From owner-chemistry@ccl.net Tue Nov 22 07:14:00 2016 From: "Daniel Morales Salazar danielmoralessalazar91^^gmail.com" To: CCL Subject: CCL: About virtual orbitals in oligomeric pi-conjugated system Message-Id: <-52503-161122071102-3954-ea5Dt9q/HLqFTCtdMK6FSw%a%server.ccl.net> X-Original-From: "Daniel Morales Salazar" Date: Tue, 22 Nov 2016 07:11:00 -0500 Sent to CCL by: "Daniel Morales Salazar" [danielmoralessalazar91[*]gmail.com] Dear all, I am performing calculations on a pi-conjugated monomer system (83 atoms of which 43 are hydrogens) with a Donor-Acceptor-Donor type of electronic structure. At the B3LYP/6-311G(d,p) level of theory the structural and optical parameters compared well with experimental X-ray data and UV-Vis- NIR spectroscopy. In the monomer case the HOMO density is located on the Donor fragments whereas the LUMO density is found on the acceptor units, naturally. I started modelling oligomeric systems, up to the tetramer. In this latter one, for example, I noticed that the LUMO, LUMO+1 LUMO+2 LUMO+3 were localized on different acceptor units. The same was true for the dimer (LUMO, LUMO+1) and trimer (LUMO, LUMO+1,LUMO+2). At first sight , these orbital densities made me think that the role of the acceptor was "lost" upon increasing the conjugation length/size. However, when I looked at the energies of these frontier virtual orbitals, the differences on the dimer (LUMO to LUMO+1), trimer (LUMO to LUMO+2) and tetramer (i.e. LUMO to LUMO+3) are very low. Less than 0.1 eV in the tetramer system. Since these energy differences are so low, can I consider all of these virtual orbitals (i.e. LUMO to LUMO+3 in the tetramer model) to be an intrinsic part of the molecular electronic structure of the system; that is of course, understanding the fact that they are unoccupied orbitals, and what I mean by intrinsic is that either three of them may be accessible and/or act as acceptors. For example if a donor of the right symmetry or energy approaches the molecular motif; or if there is an intramolecular charge transfer with the right symmetry. Therefore, one could conclude that the role of the acceptor fragments remained intact in the oligomers as compared the monomers. Is this interpretation a valid one? I would like some confirmation as I have read the virtual orbitals obtained in DFT have no physical significance (apart from the HOMO, and perhaps LUMO). Thank you very much for your help and I hope the question was somehow clear. Sincerely, Daniel Morales Salazar From owner-chemistry@ccl.net Tue Nov 22 08:38:01 2016 From: "Eric Schwegler schwegler1%%llnl.gov" To: CCL Subject: CCL: 2017 CCMS Summer Institute at LLNL Message-Id: <-52504-161121185433-8919-Rd7b42naVnMslTNvFRZBGA%a%server.ccl.net> X-Original-From: "Eric Schwegler" Date: Mon, 21 Nov 2016 18:54:32 -0500 Sent to CCL by: "Eric Schwegler" [schwegler1^-^llnl.gov] We are pleased to announce the 2017 Computational Chemistry and Material Science (CCMS) Summer Institute, which will take place from June 5 - August 11, 2017 at Lawrence Livermore National Laboratory (LLNL). The goal of the Summer Institute is to provide graduate students with the opportunity to work directly with LLNL researchers on the development and application of cutting edge methods in computational materials science and chemistry and other related areas. Each student will spend ten weeks at LLNL as a guest of an LLNL host scientist working on a computational project in the host's area of expertise. In addition, leading researchers from universities and national labs will give a series of mini-courses for the students. These courses will cover state-of-the-art and emerging computational methods in materials science and chemistry. Travel funds and a generous stipend will be provided to the participants. In order to be considered, prospective participants will need to fill out an application form that can be found at the following website: www.llnl.gov/ccms/ The application deadline is January 30, 2017. Eric Schwegler (schwegler1()llnl.gov) From owner-chemistry@ccl.net Tue Nov 22 09:13:00 2016 From: "ZhiPeng Li 979170845(0)qq.com" To: CCL Subject: CCL: reply: CCL: Gaussian 09 Frequency Jobs Message-Id: <-52505-161122024218-19025-P3RENa6VuXhxkNktFtUtQw,server.ccl.net> X-Original-From: "ZhiPeng Li" <979170845|qq.com> Date: Tue, 22 Nov 2016 02:42:17 -0500 Sent to CCL by: "ZhiPeng Li" [979170845(_)qq.com] Dear Alan: The frequency calculation is dealt by CPHF method, which Hessian matrix try to be diagonalizable. If the potential surfaces of your systems are flexible, or some numerical errors, the diagonalization will be failed, then the first derivative of energy cannot be obtained according to the model of harmonic oscillator. It may be such issues in your situation, I suppposed that: 1, The compounds must be organic molecules, which potential surfaces are flexible 2, The diffuse functions is applied such as "+" in basis set of 6-31+G* 3, The bug of program. If you are only anxious about the results which the principle of calculations or iterations is negligible, the solutions of issues are following: 1, If you can, remove the diffuse functions, whatever geometry optimization or frequency analysis 2, Try to use the key word "CPHF=grid=fine(ultrafine,300590,etc)" to aviod the issue of low precision if you failed to do as the first way 3, Try to use the key word "CPHF=conver=n" to reduce the convergence limit, where n means 10^n Detailed discusses is written in the manual of "CPHF" term. Hope you successful! sincerely, Li Zhi-Peng 2016-11-21 From owner-chemistry@ccl.net Tue Nov 22 10:29:00 2016 From: "Ulrike Salzner salzner ~~ fen.bilkent.edu.tr" To: CCL Subject: CCL: About virtual orbitals in oligomeric pi-conjugated system Message-Id: <-52506-161122092245-28824-2EDJULzJLg2FBYOH1oJFpA^_^server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=001a113f16d628f57b0541e481a0 Date: Tue, 22 Nov 2016 17:22:38 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner[]fen.bilkent.edu.tr] --001a113f16d628f57b0541e481a0 Content-Type: text/plain; charset=UTF-8 Dear Daniel, What you are describing is a system in which the conduction band states are completely localized. You get as many unoccupied orbitals with almost the same energy as you have repeat units. All of them are different linear combinations but they do not split because they do not overlap. If the occupied orbitals are localized as well, you have an insulator. If only the unoccupied orbitals are localized, you might still have a p-type system. This occurs very often in donor-acceptor systems.The low lying orbitals are acceptors but any electrons that are transferred to them will be trapped. Best regards, Ulrike Salzner On Tue, Nov 22, 2016 at 3:11 PM, Daniel Morales Salazar danielmoralessalazar91^^gmail.com wrote: > > Sent to CCL by: "Daniel Morales Salazar" [danielmoralessalazar91[*]gmai > l.com] > Dear all, > > I am performing calculations on a pi-conjugated monomer system (83 atoms > of which 43 are hydrogens) with a Donor-Acceptor-Donor type of electronic > structure. At the B3LYP/6-311G(d,p) level of theory the structural and > optical parameters compared well with experimental X-ray data and UV-Vis- > NIR spectroscopy. In the monomer case the HOMO density is located on the > Donor fragments whereas the LUMO density is found on the acceptor units, > naturally. > > I started modelling oligomeric systems, up to the tetramer. In this > latter one, for example, I noticed that the LUMO, LUMO+1 LUMO+2 LUMO+3 > were localized on different acceptor units. The same was true for the > dimer (LUMO, LUMO+1) and trimer (LUMO, LUMO+1,LUMO+2). At first sight , > these orbital densities made me think that the role of the acceptor was > "lost" upon increasing the conjugation length/size. > > However, when I looked at the energies of these frontier virtual > orbitals, the differences on the dimer (LUMO to LUMO+1), trimer (LUMO to > LUMO+2) and tetramer (i.e. LUMO to LUMO+3) are very low. Less than 0.1 eV > in the tetramer system. > > Since these energy differences are so low, can I consider all of these > virtual orbitals (i.e. LUMO to LUMO+3 in the tetramer model) to be an > intrinsic part of the molecular electronic structure of the system; that > is of course, understanding the fact that they are unoccupied orbitals, > and what I mean by intrinsic is that either three of them may be > accessible and/or act as acceptors. For example if a donor of the right > symmetry or energy approaches the molecular motif; or if there is an > intramolecular charge transfer with the right symmetry. Therefore, one > could conclude that the role of the acceptor fragments remained intact in > the oligomers as compared the monomers. > > Is this interpretation a valid one? > > I would like some confirmation as I have read the virtual orbitals > obtained in DFT have no physical significance (apart from the HOMO, and > perhaps LUMO). > > Thank you very much for your help and I hope the question was somehow > clear. > > Sincerely, > > Daniel Morales Salazar> > > -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --001a113f16d628f57b0541e481a0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Daniel,
What you are describing is= a system in which the conduction band states are completely localized. You= get as many unoccupied orbitals with almost the same energy as you have re= peat units. All of them are different linear combinations but they do not s= plit because they do not overlap.
If the occupied orbitals are localize= d as well, you have an insulator. If only the unoccupied orbitals are local= ized, you might still have a p-type system.
This occurs very often in d= onor-acceptor systems.The low lying orbitals are acceptors but any electron= s that are transferred to them will be trapped.
Best regards,=
Ulrike Salzner
On Tue, Nov 22, 2016 at 3:11 PM, Daniel Morales= Salazar danielmoralessalazar91^^gmail.com= <owner-chemistry_._ccl.net> wrote:

Sent to CCL by: "Daniel=C2=A0 Morales Salazar" [danielmoralessala= zar91[*]g= mail.com]
Dear all,

I am performing calculations on a pi-conjugated monomer system (83 atoms of which 43 are hydrogens) with a Donor-Acceptor-Donor type of electronic structure. At the B3LYP/6-311G(d,p) level of theory the structural and
optical parameters compared well with experimental X-ray data and UV-Vis- NIR spectroscopy. In the monomer case the HOMO density is located on the Donor fragments whereas the LUMO density is found on the acceptor units, naturally.

I started modelling oligomeric systems, up to the tetramer. In this
latter one, for example, I noticed that the LUMO, LUMO+1 LUMO+2 LUMO+3
were localized on different acceptor units. The same was true for the
dimer (LUMO, LUMO+1) and trimer (LUMO, LUMO+1,LUMO+2). At first sight ,
these orbital densities made me think that the role of the acceptor was
"lost" upon increasing the conjugation length/size.

However, when I looked at the energies of these frontier virtual
orbitals, the differences on the dimer (LUMO to LUMO+1), trimer (LUMO to LUMO+2) and tetramer (i.e. LUMO to LUMO+3) are very low. Less than 0.1 eV in the tetramer system.

Since these energy differences are so low, can I consider all of these
virtual orbitals (i.e. LUMO to LUMO+3 in the tetramer model) to be an
intrinsic part of the molecular electronic structure of the system; that is of course, understanding the fact that they are unoccupied orbitals,
and what I mean by intrinsic is that either three of them may be
accessible and/or act as acceptors. For example if a donor of the right
symmetry or energy approaches the molecular motif; or if there is an
intramolecular charge transfer with the right symmetry. Therefore, one
could conclude that the role of the acceptor fragments remained intact in the oligomers as compared the monomers.

=C2=A0Is this interpretation a valid one?

I would like some confirmation as I have read the virtual orbitals
obtained in DFT have no physical significance (apart from the HOMO, and
perhaps LUMO).

Thank you very much for your help and I hope the question was somehow
clear.

Sincerely,

Daniel Morales Salazar



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--
Assoc. Prof. Ulrike Salzner
D= epartment of Chemistry
Bilkent University
06800 Bilkent, Ankara
--001a113f16d628f57b0541e481a0-- From owner-chemistry@ccl.net Tue Nov 22 14:11:00 2016 From: "Horkel Ernst ernst.horkel**tuwien.ac.at" To: CCL Subject: CCL:G: AW: Gaussian 09 Frequency Jobs Message-Id: <-52507-161122140657-18083-D5Xbr2dKxWzVT9JZE8IaRg,,server.ccl.net> X-Original-From: Horkel Ernst Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 22 Nov 2016 19:06:46 +0000 MIME-Version: 1.0 Sent to CCL by: Horkel Ernst [ernst.horkel(a)tuwien.ac.at] Hi, I had a similar problem some time ago and got the following response from the Gaussian support: ************************** Hello Ernst, This is symptomatic of numerical accuracy issues. For this job you were running into poor convergence in the iterative solution of the CPHF equations when doing the differentiation with respect to nuclear coordinates. See this part of the output file: Differentiating once with respect to nuclear coordinates. ...etc... 11 vectors produced by pass 79 Test12= 2.02D-13 1.00D-09 XBig12= 3.36D-14 3.80D-09. 11 vectors produced by pass 80 Test12= 2.02D-13 1.00D-09 XBig12= 5.49D-14 4.96D-09. 11 vectors produced by pass 81 Test12= 2.02D-13 1.00D-09 XBig12= 2.65D-14 3.22D-09. 11 vectors produced by pass 82 Test12= 2.02D-13 1.00D-09 XBig12= 4.36D-14 4.36D-09. 11 vectors produced by pass 83 Test12= 2.02D-13 1.00D-09 XBig12= 4.65D-14 4.42D-09. 11 vectors produced by pass 84 Test12= 2.02D-13 1.00D-09 XBig12= 5.02D-14 5.49D-09. 11 vectors produced by pass 85 Test12= 2.02D-13 1.00D-09 XBig12= 2.14D-14 3.26D-09. 11 vectors produced by pass 86 Test12= 2.02D-13 1.00D-09 XBig12= 5.85D-14 5.20D-09. 11 vectors produced by pass 87 Test12= 2.02D-13 1.00D-09 XBig12= 3.95D-14 4.24D-09. 11 vectors produced by pass 88 Test12= 2.02D-13 1.00D-09 XBig12= 4.44D-14 5.09D-09. 11 vectors produced by pass 89 Test12= 2.02D-13 1.00D-09 XBig12= 4.34D-14 4.30D-09. The values printed after "XBig12" do not steadily approach the values printed before that (the ones between "Test12" and "XBig12"), and that these values have been oscillating near convergence for a large number of iterations ("passes"), in this case more than 89. For most frequency calculations, convergence here is achieved in less than 20 "passes". A larger number of passes and oscillations in the "XBig12" values as it approaches convergence are indicative of numerical accuracy issues. For certain molecular systems, certain combinations of computational methods and basis sets might need larger integration grids (in the case of DFT methods) and/or increased integral accuracy (especially calculations with very diffuse basis functions). The most general procedure to reduce the numerical noise in the calculation is to increase the integral accuracy. By default, the integral accuracy cutoff is 10^-10, so increasing the accuracy to 10^-11 or 10^-12 should have a positive impact in reducing numerical noise. In G09, there is a keyword to control integral accuracy, "Integral=(Acc2e=N)", which will set the accuracy to 10^-N. So, for instance, "Integral=(Acc2e=12)" sets the integral accuracy cutoff to 10^-12. Since this is a DFT calculation, the numerical integration grid is also another parameter that can impact the numerical stability of the calculation. By default, DFT energy and gradient calculations use the "Fine" grid (a pruned grid with 75 radial shells and 302 angular points, or 75,302), while the default grid for the CPHF equations in DFT frequency calculations is the "Coarse" grid (a pruned 35,110 grid). Increasing the number of points in the DFT integration grid also helps when problems due to numerical inaccuracies appear. Usually the natural increase in the number of points would be to use the "Ultrafine" grid (a pruned 99,590 grid) for the DFT energies and gradients, which would automatically set the use of the "SG1" grid (a pruned 50,194 grid) for the CPHF equations. If required (in special cases, such as using uncontracted basis sets), one can specify directly the number of radial shells and angular points. I would try first increasing integral accuracy by one or two orders of magnitude over the default ("Int=(Acc2e=11)" or "Int=(Acc2e=12)"). If you still have this issue, you may also need to increase the size of the numerical integration grid, but try first something like the following: %nprocshared=8 %mem=16GB %chk=o-PCzPOXD_DFT_b3lyp_6-311+d_freq_2ndtry.chk # freq b3lyp/6-311+g(d) geom=connectivity scf=noincfock integral=(acc2e=11) [No Title] 0 1 C 0.34900900 2.46465100 0.10154300 N -0.73346000 2.23368700 -0.57575100 N -1.08971300 0.91579800 -0.32567600 ...etc... ********************* Indeed, setting "integral=(acc2e=11)" solved the problem. So you might give this a try... Good luck an keep computing, Ernst Senior Lecturer Dipl.-Ing. Dr.techn. Ernst Horkel Institute of Applied Synthetic Chemistry, Vienna University of Technology          Tel.: +43-1-58801-163609 Getreidemarkt 9/163OC,                         +43-664-60588-7122 A-1060 Vienna, Austria                   Fax:  +43-1-58801-15499 email: ernst.horkel a tuwien.ac.at -----Ursprüngliche Nachricht----- Von: owner-chemistry+ehorkel==ioc.tuwien.ac.at a ccl.net [mailto:owner-chemistry+ehorkel==ioc.tuwien.ac.at a ccl.net] Im Auftrag von Alan Wilfred Humason ahumason*_*smu.edu Gesendet: Montag, 21. November 2016 04:56 An: Horkel, Ernst Betreff: CCL: Gaussian 09 Frequency Jobs Sent to CCL by: "Alan Wilfred Humason" [ahumason]~[smu.edu] I am running a large molecule with a large basis set. (It's an expensive calculation, but I've been given the resources.) After optimization, the program runs a set of iterations, giving the message: 3 vectors produced by pass897 Test12= 6.42D-13 1.00D-09 XBig12= 5.97D-13 1.11D-08. The calculation gets 'stuck' at 3 vectors, even after 3000 iterations, and several weeks on 24 cores. 1) What do the vectors represent? 2) What to the passes represent? 3) How can I get my job to finish? Alan Humason ahumason||smu.eduhttp://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 Tue Nov 22 17:47:00 2016 From: "John McKelvey jmmckel]^[gmail.com" To: CCL Subject: CCL: Maximum atoms in ORCA Message-Id: <-52508-161122173742-31230-OCs5QiEpSqvg3bm00q65Jg^^^server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a113dc2b25177970541eb6b18 Date: Tue, 22 Nov 2016 16:37:36 -0600 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-*-gmail.com] --001a113dc2b25177970541eb6b18 Content-Type: text/plain; charset=UTF-8 Hello.. Does one know the upper limit of how many atoms can be run in ORCA? [I want to do a semi-empirical run on 2800 atoms] Many thanks! John -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel^_^gmail.com --001a113dc2b25177970541eb6b18 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello..

Does one know the uppe= r limit of how many atoms can be run in ORCA?=C2=A0
[I want to do a sem= i-empirical run on 2800 atoms]

Many thanks!

John<= br clear=3D"all">

--
John McKelvey
545 Legacy Pointe Dr
O'Fallon,= MO 63376
636-294-5203
jmmckel^_^gmail.com
--001a113dc2b25177970541eb6b18-- From owner-chemistry@ccl.net Tue Nov 22 21:10:00 2016 From: "Jim Kress jimkress35.!^!.gmail.com" To: CCL Subject: CCL: Maximum atoms in ORCA Message-Id: <-52509-161122210847-7446-KGPTcfgibUPVm9ryJlU2Xg!^!server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0144_01D24504.93C3E3C0" Date: Tue, 22 Nov 2016 21:08:29 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35[]gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0144_01D24504.93C3E3C0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Try asking at the ORCA forum: =20 https://orcaforum.cec.mpg.de/index.php?sid=3Daa0bafb5e0c9227bf76bbe5b23a3= 902d =20 Jim =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com#%#ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com#%#ccl.net] On Behalf Of = John McKelvey jmmckel]^[gmail.com Sent: Tuesday, November 22, 2016 5:38 PM To: Kress, Jim Subject: CCL: Maximum atoms in ORCA =20 Hello.. Does one know the upper limit of how many atoms can be run in ORCA? =20 [I want to do a semi-empirical run on 2800 atoms] Many thanks! John --=20 John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel**gmail.com =20 ------=_NextPart_000_0144_01D24504.93C3E3C0 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

Try asking = at the ORCA forum:

 

https://orcaforum.cec.mpg.de/index.php?sid=3Daa0bafb5e0c922= 7bf76bbe5b23a3902d

 

Jim

 

From:<= /b> = owner-chemistry+jimkress35=3D=3Dgmail.com#%#ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com#%#ccl.net] On Behalf = Of John McKelvey jmmckel]^[gmail.com
Sent: Tuesday, = November 22, 2016 5:38 PM
To: Kress, Jim = <jimkress35#%#gmail.com>
Subject: CCL: Maximum atoms in = ORCA

 

Hello..

Does one know the upper = limit of how many atoms can be run in ORCA? 
[I want to do a = semi-empirical run on 2800 atoms]

Many = thanks!

John


--

John McKelvey
545 Legacy Pointe = Dr

O'Fallon, MO = 63376
636-294-5203
jmmckel**gmail.com

=
------=_NextPart_000_0144_01D24504.93C3E3C0--