From owner-chemistry@ccl.net Thu Sep 1 06:58:00 2016 From: "Schleife, Andre schleife]-[illinois.edu" To: CCL Subject: CCL: APS March Meeting 2017, Focus Topic Message-Id: <-52367-160831234148-30106-HwMo3iy+KgeSf1DISsAasA::server.ccl.net> X-Original-From: "Schleife, Andre" Content-ID: <77BA6EE982DBBD48BE6B7622A0709B54::mx.uillinois.edu> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 1 Sep 2016 03:41:42 +0000 MIME-Version: 1.0 Sent to CCL by: "Schleife, Andre" [schleife++illinois.edu] Dear colleagues, Abstract submission for the APS March Meeting (March 13-17, 2017 - New Orleans, LA) is now open! We would like to draw your attention to the Focus Topic "First-Principles Modeling of Excited-State Phenomena in Materials", organized by Noa Marom, Andre Schleife, Volker Blum, and Emmanuel Kioupakis (cross-listed as 16.1.6, 5.1.8, 12.1.8, and 14.1.3): https://www.aps.org/units/dcomp/meetings/focus-topics.cfm Many properties of functional materials, interfaces, and nano-structures derive from electronic excitations. These processes determine properties such as ionization potential and electron affinity, optical spectra and exciton binding energies, electron-phonon coupling, charge transition levels, and energy level alignment at interfaces. Hot carriers in semiconductors and nanostructures are generated, transition between excited states, transfer energy to the lattice, and recombine with each other. A proper description of electronic excitations requires theoretical approaches that go beyond ground state density functional theory. Advances in high performance computing and scalable implementations in several popular electronic structure packages enable further progress. While sophisticated calculations are accessible for many users and feasible for large, complex systems, these methods require cutting-edge expertise in order to successfully interpret experiments. This focus topic is dedicated to recent advances in many-body perturbation theory and electron-ion dynamics methods for electronic excitations: challenges, scalable implementations in electronic structure codes, and applications to functional materials, interfaces, molecules, and nano-structures. It aims to attract researchers working on the nexus of electronic and optical properties of materials, hot electron dynamics, and device physics. This FT is a merge of the two 2016 FTs "Many-Body Perturbation Theory for Electronic Excitations in Materials" and "Theory and Simulation of Excited-state Phenomena in Semiconductors and Nanostructures". If you are working in these fields of research, please consider submitting your contributed abstract to our focus session! Apologies for cross-posting, but a strong showing from the community will ensure the FT's success and continuity. We wish you a pleasant fall semester! With best regards, Noa Marom, Andre Schleife, Volker Blum, Emmanouil Kioupakis. -- André Schleife Blue Waters Assistant Professor Department of Materials Science and Engineering University of Illinois, Urbana-Champaign Email: schleife(_)illinois.edu Phone: +1 (217) 244 0339 Web: http://schleife.matse.illinois.edu From owner-chemistry@ccl.net Thu Sep 1 09:29:01 2016 From: "Divya . divya(-)iitk.ac.in" To: CCL Subject: CCL:G: Solvent problem in Gaussian Message-Id: <-52368-160901080025-2470-jur/QJqXPeUpciokx2/TaA+/-server.ccl.net> X-Original-From: "Divya ." Date: Thu, 1 Sep 2016 08:00:24 -0400 Sent to CCL by: "Divya ." [divya=iitk.ac.in] I am running a Dipole solvent calculation in Gaussian as follows: #p 6-31g(d,p) b97d SCRF(Dipole,A0=5.5,eps=78.39) My molecule is almost linear and approximately 11 Angstroms long. In that case, what is the optimum value of A0 that I should use ? Moreover, is there a default value of A0, where Gaussian itself decides the appropriate value for A0 based on the molecule ? If yes, how do I set A0 to the default value ? when I run a calculation without specifying A0: #p 6-31g(d,p) b97d SCRF(Dipole,eps=78.39) I get the error: WANTED A FLOATING POINT NUMBER AS INPUT. FOUND AN INTEGER AS INPUT. 1 2 1.0 3 1.0 4 1.0 9 1.0 I am fairly new to Gaussian usage and thus some of my questions may be too basic but any assistance will be very helpful divya divya .. iitk.ac.in From owner-chemistry@ccl.net Thu Sep 1 10:57:00 2016 From: "Adam Tenderholt atenderholt[a]gmail.com" To: CCL Subject: CCL: HOMO energy and redox potential Message-Id: <-52369-160901101804-8917-ueoqQ+HZW5+FrynKUsWCtw- -server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=001a113d092a45500e053b72e11a Date: Thu, 01 Sep 2016 14:17:44 +0000 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt[#]gmail.com] --001a113d092a45500e053b72e11a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Muhammad, Unless there is some underlying physical reason that allows one to derive the the relationship you proposed, I think it's just a mathematical fit. If you change the exponent on r, from say 2 to 6, you'll still get "reasonable" linear fits for IP ~ log(-k). For example, here's r^3: > k3 =3D V/(m*(r^3)) > pro <- lm(IP ~ log(-k3)) > summary(pro) Call: lm(formula =3D IP ~ log(-k3)) Residuals: 1 2 3 4 5 -11.023 27.474 -15.087 2.521 -3.885 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -1892.162 377.784 -5.009 0.01532 * log(-k3) 32.791 5.304 6.182 0.00852 ** --- Signif. codes: 0 =E2=80=98***=E2=80=99 0.001 =E2=80=98**=E2=80=99 0.01 =E2= =80=98*=E2=80=99 0.05 =E2=80=98.=E2=80=99 0.1 =E2=80=98 =E2=80=99 1 Residual standard error: 19.37 on 3 degrees of freedom Multiple R-squared: 0.9272, Adjusted R-squared: 0.903 F-statistic: 38.22 on 1 and 3 DF, p-value: 0.008523 Best, Adam On Mon, Aug 29, 2016 at 10:24 AM Muhammad Abduh Nasution abduh^ mhs.unimed.ac.id wrote: > > Sent to CCL by: "Muhammad Abduh Nasution" [abduh]~[mhs.unimed.ac.id] > Dear CCL members. > First, forgive me if this > discussion may be not too > computational chemistry. I've > read many literature states that > there are relationship between > HOMO energy and redox > potential, even this topic can be > found on CCL archive. So I try to > relate them based on data from > "Oxtoby, D. W. (2008). > Principles of Modern > Chemistry" and "Lide, David R. > (ed). (2005). CRC Handbook of > Chemistry and Physics". I found > that Ionization Potential of > alkali metal and logaritmic > function from \frac{V}{Mr\times > r^5}\ (where V is redox potential > in Volt, Mr is relative mass of > atom in kg, and r is atomic radii > in m), is have strong correlation > showed by its R-squared. Here > is script written in R, altough > basically I'm python > programmer. > # data sequences of alkali > metal properties > > element<- > c('Li','Na','K','Rb','Cs') > # Ionization Potential of alkali > metal > > IP<- > c(520.2,495.8,418.8,403,375.7) > # redox potential of alkali metal > > V<- c(-3.0401, -2.71, -2.931, - > 2.98, -3.026) > # defining Angstrom unit > > A =3D 10^-10 > # atomic radii of alkali metal > > r<- c(1.52*A, 1.86*A, 2.27*A, > 2.47*A, 2.65*A) > # atomic relative mass of alkali > metal in kg > > m<- c(0.0069412, > 0.02298977, 0.03909831, > 0.08546783, 0.132905452) > # defining k > > k =3D V/(m*(r^5)) > # relating between k and > ionization potential > > data <- data.frame(x=3Dlog(-k), > y=3DIP) > > pro <- lm(y ~ x, data=3Ddata) > > summary(pro) > Call: lm(formula =3D y ~ x, data =3D > data) Residuals: 1 2 3 4 5 - > 10.883 25.245 -13.378 2.646 - > 3.629 Coefficients: Estimate > Std. Error t value Pr(>|t|) > (Intercept) -14167.3 2164.1 - > 6.547 0.00725 ** x 3074.9 > 455.5 6.751 0.00664 ** --- > Signif. codes: 0 '***' 0.001 '**' > 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual > standard error: 17.84 on 3 > degrees of freedom Multiple R- > Squared: 0.9382, Adjusted R- > squared: 0.9177 F-statistic: > 45.58 on 1 and 3 DF, p-value: > 0.006638 > > data.entry(data) > > plot(data) > > Well, is it relationship right? or it > is just mathematical fit? If it is > right, what theory behind it? I've > search for it but until now I not > get the theory. > Best Regards > > Muhammad Abduh > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a113d092a45500e053b72e11a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Muhammad,

Unless there is some under= lying physical reason that allows one to derive the the relationship you pr= oposed, I think it's just a mathematical fit. If you change the exponen= t on r, from say 2 to 6, you'll still get "reasonable" linear= fits for IP ~ log(-k). For example, here's r^3:

> k3 =3D V/(m*(r^3))
<= font face=3D"monospace">> pro <- lm(IP ~ log(-k3))
<= font face=3D"monospace">> summary(pro)

Call:
<= div>lm(formula =3D IP ~ log(-k3))

Re= siduals:
=C2=A0 =C2=A0 =C2=A0 1 = =C2=A0 =C2=A0 =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 3 =C2=A0 =C2=A0 =C2=A0 4 =C2=A0= =C2=A0 =C2=A0 5=C2=A0
-11.023 = =C2=A027.474 -15.087 =C2=A0 2.521 =C2=A0-3.885=C2=A0

Coeffici= ents:
=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0Estimate Std. Error t value Pr(>|t|) =C2=A0=C2=A0
(Intercept) -1892.162 =C2=A0 =C2= =A0377.784 =C2=A0-5.009 =C2=A00.01532 *=C2=A0
log(-k3) =C2=A0 =C2=A0 =C2=A0 32.791 =C2=A0 =C2=A0 =C2=A05.3= 04 =C2=A0 6.182 =C2=A00.00852 **
= ---
Signif. codes: =C2=A00 =E2=80= =98***=E2=80=99 0.001 =E2=80=98**=E2=80=99 0.01 =E2=80=98*=E2=80=99 0.05 = =E2=80=98.=E2=80=99 0.1 =E2=80=98 =E2=80=99 1

Residual stan= dard error: 19.37 on 3 degrees of freedom
Multiple R-squared: =C2=A00.9272, Adjusted R-squared: =C2=A00.903=C2=A0
F-statistic: 38.22 on 1 and 3 DF, =C2= =A0p-value: 0.008523

Best,
=
Adam



On Mon, Aug 29, 2016 at 10:24 AM Muhammad= Abduh Nasution abduh^mhs.unimed.ac.id<= /a> <owner-chemistry(~)ccl.net<= /a>> wrote:

Sent to CCL by: "Muhammad Abduh Nasution" [abduh]~[mhs.unimed.ac.id= ]
Dear CCL members.
First, forgive me if this
discussion may be not too
computational chemistry. I've
read many literature states that
there are relationship between
HOMO energy and redox
potential, even this topic can be
found on CCL archive. So I try to
relate them based on data from
"Oxtoby, D. W. (2008).
Principles of Modern
Chemistry" and "Lide, David R.
(ed). (2005). CRC Handbook of
Chemistry and Physics". I found
that Ionization Potential of
alkali metal and logaritmic
function from \frac{V}{Mr\times
r^5}\ (where V is redox potential
in Volt, Mr is relative mass of
atom in kg, and r is atomic radii
in m), is have strong correlation
showed by its R-squared. Here
is script written in R, altough
basically I'm python
programmer.
# data sequences of alkali
metal properties
> element<-
c('Li','Na','K','Rb','Cs')
# Ionization Potential of alkali
metal
> IP<-
c(520.2,495.8,418.8,403,375.7)
# redox potential of alkali metal
> V<- c(-3.0401, -2.71, -2.931, -
2.98, -3.026)
# defining Angstrom unit
> A =3D 10^-10
# atomic radii of alkali metal
> r<- c(1.52*A, 1.86*A, 2.27*A,
2.47*A, 2.65*A)
# atomic relative mass of alkali
metal in kg
> m<- c(0.0069412,
0.02298977, 0.03909831,
0.08546783, 0.132905452)
# defining k
> k =3D V/(m*(r^5))
# relating between k and
ionization potential
> data <- data.frame(x=3Dlog(-k),
y=3DIP)
> pro <- lm(y ~ x, data=3Ddata)
> summary(pro)
Call: lm(formula =3D y ~ x, data =3D
data) Residuals: 1 2 3 4 5 -
10.883 25.245 -13.378 2.646 -
3.629 Coefficients: Estimate
Std. Error t value Pr(>|t|)
(Intercept) -14167.3 2164.1 -
6.547 0.00725 ** x 3074.9
455.5 6.751 0.00664 ** ---
Signif. codes: 0 '***' 0.001 '**'
0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual
standard error: 17.84 on 3
degrees of freedom Multiple R-
Squared: 0.9382, Adjusted R-
squared: 0.9177 F-statistic:
45.58 on 1 and 3 DF, p-value:
0.006638
> data.entry(data)
> plot(data)

Well, is it relationship right? or it
is just mathematical fit? If it is
right, what theory behind it? I've
search for it but until now I not
get the theory.
Best Regards

Muhammad Abduh



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(~)ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

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

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

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--001a113d092a45500e053b72e11a-- From owner-chemistry@ccl.net Thu Sep 1 11:31:00 2016 From: "Thomas Manz thomasamanz]*[gmail.com" To: CCL Subject: CCL:G: Solvent problem in Gaussian Message-Id: <-52370-160901112856-6936-GatJaWRxiRtQjRjcXaK60Q:+:server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=94eb2c08853cdcdfa0053b73de7f Date: Thu, 1 Sep 2016 09:28:49 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz++gmail.com] --94eb2c08853cdcdfa0053b73de7f Content-Type: text/plain; charset=UTF-8 Hi Divya, Onsager model is for spherical molecules, so it isn't appropriate for your system. You should look into the polarizable continuum medium (PCM) method, which can handle molecules of arbitrary shape. Best, Tom On Thu, Sep 1, 2016 at 6:00 AM, Divya . divya(-)iitk.ac.in < owner-chemistry[A]ccl.net> wrote: > > Sent to CCL by: "Divya ." [divya=iitk.ac.in] > I am running a Dipole solvent calculation in Gaussian as follows: > > #p 6-31g(d,p) b97d SCRF(Dipole,A0=5.5,eps=78.39) > > My molecule is almost linear and approximately 11 Angstroms long. In > that case, what is the optimum value of A0 that I should use ? Moreover, > is there a default value of A0, where Gaussian itself decides the > appropriate value for A0 based on the molecule ? If yes, how do I set A0 > to the default value ? > > when I run a calculation without specifying A0: > > #p 6-31g(d,p) b97d SCRF(Dipole,eps=78.39) > > I get the error: > > WANTED A FLOATING POINT NUMBER AS INPUT. > FOUND AN INTEGER AS INPUT. > 1 2 1.0 3 1.0 4 1.0 9 1.0 > > > I am fairly new to Gaussian usage and thus some of my questions may be > too basic but any assistance will be very helpful > > divya > divya|iitk.ac.in> > > --94eb2c08853cdcdfa0053b73de7f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Divya,

Onsager model is for spherica= l molecules, so it isn't appropriate for your system.
You= should look into the polarizable continuum medium (PCM) method, which can = handle molecules of arbitrary shape.

Best,

Tom

On Thu, Sep 1, 2016 at 6:00 AM, Divya . divya(-)iitk.ac.in <owner-chemistry[A]ccl.net> = wrote:

Sent to CCL by: "Divya=C2=A0 ." [divya=3Diitk.ac.in]
I am running a Dipole solvent calculation in Gaussian as follows:

#p=C2=A0 6-31g(d,p) b97d SCRF(Dipole,A0=3D5.5,eps=3D78.39)

My molecule is almost linear and approximately 11 Angstroms long.=C2=A0 In<= br> that case, what is the optimum value of A0 that I should use ?=C2=A0 Moreov= er,
is there a default value of A0, where Gaussian itself decides the
appropriate value for A0 based on the molecule ? If yes, how do I set A0 to the default value ?

when I run a calculation without specifying A0:

#p=C2=A0 6-31g(d,p) b97d SCRF(Dipole,eps=3D78.39)

I get the error:

WANTED A FLOATING POINT NUMBER AS INPUT.
=C2=A0 FOUND AN INTEGER AS INPUT.
=C2=A0 1 2 1.0 3 1.0 4 1.0 9 1.0


I am fairly new to Gaussian usage and thus some of my questions may be
too basic but any assistance will be very helpful

divya
divya|ii= tk.ac.in



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[A]ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/= ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST[A]ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/= ccl/send_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/s= ub_unsub.shtml

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

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

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/



--94eb2c08853cdcdfa0053b73de7f-- From owner-chemistry@ccl.net Thu Sep 1 12:13:00 2016 From: "Igors Mihailovs igors.mihailovs0^gmail.com" To: CCL Subject: CCL:G: Solvent problem in Gaussian Message-Id: <-52371-160901115729-26542-pbg2xXEkhUVlZ6sMJCyvtg*_*server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=94eb2c05608e02505f053b7445c4 Date: Thu, 1 Sep 2016 18:57:03 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0_+_gmail.com] --94eb2c05608e02505f053b7445c4 Content-Type: text/plain; charset=UTF-8 Dear Divya, Is there really need to use Onsager solvation model nowadays? SCRF=CPCM can provide you quite reliable results for almost no additional computational cost, as, for example, we shown in this article . With best regards, Igors Mihailovs engineer/PhD Student ISSP, University of Latvia 2016-09-01 15:00 GMT+03:00 Divya . divya(-)iitk.ac.in < owner-chemistry..ccl.net>: > > Sent to CCL by: "Divya ." [divya=iitk.ac.in] > I am running a Dipole solvent calculation in Gaussian as follows: > > #p 6-31g(d,p) b97d SCRF(Dipole,A0=5.5,eps=78.39) > > My molecule is almost linear and approximately 11 Angstroms long. In > that case, what is the optimum value of A0 that I should use ? Moreover, > is there a default value of A0, where Gaussian itself decides the > appropriate value for A0 based on the molecule ? If yes, how do I set A0 > to the default value ? > > when I run a calculation without specifying A0: > > #p 6-31g(d,p) b97d SCRF(Dipole,eps=78.39) > > I get the error: > > WANTED A FLOATING POINT NUMBER AS INPUT. > FOUND AN INTEGER AS INPUT. > 1 2 1.0 3 1.0 4 1.0 9 1.0 > > > I am fairly new to Gaussian usage and thus some of my questions may be > too basic but any assistance will be very helpful > > divya > divya|iitk.ac.in> > > --94eb2c05608e02505f053b7445c4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Divya,

Is there really need to use Onsager solvation model nowadays? SCRF=3DCPCM can provide you quite reliable results for almost no additional computational cost, as, for example, we shown in this article.

With best regards,

Igors Mihailovs

engineer/PhD Student

ISSP, University of Latvia


2016-09= -01 15:00 GMT+03:00 Divya . divya(-)iitk.ac.i= n <owner-chemistry..ccl.net>:

Sent to CCL by: "Divya=C2=A0 ." [divya=3Diitk.ac.in]
I am running a Dipole solvent calculation in Gaussian as follows:

#p=C2=A0 6-31g(d,p) b97d SCRF(Dipole,A0=3D5.5,eps=3D78.39)

My molecule is almost linear and approximately 11 Angstroms long.=C2=A0 In<= br> that case, what is the optimum value of A0 that I should use ?=C2=A0 Moreov= er,
is there a default value of A0, where Gaussian itself decides the
appropriate value for A0 based on the molecule ? If yes, how do I set A0 to the default value ?

when I run a calculation without specifying A0:

#p=C2=A0 6-31g(d,p) b97d SCRF(Dipole,eps=3D78.39)

I get the error:

WANTED A FLOATING POINT NUMBER AS INPUT.
=C2=A0 FOUND AN INTEGER AS INPUT.
=C2=A0 1 2 1.0 3 1.0 4 1.0 9 1.0


I am fairly new to Gaussian usage and thus some of my questions may be
too basic but any assistance will be very helpful

divya
divya|ii= tk.ac.in



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY..ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/= ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST..ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/= ccl/send_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/s= ub_unsub.shtml

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

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

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/



--94eb2c05608e02505f053b7445c4--