From owner-chemistry@ccl.net Sat Apr 28 01:07:01 2018 From: "Alex A. Granovsky gran::classic.chem.msu.su" To: CCL Subject: CCL: Question on OMICtools Message-Id: <-53281-180427041431-21262-3X60ZUTyXeqzFELVK5pWyg(!)server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="UTF-8"; reply-type=original Date: Fri, 27 Apr 2018 11:14:19 +0300 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran . classic.chem.msu.su] Dear Michel, thank you very much for your invaluable comments! Kind regards, Alex Granovsky -----Original Message----- > From: Michel Petitjean petitjean.chiral=gmail.com Sent: Thursday, April 26, 2018 11:06 PM To: Granovsky, Alex, A. Subject: CCL: Question on OMICtools Sent to CCL by: Michel Petitjean [petitjean.chiral^_^gmail.com] Dear Alex, OMICtools is a web database of bioinformatics resources maintained by OMICX company at Rouen (France): https://omictools.com/ See: Database 2014 (Oxford), bau069 https://doi.org/10.1093/database/bau069 They indexed several of my freewares without any counterpoart from me. They provided links to my own repository and indicated my name (as the author) and my email address (hotline), together with the full citation of the papers supporting the methods. They never requested my sources. So there no illegal use there and in my opinion it is a fair use of public data. Please check if the email you received was indeed sent from the OMICtools team (the header of the original email in source form is informative). Please do not confuse OMICtools with the OMICS Indian company (omicsgroup, omicsonline, etc.) which manages numerous journals and a huge of conferences (very diverse topics) under various names, while the name of the OMICS company is often hard to retrieve. ALL THESE JOURNALS AND CONFERENCES WERE MANY TIMES FLAGGED AS PREDATORY, SCAM, FAKE. You were probably spammed by "invitations" to submit papers or attend to conferences in various countries, and among them probably many of these "invitations" originated from OMICS, even if their name is hidden. Please be careful. Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral_._gmail.com (preferred), michel.petitjean_._univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2018-04-26 19:09 GMT+02:00 Alex A. Granovsky gran]-[classic.chem.msu.su : > Dear CCLers, > > does anybody know anything on OMICtools? > > I got a couple of strange emails from contact{}omictools.com last weeks. > > E.g.: > > ------------------- > Hi Firefly Team, > > We have some good news for you! > > The tool Firefly you engineered is now available on OMICtools (the > AI-based platform designed to help biologists identify the right > combination of tools) in the Molecular modeling category. > Feel free to visit the platform so you can discover what people are saying > about your tool. > > VISIT YOUR TOOL PAGE > > If you want to make your work more visible, sign up for free to upload > your source code and badge your skills so you can highlight your expertise > in tool development. > Got a question? We’re here to help. > > All the best, > The OMICteam > > -------------------- > > Their second email is even more suspicious. > > I did not ever get them my permission to use Firefly nor we allow Firefly > on any public (either free or commercial) computational servers or > services. > Searching the web I was not able to clarify the situation. I strongly > suspect cheating of phishing of some kind, or at least the illegal use of > our software. > I would be grateful to community for any comments. > > Kind regards, > Alex Granovskyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Apr 28 01:42:01 2018 From: "Igors Mihailovs igorsm{=}cfi.lu.lv" To: CCL Subject: CCL:G: Magnitude of static field used for calculation of polarizability Message-Id: <-53282-180427101147-12197-39RcO7Qaoy55e1JU07SZog(!)server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: en-US Content-Type: multipart/alternative; boundary="------------B9CA1C4347815BCA738367CA" Date: Fri, 27 Apr 2018 17:11:29 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm(_)cfi.lu.lv] This is a multi-part message in MIME format. --------------B9CA1C4347815BCA738367CA Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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. --------------B9CA1C4347815BCA738367CA Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit 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. 
--------------B9CA1C4347815BCA738367CA-- From owner-chemistry@ccl.net Sat Apr 28 05:28:00 2018 From: "Steve Williams willsd:-:appstate.edu" To: CCL Subject: CCL:G: Magnitude of static field used for calculation of polarizability Message-Id: <-53283-180428052645-6221-dV8PwI867S3IVPIMw2bkYw]|[server.ccl.net> X-Original-From: Steve Williams Content-Type: multipart/alternative; boundary="000000000000ccd0c7056ae537c6" Date: Sat, 28 Apr 2018 09:26:29 +0000 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd[A]appstate.edu] --000000000000ccd0c7056ae537c6 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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{=3D}cfi.lu.lv < owner-chemistry#%#ccl.net> wrote: > Dear Dr. Lehtola, > > Can You please suggest something good to read about the theory of CPHF an= d > 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 =E2=80=93 /can anyone comme= nt on > that?/) > > CPHF *is* linear response. > > --000000000000ccd0c7056ae537c6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I think Chris Farmer's book "Essentials of Compu= tational Chemistry" would be a good place to start. It have quite a bi= t on how various methods work and does not have a great deal of mathematica= l details.=C2=A0
Steve Williams=C2=A0

On Sat, Apr 28, 2018, 2:58 AM Igors = Mihailovs igorsm{=3D}cfi.lu.lv <owner-chemistry#%#ccl.net> wrote:<= br>
=20 =20 =20
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 =E2=80= =93 /can anyone comment on that?/)
CPHF *is* linear response.=C2=A0
--000000000000ccd0c7056ae537c6-- From owner-chemistry@ccl.net Sat Apr 28 09:58:00 2018 From: "Susi Lehtola susi.lehtola/./alumni.helsinki.fi" To: CCL Subject: CCL: Magnitude of static field used for calculation of polarizability Message-Id: <-53284-180428094459-30370-lph1d/9M5cpjiJA+e9QFsw{:}server.ccl.net> X-Original-From: Susi Lehtola Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sat, 28 Apr 2018 16:44:45 +0300 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola#%#alumni.helsinki.fi] On 04/27/2018 05:11 PM, 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. If you haven't studied quantum mechanics, then understanding wave function response might be a bit tricky. CPHF and response functions are molecular properties, and so good places to start are any books written on (the calculation of) molecular properties, or the molecular properties sections of introductory quantum chemistry textbooks. By googling around I found e.g. these lecture notes by Julien Toulose which appear rather well written http://surya.lct.jussieu.fr/pagesperso/toulouse/enseignement/molecular_properties.pdf and which presents CPHF as one example. -- ------------------------------------------------------------------ Mr. Susi Lehtola, PhD Junior Fellow, Adjunct Professor susi.lehtola[a]alumni.helsinki.fi University of Helsinki http://www.helsinki.fi/~jzlehtol Finland ------------------------------------------------------------------ Susi Lehtola, dosentti, FT tutkijatohtori susi.lehtola[a]alumni.helsinki.fi Helsingin yliopisto http://www.helsinki.fi/~jzlehtol ------------------------------------------------------------------ From owner-chemistry@ccl.net Sat Apr 28 13:18:00 2018 From: "John Keller jwkeller**alaska.edu" To: CCL Subject: CCL:G: Magnitude of static field used for calculation ofpolarizability Message-Id: <-53285-180428124716-7706-eVSsykVV6fwoYB7zBlM3Ug__server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary="_E90755C9-B57E-4B08-B972-5F29E86F371D_" Date: Sat, 28 Apr 2018 08:47:11 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller#alaska.edu] --_E90755C9-B57E-4B08-B972-5F29E86F371D_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Hi, Actually, Chris Cramer is the author of =E2=80=9CEssentials..=E2=80=9D. Errol Lewars=E2=80=99 =E2=80=9CComputational Chemistry=E2=80=9D is another= good intro to the mathematics of Hartree-Fock MO method and basis function= s. It has exercises for the student, with answers in the back of the book. John Keller Sent from Mail for Windows 10 > 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 ofpolarizabi= lity I think Chris Farmer's book "Essentials of Computational Chemistry" would b= e a good place to start. It have quite a bit on how various methods work an= d does not have a great deal of mathematical details.=C2=A0 Steve Williams=C2=A0 On Sat, Apr 28, 2018, 2:58 AM Igors Mihailovs igorsm{=3D}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 quit= e hard to me to sum it up to get at least some understanding of "how it wor= ks": I have never attended any serious course on quantum mechanics or chemi= stry, and I didn't find much literature for laymen like me either. Most boo= ks I have read contain either the essential basics or deep discussion, bein= g 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]=20 On 04/26/2018 03:46 PM, Igors Mihailovs igorsm : cfi.lu.lv wrote:=20 Dear Suresh,=20 By default, Gaussian uses CPHF for polarizabilities (quite different from t= he response formalism, as far as I can judge =E2=80=93 /can anyone comment = on that?/)=20 CPHF *is* linear response.=C2=A0 --_E90755C9-B57E-4B08-B972-5F29E86F371D_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8"

Hi,

Actually= , Chris Cramer is the author of =E2=80=9CEssentials..=E2=80=9D.

Errol Lewars=E2=80=99=C2=A0 =E2=80=9CComputational Chemistry= =E2=80=9D is another good intro to the mathematics of Hartree-Fock MO metho= d and basis functions. It has exercises for the student, with answers in th= e back of the book.

John Keller

 

 

Sent from Mail for Windows 10

 

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

&= nbsp;

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 Will= iams 

 

On Sat, Apr 28, 2018, 2:58 AM Igors Mihailovs igors= m{=3D}cfi.lu.lv <owner-chemistry^^ccl.net> wrote:

=

Dear Dr. Lehtola,

Can You please suggest something good t= o read about the theory of CPHF and response functions? I have performed so= me literature search but it was quite hard to me to sum it up to get at lea= st some understanding of "how it works": I have never attended an= y 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:<= o:p>


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 Sures= h,

By default, Gaussian uses CPHF for polarizabilities (quite diffe= rent from the response formalism, as far as I can judge =E2=80=93 /can anyo= ne comment on that?/)

CPHF *is* linear response. 

<= p class=3DMsoNormal> 

= --_E90755C9-B57E-4B08-B972-5F29E86F371D_-- From owner-chemistry@ccl.net Sat Apr 28 14:22:01 2018 From: "Steve Williams willsd,appstate.edu" To: CCL Subject: CCL:G: Magnitude of static field used for calculation ofpolarizability Message-Id: <-53286-180428142134-3062-50YMMFyCrIh58EcG9s23UQ]|[server.ccl.net> X-Original-From: Steve Williams Content-Type: multipart/alternative; boundary="0000000000004c75d7056aecb00c" Date: Sat, 28 Apr 2018 18:21:15 +0000 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd[*]appstate.edu] --0000000000004c75d7056aecb00c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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-chemistry[*]ccl.net> wrote: > Hi, > > Actually, Chris Cramer is the author of =E2=80=9CEssentials..=E2=80=9D. > > Errol Lewars=E2=80=99 =E2=80=9CComputational Chemistry=E2=80=9D is anoth= er good intro to the > mathematics of Hartree-Fock MO method and basis functions. It has exercis= es > for the student, with answers in the back of the book. > > John Keller > > > > > > Sent from Mail for > Windows 10 > > > > *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{=3D}cfi.lu.lv < > owner-chemistry^^ccl.net> wrote: > > Dear Dr. Lehtola, > > Can You please suggest something good to read about the theory of CPHF an= d > 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 =E2=80=93 /can anyone comme= nt on > that?/) > > CPHF *is* linear response. > > > --0000000000004c75d7056aecb00c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Yes....fat fingers,=C2=A0 small on-screen keyboard, aggre= ssive autocorrect, and poor proofreading is not a good combination. I have = given copies of this book to half a dozen or so undergraduate research stud= ents as graduation presents over the past several years. Sorry for mangling= your name Chris Cramers....your book is a nice, quite readable introductio= n to our broad field.
Steve

On Sat, Apr 28, 2018, 1:53 PM John Keller jwke= ller**alaska.edu <owner-chemistry[*]ccl.net> wrote:

Hi,

Actually, Chris Cramer is the author of =E2= =80=9CEssentials..=E2=80=9D.

Errol Lewars=E2=80= =99=C2=A0 =E2=80=9CComputational Chemistry=E2=80=9D is another good intro t= o the mathematics of Hartree-Fock MO method and basis functions. It has exe= rcises for the student, with answers in the back of the book.

John Keller

=C2=A0

=C2=A0

Sen= t from Mail for Windows 10

=C2=A0

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

=C2= =A0

I think Chris Farmer's book &= quot;Essentials of Computational Chemistry" would be a good place to s= tart. It have quite a bit on how various methods work and does not have a g= reat deal of mathematical details.=C2=A0

Ste= ve Williams=C2=A0

=C2=A0

On Sat, Apr 28, 2018, 2:58 AM Igors M= ihailovs igorsm{=3D}cfi.lu.lv <owner-chemistry^^ccl.net> wro= te:

Dear Dr. Lehtola,

Can You please= suggest something good to read about the theory of CPHF and response funct= ions? I have performed some literature search but it was quite hard to me t= o 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 boo= ks I have read contain either the essential basics or deep discussion, bein= g quite sparse in between.

With deep gratitude,
Igors MihailovsISSP UL

On 26/04/18 20:54, Susi Leh= tola 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:

<= /p>

Dear Suresh,

By default, Gaussian uses CPHF for polarizab= ilities (quite different from the response formalism, as far as I can judge= =E2=80=93 /can anyone comment on that?/)

CPHF *is* linear response.=C2=A0

=C2=A0

--0000000000004c75d7056aecb00c--