From owner-chemistry@ccl.net Wed Sep 30 00:33:01 2015 From: "Michele Pavanello m.pavanello(_)rutgers.edu" To: CCL Subject: CCL: constrained DFT and diabatic states Message-Id: <-51795-150929185917-12360-c7YHq2x+tZmx3E9r2fj8rA|a|server.ccl.net> X-Original-From: Michele Pavanello Content-Type: multipart/alternative; boundary=001a1142696622443d0520eac3cc Date: Tue, 29 Sep 2015 18:59:11 -0400 MIME-Version: 1.0 Sent to CCL by: Michele Pavanello [m.pavanello+*+rutgers.edu] --001a1142696622443d0520eac3cc Content-Type: text/plain; charset=UTF-8 Dear Xing, There is literature on diabatic states and their meaning, but little on whether they indeed minimize the vibronic coupling. A proof has been worked out for outer sphere charge and excitation energy transfer in Pavanello, M. and Neugebauer, J., "Linking the Historical and Chemical Definitions of Diabatic States for Charge and Excitation Energy Transfer Reactions in Condensed Phase", J. Chem. Phys. Vol. 135, pp. 134113, year 2011. In there, you will find also several important references. There are additional references that arose after 2011 - but perhaps those can be shared privately if you like. I hope this helps. Best, Michele > > > -------- Forwarded Message -------- > Subject: > CCL: constrained DFT and diabatic states > Date: > Mon, 28 Sep 2015 10:00:43 -0400 > From: > Xing Yin xiy726*|*gmail.com > Reply-To: > CCL Subscribers > To: > Goumans, Fedor > > > Sent to CCL by: Xing Yin [xiy726=-=gmail.com] > Dear all, > > I'm learning constrained DFT to study electron transfer transitions now. I know that the results calculated by cDFT are usually called diabatic states. However, the diabatic states are usually defined > as the states without vibronic couplings in non-adiabatic dynamics. Is there any rigorous proof that the diabatic states constructed by cDFT methods do no have (or only have minimal) vibornic > couplings between them? > > -- > Best wishes, > Xing> > > > --001a1142696622443d0520eac3cc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Xing,

There is literature on diabatic states and their meaning, bu= t little on whether they indeed minimize the vibronic coupling.

A proof has been worked out for outer sphere charge and exci= tation energy transfer in

Pavanello, M. and Neugebauer, J., "Linking the Historic= al and Chemical Definitions of Diabatic States for Charge and Excitation En= ergy Transfer Reactions in Condensed Phase", J. Chem. Phys. Vol. 135, = pp. 134113, year 2011.

In there, you will find also several important references. T= here are additional references that arose after 2011 - but perhaps those ca= n be shared privately if you like.

I hope this helps.

Best,
Michele

>
>
> -------- Forwarded Message --------
> Subject:
> CCL: constrained DFT and diabatic states
> Date:
> Mon, 28 Sep 2015 10:00:43 -0400
> From:
> Xing Yin xiy726*|*gmail.com <owner-chemistry*_*ccl.net>
> Reply-To:
> CCL Subscribers <chemistry*_*ccl= .net>
> To:
> Goumans, Fedor <goumans= *_*scm.com>
>
>
> Sent to CCL by: Xing Yin [xiy726=3D-=3Dgm= ail.com]
> Dear all,
>
> I'm learning constrained DFT to study electron transfer transition= s now. I know that the results calculated by cDFT are usually called diabat= ic states. However, the diabatic states are usually defined
> as the states without vibronic couplings in non-adiabatic dynamics. Is= there any rigorous proof that the diabatic states constructed by cDFT meth= ods do no have (or only have minimal) vibornic
> couplings between them?
>
> --
> Best wishes,
> Xing
>
>
>
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--001a1142696622443d0520eac3cc-- From owner-chemistry@ccl.net Wed Sep 30 04:28:01 2015 From: "Grant Hill grant.hill||sheffield.ac.uk" To: CCL Subject: CCL:G: External basis set - error - BadBas Message-Id: <-51796-150930042554-28831-DWxXdiUKSO2NbKMUc7JeMQ,server.ccl.net> X-Original-From: Grant Hill Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 30 Sep 2015 09:25:44 +0100 Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2104\)) Sent to CCL by: Grant Hill [grant.hill-#-sheffield.ac.uk] The basis set in question has 8s5p3d Gaussian primitives contracted to 5s4p2d. From the table you attached it can be seen that the tightest (largest exponent) four exponents in the s shell have been contracted to a single function (non-zero entries in the second column). The remaining four s functions are all uncontracted, hence only a single non-zero entry in the contraction coefficients. For more on basis sets and their construction, I suggest the following two reviews (please excuse the self-publicity): Hill, J. G., Int. J. Quantum Chem. 113, 21 (2013) Jensen, F., WIREs Comput. Mol. Sci. 3, 273 (2013) The two are quite complementary. HTH, Grant > On 29 Sep 2015, at 17:29, Mohan maruthi sena wrote: > > Dear Sir, > Thanks for a quick reply. I have used the format mentioned in your earlier mail and the job is running now, but still I have the following queries, > > 1) In the article they have mentioned 8 columns ( please find the attachment), what does zeros in the column signify? > > 2) Why we are dividing 'S' into 4 types and writing 4 lines (coefficients) in the first S and 1 line in the rest of S? > > > The link for the article is : "http://pubs.acs.org/doi/abs/10.1021/jp961417n" > > Please find the attachment containing the screenshot of the basis set mentioned in the article. > > Thanks & Regards, > Mohan > > On Tue, Sep 29, 2015 at 6:41 PM, Grant Hill grant.hill+*+sheffield.ac.uk wrote: > > Sent to CCL by: Grant Hill [grant.hill%a%sheffield.ac.uk] > The basis you are specifying is not in Gaussian format. You could try the following (I haven’t tested it): > > Li 0 > S 4 1.00 > 1360.306 0.000844 > 204.1193 0.006491 > 46.45243 0.032691 > 13.10943 0.119676 > S 1 1.00 > 4.189925 1.0 > S 1 1.00 > 1.434060 1.0 > S 1 1.00 > 0.509171 1.0 > S 1 1.00 > 0.203668 1.0 > P 2 1.00 > 10.0 0.150873 > 4.0 0.372952 > P 1 1.00 > 1.6 1.0 > P 1 1.00 > 0.3079 1.0 > D 2 1.00 > 8.53815 0.277606 > 3.41526 0.785589 > D 1 1.00 > 0.6573 1.0 > **** > > HTH, > > Grant > > > > On 29 Sep 2015, at 11:24, Mohan maruthi sena maruthi.sena]~[gmail.com wrote: > > > > Hi all, > > I am trying to use external basis set for Li atom as mentioned in the article, http://pubs.acs.org/doi/abs/10.1021/jp961417n. > > > > The input file is as follows: > > %nprocshared=12 > > %mem=20GB > > %chk=test.chk > > # opt b3pw91/gen geom=connectivity symm=follow > > > > optmization > > > > 0 1 > > F 0.00000000 1.72486459 -0.03772611 > > F 1.21837255 0.00000000 -1.25783532 > > F -1.21837255 0.00000000 -1.25783532 > > F 0.00000000 -1.72486459 -0.03772611 > > F -1.21900832 0.00000000 1.18238310 > > F 1.21900832 0.00000000 1.18238310 > > Si 0.00000000 0.00000000 -0.03772611 > > Li 0.00000000 0.00000000 -1.53771914 > > Li 0.00000000 0.00000000 2.39284425 > > > > 1 7 1.0 > > 2 7 1.0 > > 3 7 1.0 > > 4 7 1.0 > > 5 7 1.0 > > 6 7 1.0 > > 7 > > 8 > > 9 > > > > Li 0 > > S 8 1.00 > > 1360.306 0.000844 0.0 0.0 0.0 0.0 > > 204.1193 0.006491 0.0 0.0 0.0 0.0 > > 46.45243 0.032691 0.0 0.0 0.0 0.0 > > 13.10943 0.119676 0.0 0.0 0.0 0.0 > > 4.189925 0.0 1.0 0.0 0.0 0.0 > > 1.434060 0.0 0.0 1.0 0.0 0.0 > > 0.509171 0.0 0.0 0.0 1.0 0.0 > > 0.203668 0.0 0.0 0.0 0.0 1.0 > > P 4 1.00 > > 10.0 0.150873 0.0 0.0 > > 4.0 0.372952 0.0 0.0 > > 1.6 0.0 1.0 0.0 > > 0.3079 0.0 0.0 1.0 > > D 3 1.00 > > 8.53815 0.277606 0.0 > > 3.41526 0.785589 0.0 > > 0.6573 0.0 1.0 > > **** > > Si F 0 > > 6-311++G(2df) > > **** > > > > > > When i run the job, I got the following error" > > > > "Integral buffers will be 131072 words long. > > Raffenetti 2 integral format. > > Two-electron integral symmetry is turned on. > > 264 basis functions, 454 primitive gaussians, 301 cartesian basis functions > > 37 alpha electrons 37 beta electrons > > nuclear repulsion energy 583.9077027939 Hartrees. > > IS= 64 IAt= 8 ISR= 1 T=0 IP= 5 IndIP= 121 IndIPD= 4 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 64 IAt= 8 ISR= 1 T=0 IP= 6 IndIP= 122 IndIPD= 5 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 64 IAt= 8 ISR= 1 T=0 IP= 7 IndIP= 123 IndIPD= 6 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 64 IAt= 8 ISR= 1 T=0 IP= 8 IndIP= 124 IndIPD= 7 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 65 IAt= 8 ISR= 2 T=1 IP= 3 IndIP= 127 IndIPD= 2 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 65 IAt= 8 ISR= 2 T=1 IP= 4 IndIP= 128 IndIPD= 3 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 66 IAt= 8 ISR= 3 T=2 IP= 3 IndIP= 131 IndIPD= 24 C= 0.000000D+00 0.000000D+00 0.000000D+00 0.000000D+00 NZ=F > > IS= 67 IAt= 9 ISR= 1 T=0 IP= 5 IndIP= 136 IndIPD= 4 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 67 IAt= 9 ISR= 1 T=0 IP= 6 IndIP= 137 IndIPD= 5 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 67 IAt= 9 ISR= 1 T=0 IP= 7 IndIP= 138 IndIPD= 6 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 67 IAt= 9 ISR= 1 T=0 IP= 8 IndIP= 139 IndIPD= 7 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 68 IAt= 9 ISR= 2 T=1 IP= 3 IndIP= 142 IndIPD= 2 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 68 IAt= 9 ISR= 2 T=1 IP= 4 IndIP= 143 IndIPD= 3 C= 0.000000D+00 0.000000D+00 NZ=F > > IS= 69 IAt= 9 ISR= 3 T=2 IP= 3 IndIP= 146 IndIPD= 27 C= 0.000000D+00 0.000000D+00 0.000000D+00 0.000000D+00 NZ=F > > Error in basis set or dimensioning detected by BadBas." > > > > Could some one help me to understand this error. > > > > Thanks for a reply in advance, > > Mohan> > > > From owner-chemistry@ccl.net Wed Sep 30 07:26:01 2015 From: "Susi Lehtola susi.lehtola],[alumni.helsinki.fi" To: CCL Subject: CCL: External basis set - error - BadBas Message-Id: <-51797-150930013816-1953-5rM+u37PIfjwGLrOul5r8A * server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 29 Sep 2015 22:38:03 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola(_)alumni.helsinki.fi] On 09/29/2015 09:29 AM, Mohan maruthi sena maruthi.sena]|[gmail.com wrote: > Dear Sir, > Thanks for a quick reply. I have used the format > mentioned in your earlier mail and the job is running now, but still I > have the following queries, > > 1) In the article they have mentioned 8 columns ( please find the > attachment), what does zeros in the column signify? > > 2) Why we are dividing 'S' into 4 types and writing 4 lines > (coefficients) in the first S and 1 line in the rest of S? The reason is that you can represent basis functions either as segmented contractions (same primitives used only on one contracted basis function), or as a general contractions (all primitives used on all the contractions). Let's say you have 8 S-type exponents (i.e. primitives) 1360.306 204.1193 46.45243 13.10943 0.119676 4.189925 1.434060 0.509171 0.203668 > from which you build 5 functions using segmented functions: the first four primitives are used to represent the core part of the 1s orbital, and the outermost 4 primitives are left as free functions. You can write the matrix that takes you from the primitives to the contracted basis (i.e. general contraction pattern) as an 8x5 matrix: 0.000844 0 0 0 0 0.006491 0 0 0 0 0.032691 0 0 0 0 0.119676 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 Or, alternatively, you can represent the basis set by writing out all the columns in the matrix as S 4 1.00 1360.306 0.000844 204.1193 0.006491 46.45243 0.032691 13.10943 0.119676 S 1 1.00 4.189925 1.0 S 1 1.00 1.434060 1.0 S 1 1.00 0.509171 1.0 S 1 1.00 0.203668 1.0 These are mathematically totally equivalent ways to express basis set. *** As to your original purpose, I'm not quite sure why you would want to use a custom basis set instead of the standard correlation consistent cc-pVXZ sets, if you're just doing energy calculations. The sets in the paper you linked are smaller than cc-pVTZ, which is typically the smallest you'd consider for calculations at the post-HF level of theory (e.g. MP2). For anions, you need the augmented aug-cc-pVXZ sets, which describe the loosely bound additional electrons. If you are worried that the core part is not represented accurately enough, you can decontract the basis set for the center you are interested in. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola(0)alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 30 12:21:01 2015 From: "V ctor Mor n Tejero v.morontejero!A!acellera.com" To: CCL Subject: CCL: 2nd Workshop on High-Throughput Molecular Dynamics Message-Id: <-51798-150930114914-18223-aQUa0IikKpJmmXOjpmUtZw!A!server.ccl.net> X-Original-From: "V ctor Mor n Tejero" Date: Wed, 30 Sep 2015 11:49:13 -0400 Sent to CCL by: "V ctor Mor n Tejero" [v.morontejero- -acellera.com] Dear all, I am pleased to announce the 2nd Workshop on High-Throughput Molecular Dynamics. This workshop is a great opportunity for the users to get an overview of the state-of-the-art in molecular simulations. The aim of this workshop is to learn the latest developments of high-throughput molecular dynamics simulations, and to give scientists the opportunity to exchange their experiences. Environments like HTMD are designed to get the scientist to focus on the science and applications, rather than the technicalities. More information at: http://workshop.htmd.org/ Best Wishes, Victor Moron Acellera Labs v.morontejero]=[acellera.com Dr. Aiguader, 88 08003 Barcelona, Spain