From owner-chemistry@ccl.net Thu Mar 10 02:12:01 2011 From: "Arun Manna arun.manna17{}gmail.com" To: CCL Subject: CCL:G: How to get band diagram in g09? Message-Id: <-44100-110310020934-21946-yFD6jXmKhfYJKgSZJN2kHg=-=server.ccl.net> X-Original-From: Arun Manna Content-Type: multipart/alternative; boundary=bcaec5299f8baa7075049e1b866e Date: Thu, 10 Mar 2011 12:39:27 +0530 MIME-Version: 1.0 Sent to CCL by: Arun Manna [arun.manna17-*-gmail.com] --bcaec5299f8baa7075049e1b866e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bandeira, Thank you very much for your prompt reply that helped me a lot to understand the things. With this IOP(5/103=3DN), I am able to get the energy eigenvalue at each k-points. It looks that the program has generated an automatic 3D k-mesh grid. From there using excel, I can get the 3D plot of band structure. But I want to know is it possible to specify the k-path line joining the high symmetric k-points in Brillouin zone for a system? Let's say for graphene; Gamma-->M--->K. i.e.; to have a 2D band diagram showing the popular Dirac cone picture at high symmetric K-point of Brillouin zone. Or, do I have to calculate the magnitude of k-vector from the Kxyz values printed in output file, and then plot the eigenvalues with increasing oder of k-vector magnitude to get the 2D band structure? Could you please help me to understand these points also too? Thanking you very much Arun Bandeira On Thu, Mar 10, 2011 at 3:44 AM, Nuno A. G. Bandeira nuno.bandeira|a| ist.utl.pt wrote: > You can get band structures from Gaussian using the following iop key > IOP(5/103=3DN) where N can take these values: > (Number of occupied and virtual orbitals to print for each k-point.) > > -1 Default of 5 occupieds and 5 virtuals. > 0 Default is 5 if printing turned up; otherwise 0. > N N occupieds and N virtuals. > this will give you the list of energy eigenvalues per k point. The energ= y > units are eV and you should be able to plot them using common excel > features. The k point mapping should be self evident. > > Then just excel to plot them using the output file. > > > On 09-03-2011 19:04, Arun Manna arun.manna17-$-gmail.com wrote: > > > Dear All, > > Could anyone please tell me how do I plot band structure for graphene > using g09? > I have successfully done a periodic geometry optimization of 2 atom > unit cell of graphene. > Now I want to plot the band diagram for this system along the various > high symmetric k-points > (e.g; Gamma-->M--->K). > Even if I don't know how do I specify k-path along these hight > symmetric k-points in Brillouin zone. > > Could anybody help me to solve this problem? > > Thanks in advance > > Best regards, > Arun > > > > > > > -- > Nuno A. G. Bandeira, AMRSC > Departamento de Qu=EDmica F=EDsica i Inorg=E1nica > Despatx 207, N4 - Universitat Rovira i Virgili > Campus Sescelades, Carrer Marcel.l=ED Domingo > 43007 Tarragona - SPAIN > -- > > > --=20 Arun K Manna PhD Student, TSU, JNCASR, Bangalore - 560064, India --bcaec5299f8baa7075049e1b866e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
=A0Dear Bandeira,

=A0 Thank you very much for your prompt reply = that helped me a lot to understand the
=A0 things.

=A0 With this= IOP(5/103=3DN), I am able to get the energy eigenvalue at each k-points.=A0 It looks that the program has generated an automatic 3D k-mesh grid. = > From there
=A0 using excel, I can get the 3D plot of band structure.

=A0 But I = want to know is it possible to specify the k-path line joining the high sym= metric
=A0 k-points in Brillouin zone for a system? Let's say for g= raphene; Gamma-->M--->K.
=A0 i.e.; to have a 2D band diagram showing the popular Dirac cone picture = at high symmetric
=A0 K-point of Brillouin zone.
=A0
=A0 Or, do I= have to calculate the magnitude of k-vector from the Kxyz values printed i= n output
=A0=A0 file, and then plot the eigenvalues with increasing oder of k-vector= magnitude to get the 2D band
=A0=A0 structure?

=A0 Could you pl= ease help me to understand these points also too?

=A0 Thanking you v= ery much
=A0 Arun
Bandeira
On Th= u, Mar 10, 2011 at 3:44 AM, Nuno A. G. Bandeira nuno.bandeira|a|ist.utl.pt <owner-chemistry=-=ccl.net> wrote:
=20 =20 =20 =20
You can get band structures from Gaussian using the following iop key
IOP(5/103=3DN) where N can take these values:
(Number of occupied and virtual orbitals to print for each k-point.)

-1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Default of 5 occupieds and 5 virtuals.
0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Def= ault is 5 if printing turned up; otherwise 0.
N=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 N occu= pieds and N virtuals.

this will give you the list of energy eigenvalues per k point. The energy units are eV and you should be able to plot them using common excel features.=A0 The k point mapping should be self evident.

Then just excel to plot them using the output file.


On 09-03-2011 19:04, Arun Manna arun.manna17-$-gmail.com wrote:

=A0Dear All,

=A0=A0=A0 Could anyone please tell me how do I plot band structure = for graphene using g09?
=A0=A0=A0 I have successfully done a periodic geometry optimization= of 2 atom unit cell of graphene.
=A0=A0=A0 Now I want to plot the band diagram for this system along the various high symmetric k-points
=A0=A0=A0 (e.g; Gamma-->M--->K).
=A0=A0=A0 Even if I don't know how do I specify k-path along th= ese hight symmetric k-points in Brillouin zone.
=A0 =A0=A0
=A0=A0=A0 Could anybody help me to solve this problem?
=A0=A0=A0
=A0=A0=A0 Thanks in advance

=A0=A0 Best regards,
=A0=A0 Arun 






--=20
Nuno A. G. Bandeira, AMRSC =20
Departamento de Qu=EDmica F=EDsica i Inorg=E1nica
Despatx 207, N4 - Universitat Rovira i Virgili
Campus Sescelades, Carrer Marcel.l=ED Domingo
43007 Tarragona - SPAIN
--



--
Arun K Manna
PhD Stu= dent, TSU, JNCASR,
Bangalore - 560064, India

--bcaec5299f8baa7075049e1b866e-- From owner-chemistry@ccl.net Thu Mar 10 05:45:01 2011 From: "aloysius bella a aloysius.bella{:}gmail.com" To: CCL Subject: CCL:G: emission spectra in gaussian 09 Message-Id: <-44101-110310054248-20080-KTXAtkF0z8L3tkHfOzIdJQ=server.ccl.net> X-Original-From: "aloysius bella a" Date: Thu, 10 Mar 2011 05:42:46 -0500 Sent to CCL by: "aloysius bella a" [aloysius.bella,+,gmail.com] Hello all, I have done tddft calculations for some (organic )pi conjugated systems using gaussian 09. Can anyone suggest me how to find emission spectra values from tddft output? What is the appropriate key word to find both absorption and emission wavelength? Lot of thanks in advance. -------------------------- A. Bella, aloysius.bella:_:gmail.com From owner-chemistry@ccl.net Thu Mar 10 06:19:00 2011 From: "Jens Bredenbeck jbreden:+:gmx.de" To: CCL Subject: CCL:G: Gaussian: Error in internal coordinate system Message-Id: <-44102-110310061517-22647-Aiu6IRbELAkuJ+RLU1Gbfw a server.ccl.net> X-Original-From: "Jens Bredenbeck" Date: Thu, 10 Mar 2011 06:15:15 -0500 Sent to CCL by: "Jens Bredenbeck" [jbreden*_*gmx.de] Dear CCL, when performing a geometry optimization, I encounter the error message "Error in internal coordinate system". It seems to occur when parts of the molecule are close to becoming linear (Angles approaching 180 degrees). Optimization with Opt=Z-Matrix seems to fail for a similar reason, with gaussian reporting that an angle is outside the range of 0-180 degree. Optimization in cartesian coordinates is terribly slow or fails, as the system contains 156 degrees of freedom. Does anybody have an idea how to fix the problem? Thanks and best regards, Jens From owner-chemistry@ccl.net Thu Mar 10 08:04:01 2011 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL:G: How to get band diagram in g09? Message-Id: <-44103-110310080138-19135-nG3Pwo15+Uxzf8UEA5/YBA|*|server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Mar 2011 14:01:27 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira-,-ist.utl.pt] On 10-03-2011 08:09, Arun Manna arun.manna17{}gmail.com wrote: > > Or, do I have to calculate the magnitude of k-vector from the Kxyz > values printed in output > file, and then plot the eigenvalues with increasing oder of > k-vector magnitude to get the 2D band > structure? > > Could you please help me to understand these points also too? Gaussian calculates the number of k points "automagically". That is without need for specific intervention from the user. The method by which they do so is written in a paper by Gustavo Scuseria. You can at most specify the number of k points you want in the calculation but not their symmetries. You always get the Gamma point but I'm not sure about the rest of them. -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Thu Mar 10 08:38:00 2011 From: "Tian Lu sobjubao..yahoo.com.cn" To: CCL Subject: CCL:G: Multiwfn 2.0 released Message-Id: <-44104-110310021535-28139-fpUGS4QmSpjaCMEn/KzFbQ-,-server.ccl.net> X-Original-From: "Tian Lu" Date: Thu, 10 Mar 2011 02:15:33 -0500 Sent to CCL by: "Tian Lu" [sobjubao/a\yahoo.com.cn] Dear CCLers, Multiwfn version 2.0 is now available on http://multiwfn.codeplex.com Multiwfn is a free, open-source, user-friendly program aims for wavefunction analysis, current version is based on Windows platform. Main file types supported by Multiwfn including .wfn/.wfx (Conventional / Extended PROAIM wavefunction file), .31~.40 (NBO plot file) and .fch (Gaussian formatted check file). Main features of Multiwfn 2.0 1) Showing molecular structure and previewing orbitals (MO, NBO, natural orbital, etc.). 2) Outputting all supported properties at a point. 3) Outputting properties in a line and plotting curve map. 4) Outputting properties in a plane and plotting graph. Supported graph types including filled-color map, contour map, relief map (with/without projection), gradient map. 5) Outputting properties in a spatial scope, data can be exported to Gaussian-type grid file (.cub) and can be viewed in terms of isosurface. Setting up grid is very flexible and convenient. 6) For property calculation in one, two and three dimension, the operations between data generated from multiple files can be defined. 7) Promolecular and deformation properties of all built-in functions are supported. 8) User can decide the wavefunction informations belong to which atoms and which orbitals will be used for subsequent analysis, uninteresting parts can be discarded. 9) Checking and modifying wavefunction. Including assigning, exchanging, translating & duplicating, etc. 10) Population analysis. Hirshfeld, Voronoi deformation density (VDD), Mulliken, Lowdin, SCPA, Modified MPA (SCPA, Stout & Politzer, Bickelhaupt) and Becke population are supported. 11) Orbital composition analysis. Multiwfn outputs composition of basis functions, shells, atoms and intra-/inter-fragments in each orbital. Partition methods defined by Mulliken, Stout & Politzer, Ros & Schuit (SCPA) and Hirshfeld are supported. 12) Bond order analysis. Mayer bond order (up to 6-centers), Wiberg bond order in Lowdin orthogonalized basis and Mulliken bond order (can be decomposed to orbital contributions) are supported. 13) Plotting Total/Partial/Overlap population density-of-states (DOS). 14) Plotting IR/Raman/UV-Vis spectrum, parameters (broadening function, FWHM, etc.) can be controlled by user. 15) Some utilities functions: Plotting scatter map for two functions in specific spatial scope, integrating a function in whole space by Becke method, evaluating overlap integral between alpha and beta orbital, monitoring SCF convergence process, generating Gaussian input file with initial guess from converged wavefunction or multiple fragment wavefunctions, etc. The real space functions supported by Multiwfn including electron density (and its gradient and laplacian), electrostatic potential, electron localization function(ELF), localized orbital locator(LOL), Fermi hole, etc. please visit http://multiwfn.codeplex.com for detail. ------------ Tian Lu sobereva]|[sina.com Institute of chemical and biological technology, University of Science and Technology Beijing, China ------------ From owner-chemistry@ccl.net Thu Mar 10 09:13:00 2011 From: "Jean Jules FIFEN julesfifen/a\gmail.com" To: CCL Subject: CCL:G: Gaussian: Error in internal coordinate system Message-Id: <-44105-110310082418-11928-UK+IxeeK4I6oLJ1mTW0pgA!A!server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=001636d33a55c926eb049e20c25d Date: Thu, 10 Mar 2011 14:24:10 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen * gmail.com] --001636d33a55c926eb049e20c25d Content-Type: text/plain; charset=ISO-8859-1 Would you please give more details of your input file and the 20 last lines of the output file? On 10 March 2011 12:15, Jens Bredenbeck jbreden:+:gmx.de < owner-chemistry||ccl.net> wrote: > > Sent to CCL by: "Jens Bredenbeck" [jbreden*_*gmx.de] > Dear CCL, > > when performing a geometry optimization, I encounter the error message > "Error in internal coordinate system". It seems to occur when parts of the > molecule are close to becoming linear (Angles approaching 180 degrees). > Optimization with Opt=Z-Matrix seems to fail for a similar reason, with > gaussian reporting that an angle is outside the range of 0-180 degree. > Optimization in cartesian coordinates is terribly slow or fails, as the > system contains 156 degrees of freedom. Does anybody have an idea how to fix > the problem? > > Thanks and best regards, > Jens> > > -- Jules. --001636d33a55c926eb049e20c25d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Would you please give more details of your input file and = the 20 last lines of the output file?

On = 10 March 2011 12:15, Jens Bredenbeck jbreden:+:gm= x.de <o= wner-chemistry||ccl.net> wrote:

Sent to CCL by: "Jens =A0Bredenbeck" [jbreden*_*gmx.de]
Dear CCL,

when performing a geometry optimization, I encounter the error message &quo= t;Error in internal coordinate system". It seems to occur when parts o= f the molecule are close to becoming linear (Angles approaching 180 degrees= ). Optimization with Opt=3DZ-Matrix seems to fail for a similar reason, wit= h gaussian reporting that an angle is outside the range of 0-180 degree. Op= timization in cartesian coordinates is terribly slow or fails, as the syste= m contains 156 degrees of freedom. Does anybody have an idea how to fix the= problem?

Thanks and best regards,
Jens



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--
Jules.
--001636d33a55c926eb049e20c25d-- From owner-chemistry@ccl.net Thu Mar 10 10:18:00 2011 From: "Ralf Tonner ralf.tonner%googlemail.com" To: CCL Subject: CCL: IR intensities from VASP Message-Id: <-44106-110310101541-8784-gJ86XGl4Y+BYEU28mnDFiA .. server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 10 Mar 2011 16:15:05 +0100 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [ralf.tonner(!)googlemail.com] Dear CCL-members, in moving from molecular quantum chemistry to surface and solid state problems I am investigating vibrational properties of molecular crystals with VASP. Now I would like to extract the infrared intensities of the respective modes but this is unfortunately not given directly. Is anyone out there with experience in extracting IR intensities from VASP calculations ? Thank you in advance, Ralf. -- Dr. Ralf Tonner Philipps-Universität Marburg GERMANY Ph +49-(0)6421-28-25418 Fax +49-(0)6421-28-25566 http://www.uni-marburg.de/fb15/ag-tonner ---- From owner-chemistry@ccl.net Thu Mar 10 10:52:01 2011 From: "Nuno A. G. Bandeira nuno.bandeira:+:ist.utl.pt" To: CCL Subject: CCL: Multiwfn 2.0 released Message-Id: <-44107-110310104436-19059-QHWnDoqpkxCJLwYXj4avsg]-[server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Mar 2011 16:44:21 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]=[ist.utl.pt] Dear Tian Lu, Thank you for your program and I take a keen interest in it. The auxiliary program molden2wfn leads to a forum in chinese and there seems to be no download link from what I see with google translator. Could you make this program available through your site ? Thanks. Best wishes, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Thu Mar 10 16:32:00 2011 From: "Adrian Stevens adrian.stevens:-:accelrys.com" To: CCL Subject: CCL: Accelrys Free Discovery Studio Visualizer 3.0 Now Available Message-Id: <-44108-110310154113-7217-PtGqq847BwM8mvu7ADtchQ ~~ server.ccl.net> X-Original-From: "Adrian Stevens" Date: Thu, 10 Mar 2011 15:41:10 -0500 Sent to CCL by: "Adrian Stevens" [adrian.stevens[-]accelrys.com] Dear Colleagues, We are very pleased to announce that the latest release of our free Discovery Studio Visualizer software, version 3.0, is now available for download at: http://accelrys.com/products/discovery-studio/visualization-download.php With Discovery Studio (DS) Visualizer, the following features are available for free: * Visualization: - Advanced, flexible molecular visualization tools - Publication quality molecular images - Hardware acceleration and stereo support * Ligand-based design: - Sketching and fragment building tools - Manual pharmacophore generation * Macromolecule design: - View and edit molecular sequences - Superimpose and edit protein structures * Web ActiveX Control (New update coming soon!) - Visualize and interact with molecules in Microsoft Office documents and Internet Explorer New with version 3.0: * Advanced graphics rendering: - On supported graphics cards we can now offer depth cue, depth-blur and shading effects * 2D Diagram: - Create 2D ligand-receptor interaction diagrams directly in the free Visualizer. * New Storyboard mode: - Capture key scenes in the Molecule Window and save them to share with colleagues. * Sequence window: - Handle and align sequences with multiple chains (e.g., Antibodies). - In Chain view, you can swap chain order and align independently. All this is available for free! To learn more about the visualization capabilities in DS Visualizer 3.0 download our data sheet: http://accelrys.com/products/datasheets/discovery-studio-visualizer-30.pdf Download DS Visualizer 3.0 today at: http://accelrys.com/products/discovery-studio/visualization-download.php Best regards, Adrian Stevens Product Marketing Manager, Discovery Studio