From owner-chemistry@ccl.net Tue Jul 15 10:10:00 2014 From: "J. Phoenix himphoenixCCL\a/gmail.com" To: CCL Subject: CCL:G: Tozer's diagnostic test in Gaussian Message-Id: <-50324-140715100917-19125-pCLu+6gKjFDIg5igb/zJAQ**server.ccl.net> X-Original-From: "J. Phoenix" Date: Tue, 15 Jul 2014 10:09:16 -0400 Sent to CCL by: "J. Phoenix" [himphoenixCCL_._gmail.com] Dear CCLs, I am trying to compute the Tozer's lambda parameter that relates the spatial overlap between orbitals in a certain excitation using TDDFT calculations (JCP, 128, 044118 (2008)). The procedure I am following is to extract the overlap matrix of AOs in the Gaussian output and then compute for each MO pair: = sum_i sum_j c_1_i c_2_j , using the MO coefficients. When coefficients are taken with their sign, I get an overlap of one between the same MO, and zero between different MOs. However, when I use the absolute value of the coefficients to compute the inner product of the moduli, overlaps larger than 1 are obtained in some cases. Is there anything wrong in my procedure for computing the inner product of the moduli of two orbitals or is not expected to be a value between 0 and 1? Thanks in advance, J. From owner-chemistry@ccl.net Tue Jul 15 11:55:00 2014 From: "Susi Lehtola susi.lehtola#alumni.helsinki.fi" To: CCL Subject: CCL:G: Tozer's diagnostic test in Gaussian Message-Id: <-50325-140715114428-27229-jur/QJqXPeUpciokx2/TaA _ server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 15 Jul 2014 08:44:04 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola-#-alumni.helsinki.fi] On Tue, 15 Jul 2014 10:09:16 -0400 "J. Phoenix himphoenixCCL\a/gmail.com" wrote: > Sent to CCL by: "J. Phoenix" [himphoenixCCL_._gmail.com] > Dear CCLs, > > I am trying to compute the Tozer's lambda parameter that relates the > spatial overlap between orbitals in a certain excitation using TDDFT > calculations (JCP, 128, 044118 (2008)). The procedure I am following > is to extract the overlap matrix of AOs in the Gaussian output and > then compute for each MO pair: = sum_i sum_j c_1_i > c_2_j , using the MO coefficients. When coefficients are > taken with their sign, I get an overlap of one between the same MO, > and zero between different MOs. However, when I use the absolute > value of the coefficients to compute the inner product of the moduli, > overlaps larger than 1 are obtained in some cases. > > Is there anything wrong in my procedure for computing the inner > product of the moduli of two orbitals or is not expected to be a > value between 0 and 1? Yes, there is. Just taking the absolute value of the coefficients is meaningless, there's no connection to the physics. What you need to do is calculate the absolute value of the *orbitals*, meaning that you need to sum over ALL the contributions from the different coefficients AND the basis functions in a single point. As Tozer et al discuss, this is easily done using standard numerical integration techniques that are used to evaluate the exchange-correlation contribution in molecular DFT calculations. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Research Associate susi.lehtola===alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University ----------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 15 12:29:00 2014 From: "John McKelvey jmmckel|-|gmail.com" To: CCL Subject: CCL:G: Tozer's diagnostic test in Gaussian Message-Id: <-50326-140715122408-8122-l1+5zn3nN7gd/fIkuQHvPQ]-[server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=089e0160c4a0ee068004fe3dd53d Date: Tue, 15 Jul 2014 12:24:02 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel#,#gmail.com] --089e0160c4a0ee068004fe3dd53d Content-Type: text/plain; charset=UTF-8 Might the sum be zero because all the converged DFT MO's are orthogonal? It seems like this orthogonality condition is just what you computed. John McKelvey . On Tue, Jul 15, 2014 at 10:09 AM, J. Phoenix himphoenixCCLa/gmail.com < owner-chemistry(!)ccl.net> wrote: > > Sent to CCL by: "J. Phoenix" [himphoenixCCL_._gmail.com] > Dear CCLs, > > I am trying to compute the Tozer's lambda parameter that relates the > spatial overlap between orbitals in a certain excitation using TDDFT > calculations (JCP, 128, 044118 (2008)). The procedure I am following is to > extract the overlap matrix of AOs in the Gaussian output and then compute > for each MO pair: = sum_i sum_j c_1_i c_2_j , using > the MO coefficients. When coefficients are taken with their sign, I get an > overlap of one between the same MO, and zero between different MOs. > However, when I use the absolute value of the coefficients to compute the > inner product of the moduli, overlaps larger than 1 are obtained in some > cases. > > Is there anything wrong in my procedure for computing the inner product of > the moduli of two orbitals or is not expected to be a value between 0 and 1? > > Thanks in advance, > J.> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(!)gmail.com --089e0160c4a0ee068004fe3dd53d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Might the sum be zero because all the converged DFT M= O's are orthogonal?=C2=A0 It seems like this orthogonality condition is= just what you computed.

John McKelvey
.


On Tue, Jul 15, 2014 at 10:09 AM, J. Pho= enix himphoenixCCLa/gmail.com <owne= r-chemistry(!)ccl.net> wrote:

Sent to CCL by: "J. =C2=A0Phoenix" [himphoenixCCL_._gmail.com]
Dear CCLs,

I am trying to compute the Tozer's lambda parameter that relates the sp= atial overlap between orbitals in a certain excitation using TDDFT calculat= ions (JCP, 128, 044118 (2008)). The procedure I am following is to extract = the overlap matrix of AOs in the Gaussian output and then compute for each = MO pair: <Psi_1|Psi_2> =3D sum_i sum_j c_1_i c_2_j <X_i|X_j>, u= sing the MO coefficients. When coefficients are taken with their sign, I ge= t an overlap of one between the same MO, and zero between different MOs. Ho= wever, when I use the absolute value of the coefficients to compute the inn= er product of the moduli, overlaps larger than 1 are obtained in some cases= .

Is there anything wrong in my procedure for computing the inner product of = the moduli of two orbitals or is not expected to be a value between 0 and 1= ?

Thanks in advance,
J.



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--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel(!)gmail.com --089e0160c4a0ee068004fe3dd53d-- From owner-chemistry@ccl.net Tue Jul 15 13:05:00 2014 From: "=?ISO-8859-15?Q?Bj=F6rn_Sommer?= bjoern a CELLmicrocosmos.org" To: CCL Subject: CCL: CELLmicrocosmos neXt: 1st Call for Abstracts Message-Id: <-50327-140715095555-24821-Kug0PWvpHn1i1tXCxAt5Bw|*|server.ccl.net> X-Original-From: =?ISO-8859-15?Q?Bj=F6rn_Sommer?= Content-type: multipart/alternative; boundary="Boundary_(ID_cyEAbPoucgrpdmi9XqZ1Bg)" Date: Tue, 15 Jul 2014 15:55:47 +0200 MIME-version: 1.0 Sent to CCL by: =?ISO-8859-15?Q?Bj=F6rn_Sommer?= [bjoern(a)CELLmicrocosmos.org] This is a multi-part message in MIME format. --Boundary_(ID_cyEAbPoucgrpdmi9XqZ1Bg) Content-type: text/plain; charset=ISO-8859-15; format=flowed Content-transfer-encoding: 8BIT Dear Colleagues, I would like to invite your contributions to our workshop which will celebrate the first 10 years of our CELLmicrocosmos project. It will take place at the German Conference on Bioinformatics in Bielefeld, Germany at the 28th September 2014. CELLmicrocosmos neXt workshop: 1st Call for Abstracts A primary vision of Integrative Bioinformatics is the creation of a virtual cell. Cell Modeling and Visualization is an immense interdisiplinary task. For this purpose, in the context of the /German Conference of Bioinformatics (28.09. - 01.10.2014)/, the first CELLmicrocosmos neXt workshop will take place in /Bielefeld at the 28.09.2014/. During this event, 10 years of the CELLmicrocosmos project will be celebrated by presenting CELLmicrocosmos X and an additional hands-on workshop session. The submission for extended abstracts is now open! All topics related to cell visualization, modeling and simulation are welcome! These topics include e.g.: * Integrative Bioinformatics * Structural Bioinformatics * Cell Modeling and Visualization * Molecular Modeling and Visualization * Membrane and Vesicle Simulation * Network Analysis and Visualization * Data Integration * Text mining * Microscopic Image Segmentation * Biological Interactive Web Visualization * Stereoscopic 3D Visualization * Subcellular Localization More information and the complete call you will find at: http://neXt.CELLmicrocosmos.org The submission deadline is the 10th August 2014. For questions and submissions, please contact us at: next..CELLmicrocosmos.org On behalf of the program committee, Björn Sommer --Boundary_(ID_cyEAbPoucgrpdmi9XqZ1Bg) Content-type: text/html; charset=ISO-8859-15 Content-transfer-encoding: 8BIT Dear Colleagues,

I would like to invite your contributions to our workshop which will celebrate the first 10 years of our CELLmicrocosmos project. It will take place at the German Conference on Bioinformatics in Bielefeld, Germany at the 28th September 2014.

CELLmicrocosmos neXt workshop: 1st Call for Abstracts

A primary vision of Integrative Bioinformatics is the creation of a virtual cell. Cell Modeling and Visualization is an immense interdisiplinary task. For this purpose, in the context of the German Conference of Bioinformatics (28.09. - 01.10.2014), the first CELLmicrocosmos neXt workshop will take place in Bielefeld at the 28.09.2014. During this event, 10 years of the CELLmicrocosmos project will be celebrated by presenting CELLmicrocosmos X and an additional hands-on workshop session.

The submission for extended abstracts is now open! All topics related to cell visualization, modeling and simulation are welcome! These topics include e.g.:
  •     Integrative Bioinformatics
  •     Structural Bioinformatics
  •     Cell Modeling and Visualization
  •     Molecular Modeling and Visualization
  •     Membrane and Vesicle Simulation
  •     Network Analysis and Visualization
  •     Data Integration
  •     Text mining
  •     Microscopic Image Segmentation
  •     Biological Interactive Web Visualization
  •     Stereoscopic 3D Visualization
  •     Subcellular Localization
More information and the complete call you will find at:

http://neXt.CELLmicrocosmos.org

The submission deadline is the 10th August 2014.

For questions and submissions, please contact us at:

next..CELLmicrocosmos.org

On behalf of the program committee,

Björn Sommer

--Boundary_(ID_cyEAbPoucgrpdmi9XqZ1Bg)--