finland > ------------------------------------------------------------------ > Susi Lehtola, dosentti, FT tutkijatohtori > susi.lehtola() alumni.helsinki.fi Helsingin > yliopisto > http://susilehtola.github.io/ > ------------------------------------------------------------------ > > > > > > the strange characters on the top line to the /a\ sign. You can also > > > E-mail to subscribers: CHEMISTRY/a\ccl.net or use:E-mail > to administrators: CHEMISTRY-REQUEST/a\ccl.net or > use http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/spammers.txt-- > Ar cieňu, > Igors Mihailovs > Zinâtniskais asistents > Organisko materiâlu laboratorija > LU Cietvielu fizikas institűts > Yours faithfully, > Igors Mihailovs > Research assistant > Laboratory of Organic Materials > Institute of Solid State Physics, University of Latvia > > -- Achintya Kumar Dutta Assistant Professor Chemistry Department IIT Bombay, Powai Mumbai-400076 http://www.chem.iitb.ac.in/?q=facultyuserview/183 ----------------------------------------- This email was sent using SquirrelMail. "Webmail for nuts!" http://squirrelmail.org/ From owner-chemistry@ccl.net Sat Jan 11 16:20:00 2020 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard=u-bourgogne.fr" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gauss Message-Id: <-53946-200111161924-28802-c6EHEPHW19INTVPoDCdd4g=server.ccl.net> X-Original-From: "Paul Fleurat-Lessard" Date: Sat, 11 Jan 2020 16:19:22 -0500 Sent to CCL by: "Paul Fleurat-Lessard" [Paul.Fleurat-Lessard=u-bourgogne.fr] Dear All, Thanks a lot for your quick answers. Here is a short summary: I asked for a script to parse Gaussian output file from a frequencies calculations to estimate the free energy at any temperature. * Mariusz Radon suggested to use the powerful cclib library (https://cclib.github.io) This looks very powerful, but a bit too involved for me as I do not known python :( * Grant Hill, Uche Anene and Francisco Guzman pointed me to the NIST website for "Using the output file > from a Gaussian frequency calculation to compute ideal-gas thermodynamic functions https://www.nist.gov/mml/csd/chemical-informatics-research-group/products- and-services/program-computing-ideal-gas and to the very practical (to me) Perl script thermo.pl itself: https://www.nist.gov/system/files/documents/2017/03/01/thermo.txt * John Keller suggested the very nice WebMo interface : https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi but I want a scriptable tool so I will not use it for now. * Andrew Rosen advised to use the program GoodVibes (https://github.com/bobbypaton/GoodVibes) I have not yet tested it (I have to install it) but it looks very promising for my problem. * Prof. Gabriel Merino pointed out the EyringPy program, that is quite powerful too: https://www.theochemmerida.org/eyringpy-1-0 I have tried thermo.pl and it works nicely for now. I will surely try some other options but I have to get more acquainted to Python first. Best regards, Paul. -- Fleurat-Lessard Paul, Professor Universite Bourgogne Franche Comte tel: 03 80 39 37 20 e-mail:Paul.Fleurat-Lessard++u-bourgogne.fr ICMUB, 9 avenue Alain Savary - BP 47870 21078 DIJON Cedex - FRANCE