From owner-chemistry@ccl.net Thu Jan 23 09:30:01 2014
From: "Johannes Johansson johjo76(a)gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: negative values in Mulliken spin distribution
Message-Id: <-49598-140123031216-3686-N3WZIqGVr1dGbTtPpoKNhw/a\server.ccl.net>
X-Original-From: Johannes Johansson <johjo76~~gmail.com>
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Date: Thu, 23 Jan 2014 09:12:10 +0100
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Sent to CCL by: Johannes Johansson [johjo76 * gmail.com]
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Dear Haya and others,

as I understood Hayas original question it was concerning negative values
in the spin distribution on some atoms. In, for example, the Mulliken
population scheme, that only means that the net spin on those atoms is
"down" or "beta".

It is very common, normal I would say, that you get polarisation among the
spin orbitals in a unrestricted calculation. For example, even if you have
a net "alpha" spin on the central transition metal in a coordination
compound, you can find states in which the spin on a second metal ion or
ligand donor atoms (typically S, N, O) is "beta", i.e. antiferromagnetic
coupling.

"Spin down" is not the same a "negative spin density". I got the impression
that what Haya asked for was the appearance of "spin down" on some atoms,
but I might have misunderstood that.

Kind regards

Johannes Johansson

-- 
Adam Johannes Johansson
Ph.D., M.Sc.
Linkedin: http://se.linkedin.com/pub/adam-johannes-johansson/22/209/395
**************************************************************************************
Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish Pharmacist,
Humanist and Pioneer Quantum Chemist:
http://pubs.acs.org/doi/abs/10.1021/ed300024g
**************************************************************************************

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<div dir=3D"ltr">Dear Haya and others,<div><br></div><div>as I understood H=
ayas original question it was concerning negative values in the spin distri=
bution on some atoms. In, for example, the Mulliken population scheme, that=
 only means that the net spin on those atoms is &quot;down&quot; or &quot;b=
eta&quot;.</div>
<div><br></div><div>It is very common, normal I would say, that you get pol=
arisation among the spin orbitals in a unrestricted calculation. For exampl=
e, even if you have a net &quot;alpha&quot; spin on the central transition =
metal in a coordination compound, you can find states in which the spin on =
a second metal ion or ligand donor atoms (typically S, N, O) is &quot;beta&=
quot;, i.e. antiferromagnetic coupling.</div>
<div><br></div><div>&quot;Spin down&quot; is not the same a &quot;negative =
spin density&quot;. I got the impression that what Haya asked for was the a=
ppearance of &quot;spin down&quot; on some atoms, but I might have misunder=
stood that.</div>
<div><br></div><div>Kind regards</div><div><br></div><div>Johannes Johansso=
n</div><div><br></div><div class=3D"gmail_extra">-- <br>Adam Johannes Johan=
sson<br>Ph.D., M.Sc.<br>Linkedin: <a href=3D"http://se.linkedin.com/pub/ada=
m-johannes-johansson/22/209/395" target=3D"_blank">http://se.linkedin.com/p=
ub/adam-johannes-johansson/22/209/395</a><br>
***************************************************************************=
***********<br>Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swed=
ish Pharmacist, Humanist and Pioneer Quantum Chemist: <a href=3D"http://pub=
s.acs.org/doi/abs/10.1021/ed300024g" target=3D"_blank">http://pubs.acs.org/=
doi/abs/10.1021/ed300024g</a><br>
***************************************************************************=
***********<br><br>
</div></div>

--001a113322b05a65fe04f09ecc6b--


From owner-chemistry@ccl.net Thu Jan 23 10:05:01 2014
From: "Ariel Sarotti sarotti+*+iquir-conicet.gov.ar" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL:G: Problems with NBO calculations!!!
Message-Id: <-49599-140123081353-10469-4skGL+qcXTiWB/6PPj0oCw[*]server.ccl.net>
X-Original-From: "Ariel  Sarotti  " <sarotti()iquir-conicet.gov.ar>
Date: Thu, 23 Jan 2014 08:13:52 -0500


Sent to CCL by: "Ariel  Sarotti  " [sarotti|iquir-conicet.gov.ar]
Dear all,
I am trying to run NBO calculations at the M06-2X/6-311+G(d,p) level, with 
Gaussian09. The problem is that with some systems the NATURAL BOND ORBITAL 
ANALYSIS fails, and appears the following legend:

 "A bond orbital with an occupancy of  2.33066 electrons was found!
 Please check you input data"

However, when I run the NBO calculations using other basis sets, such as 6-
31+G(d), 6-311G(d), 6-311G(d,p), I have no problems at all.

The input that I am using is

# M062X/6-311+G(d,p) pop=nboread

$nbo bndidx $end

Can anyone give me some advice with this issue?

Thank you very much,

best regards,

ariel


From owner-chemistry@ccl.net Thu Jan 23 10:45:01 2014
From: "Susi Lehtola susi.lehtola**alumni.helsinki.fi" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: negative values in Mulliken spin distribution
Message-Id: <-49600-140123102622-24150-b72Rc6YnYsR4LuM0Ezoa5A%a%server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola\a/alumni.helsinki.fi>
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Date: Thu, 23 Jan 2014 17:26:12 +0200
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Sent to CCL by: Susi Lehtola [susi.lehtola * alumni.helsinki.fi]
On Thu, 23 Jan 2014 09:12:10 +0100
"Johannes Johansson johjo76(a)gmail.com" <owner-chemistry!^!ccl.net>
wrote:
> "Spin down" is not the same a "negative spin density". I got the impression
> that what Haya asked for was the appearance of "spin down" on some atoms,
> but I might have misunderstood that.

Oh but it is, since the "spin density" is defined as
 spin density = density(spin up) - density(spin down)
where both the up and down densities are non-negative.

Also, as I tried to convey in my last mail was that you can then
analyze this "density" [1] with e.g. the Mulliken method, which assigns
the density scattered all over the systems to point-like "charges"
centered on the atoms.

[1] It's not a real density since it can - and often is - negative.
-- 
---------------------------------------------------------------
Mr. Susi Lehtola, PhD             Research Associate
susi.lehtola!^!alumni.helsinki.fi   Department of Applied Physics
http://www.helsinki.fi/~jzlehtol  Aalto University
                                  Finland
---------------------------------------------------------------
Susi Lehtola, FT                  Tutkijatohtori
susi.lehtola!^!alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Aalto-yliopisto
---------------------------------------------------------------


From owner-chemistry@ccl.net Thu Jan 23 12:16:00 2014
From: "Marcel Swart marcel.swart _ icrea.cat" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: negative values in Mulliken spin distribution
Message-Id: <-49601-140123121250-24442-++VW2ui4ZzaA+2eCZTbOow]_[server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart::icrea.cat>
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Date: Thu, 23 Jan 2014 18:12:41 +0100
Mime-Version: 1.0 (Mac OS X Mail 7.1 \(1827\))


Sent to CCL by: Marcel Swart [marcel.swart|icrea.cat]

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First of all, to set things straight, it is a simplification of the
charge density, which are being assigned to atoms. Hence,
yes, it is not a real density.

The fact that it is =93negative=94 does not imply that it could not
be related to a density. In the end the charges are obtained=20
*relative* to the total number of electrons the elements have.

Simple example: water, where oxygen may have a total
Mulliken population of 8.8 electrons, and each of the
hydrogens a Mulliken population of 0.6 electrons.

These populations could be regarded as a simplification
of the charge density indeed. The fact that for the total
atomic charge we also take the nuclear charge into
account (hence leading to Mulliken charges of -0.8 for
oxygen and +0.4 for hydrogen in this case), does not
mean that these charges do not relate to a real density.
The Mulliken (spin) charges are one of a variety of
different representations of the charge (spin) density.

Marcel

On 23 Jan 2014, at 16:26 , Susi Lehtola susi.lehtola**alumni.helsinki.fi =
<owner-chemistry*o*ccl.net> wrote:

>=20
>> "Spin down" is not the same a "negative spin density". I got the =
impression
>> that what Haya asked for was the appearance of "spin down" on some =
atoms,
>> but I might have misunderstood that.
>=20
> Oh but it is, since the "spin density" is defined as
> spin density =3D density(spin up) - density(spin down)
> where both the up and down densities are non-negative.
>=20
> Also, as I tried to convey in my last mail was that you can then
> analyze this "density" [1] with e.g. the Mulliken method, which =
assigns
> the density scattered all over the systems to point-like "charges"
> centered on the atoms.
>=20
> [1] It's not a real density since it can - and often is - negative.


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Prof. Dr. Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica Computacional i Cat=E0lisi
Universitat de Girona

Facultat de Ci=E8ncies
Campus Montilivi
17071 Girona
Catalunya (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mail
marcel.swart*o*icrea.cat
marcel.swart*o*udg.edu
web
http://www.marcelswart.eu

vCard
addressbook://www.marcelswart.eu/MSwart.vcf
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


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<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Dwindows-1252"></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">First =
of all, to set things straight, it is a simplification of the<div>charge =
density, which are being assigned to atoms. Hence,</div><div>yes, it is =
not a real density.</div><div><br></div><div>The fact that it is =
=93negative=94 does not imply that it could not</div><div>be related to =
a density. In the end the charges are =
obtained&nbsp;</div><div>*relative* to the total number of electrons the =
elements have.</div><div><br></div><div>Simple example: water, where =
oxygen may have a total</div><div>Mulliken population of 8.8 electrons, =
and each of the</div><div>hydrogens a Mulliken population of 0.6 =
electrons.</div><div><br></div><div>These populations could be regarded =
as a simplification</div><div>of the charge density indeed. The fact =
that for the total</div><div>atomic charge we also take the nuclear =
charge into</div><div>account (hence leading to Mulliken charges of -0.8 =
for</div><div>oxygen and +0.4 for hydrogen in this case), does =
not</div><div>mean that these charges do not relate to a real =
density.</div><div>The Mulliken (spin) charges are one of a variety =
of</div><div>different representations of the charge (spin) =
density.</div><div><br></div><div>Marcel</div><div><br><div><div>On 23 =
Jan 2014, at 16:26 , Susi Lehtola susi.lehtola**<a =
href=3D"http://alumni.helsinki.fi">alumni.helsinki.fi</a> &lt;<a =
href=3D"mailto:owner-chemistry*o*ccl.net">owner-chemistry*o*ccl.net</a>&gt; =
wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite"><br><blockquote type=3D"cite">"Spin down" is not the same =
a "negative spin density". I got the impression<br>that what Haya asked =
for was the appearance of "spin down" on some atoms,<br>but I might have =
misunderstood that.<br></blockquote><br>Oh but it is, since the "spin =
density" is defined as<br> spin density =3D density(spin up) - =
density(spin down)<br>where both the up and down densities are =
non-negative.<br><br>Also, as I tried to convey in my last mail was that =
you can then<br>analyze this "density" [1] with e.g. the Mulliken =
method, which assigns<br>the density scattered all over the systems to =
point-like "charges"<br>centered on the atoms.<br><br>[1] It's not a =
real density since it can - and often is - =
negative.<br></blockquote></div><br><div apple-content-edited=3D"true">
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica;  font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-align: -webkit-auto; =
text-indent: 0px; text-transform: none; white-space: normal; widows: 2; =
word-spacing: 0px; -webkit-text-size-adjust: auto; =
-webkit-text-stroke-width: 0px; word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; =
border-spacing: 0px;"><div style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: =
normal; font-weight: normal; letter-spacing: normal; line-height: =
normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; =
text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; =
border-spacing: 0px; -webkit-text-decorations-in-effect: none; =
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;  "><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><br =
class=3D"Apple-interchange-newline">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>Prof=
. Dr. Marcel Swart<br><br>ICREA Research Professor at<br>Institut de =
Qu=EDmica Computacional i Cat=E0lisi<br>Universitat de =
Girona<br><br>Facultat de Ci=E8ncies<br>Campus Montilivi</div><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">17071 Girona</div><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">Catalunya =
(Spain)<br><br>tel<br>+34-972-418861<br>fax<br>+34-972-418356<br>e-mail<br=
><a =
href=3D"mailto:marcel.swart*o*icrea.cat">marcel.swart*o*icrea.cat</a><br>marce=
l.swart*o*udg.edu<br>web<br>http://www.marcelswart.eu</div><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><br></div><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">vCard<br><a =
href=3D"addressbook://www.marcelswart.eu/MSwart.vcf">addressbook://www.mar=
celswart.eu/MSwart.vcf</a><br>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br></div></sp=
an></div></span></div>
</div>
<br></div></body></html>=

--Apple-Mail=_49C19ED1-FE46-41F7-B37E-D9984E255BC1--


From owner-chemistry@ccl.net Thu Jan 23 13:31:00 2014
From: "Susi Lehtola susi.lehtola_._alumni.helsinki.fi" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: negative values in Mulliken spin distribution
Message-Id: <-49602-140123132723-23534-+1JNJ+GJr8niOPfHyMaiCw===server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola**alumni.helsinki.fi>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Thu, 23 Jan 2014 20:27:10 +0200
MIME-Version: 1.0


Sent to CCL by: Susi Lehtola [susi.lehtola*alumni.helsinki.fi]
On Thu, 23 Jan 2014 18:12:41 +0100
"Marcel Swart marcel.swart _ icrea.cat" <owner-chemistry##ccl.net> wrote:
> First of all, to set things straight, it is a simplification of the
> charge density, which are being assigned to atoms. Hence,
> yes, it is not a real density.

No, it is not. You're mixing concepts. Mulliken charges and Mulliken
spin charges are not the same thing. The first deals with
electric charge, while the second deals with spin. (Also, I was
talking about a probability density, which is always non-negative.)

In the former you substract electronic charge from the nuclear
charge to get the net atomic charge. For instance, O in H2O has a
negative charge due to a relative surplus of electrons. (Here,
different methods give a variety of different answers, for example
Löwdin can assign O to be positive!)

In the latter you substract the amount of spin down electrons from the
amount of spin up electrons. The value 0 will mean that there are an
equal amount of spin up and down electrons for the atom. A positive
value will mean that spin up electrons are in surplus for the atom,
while a negative value will mean that spin down electrons are in
surplus.

If you calculate a spin polarized system, e.g. the oxygen molecule with
spin multiplicity M=3, you'll have a net positive spin charge in the
system, since you'll have two more spin up electrons than spin down
electrons. Here, both oxygen atoms will have spin charge +1, although
the electric charge is 0.

On the other hand, even spin neutral systems may have atoms with large
negative and large positive charges, e.g. in the case of
antiferromagnetic couplings between atoms.
-- 
---------------------------------------------------------------
Mr. Susi Lehtola, PhD             Research Associate
susi.lehtola##alumni.helsinki.fi   Department of Applied Physics
http://www.helsinki.fi/~jzlehtol  Aalto University
                                  Finland
---------------------------------------------------------------
Susi Lehtola, FT                  Tutkijatohtori
susi.lehtola##alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Aalto-yliopisto
---------------------------------------------------------------


From owner-chemistry@ccl.net Thu Jan 23 16:24:00 2014
From: "may abdelghani may01dz]~[yahoo.fr" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: ADF in HPC
Message-Id: <-49603-140123162222-31144-9TmMKF1By5VFzWHVWrPAjw*o*server.ccl.net>
X-Original-From: "may  abdelghani" <may01dz%%yahoo.fr>
Date: Thu, 23 Jan 2014 16:22:20 -0500


Sent to CCL by: "may  abdelghani" [may01dz.:.yahoo.fr]
Dear CCL'ers
I look for a high-performance computing  clusters  that contains the Amsterdam density functional (ADF)  program
thanks