From owner-chemistry@ccl.net Sun Jan 25 17:47:01 2015 From: "Alberto Otero de la Roza alberto#carbono.quimica.uniovi.es" To: CCL Subject: CCL:G: gaussian basis set less charged Pseudopotentials Message-Id: <-50959-150125174407-11771-a6J80qY9t0/CxAyrLbHK/g]=[server.ccl.net> X-Original-From: Alberto Otero de la Roza Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=utf-8 Date: Sun, 25 Jan 2015 15:41:35 -0700 MIME-version: 1.0 Sent to CCL by: Alberto Otero de la Roza [alberto|carbono.quimica.uniovi.es] Hi Vijay, I'm not sure if this reply comes a bit too late, but here it goes in any case. I found the inputs for embedding calculations in ionic crystals with embedding ECPs using Gaussian03 that Víctor mentioned in a previous e-mail. Unfortunately, things seem to have changed in Gaussian09 regarding the use of pseudopotentials and point charges. However, I think I managed to reproduce the old results in g09 with some changes, and also simplified the input a little bit. I suggest that you check the outputs yourself carefully and that you keep an eye out for possible errors. Consider a cluster of magnesium oxide (a = 4.213 ang) centered on the O. Say you want to treat the central oxygen and its first (Mg) and second (O) shells of neighbors with your QM method of choice (B3LYP/6-31+g*, for instance). Then, for the next four shells (two O and two Mg), you want to use a combination of the ECPs in PRB 64 (2001) 104102, which replace all the electrons, and point charges. Around this model, you add a number of shells (10+) composed only of point charges at the atomic positions. Finally, you add ghost charges far away from the model in order to reproduce the potential at the center of the cluster, as done in the article. This is what a simple input for this looks like in Gaussian09: #P b3lyp 6-31+g* units=bohr pseudo=read charge title -2 1 O 0.000000000 0.000000000 0.000000000 Mg 3.980708083 0.000000000 0.000000000 Mg 0.000000000 0.000000000 3.980708083 Mg -0.000000000 -0.000000000 -3.980708083 Mg -0.000000000 -3.980708083 0.000000000 Mg 0.000000000 3.980708083 0.000000000 Mg -3.980708083 0.000000000 0.000000000 O 0.000000000 0.000000000 7.961416165 O -7.961416165 0.000000000 0.000000000 O 0.000000000 7.961416165 0.000000000 O -0.000000000 -0.000000000 -7.961416165 O -0.000000000 -7.961416165 0.000000000 O 7.961416165 0.000000000 0.000000000 Bq 3.980708083 3.980708083 0.000000000 Bq 3.980708083 0.000000000 3.980708083 Bq -3.980708083 -3.980708083 0.000000000 Bq 0.000000000 3.980708083 3.980708083 Bq -0.000000000 -3.980708083 -3.980708083 Bq -3.980708083 -0.000000000 -3.980708083 Bq 0.000000000 -3.980708082 3.980708083 Bq -3.980708082 0.000000000 3.980708083 Bq 0.000000000 3.980708082 -3.980708083 Bq -3.980708082 3.980708083 0.000000000 Bq 3.980708082 -0.000000000 -3.980708083 Bq 3.980708082 -3.980708083 0.000000000 Bq -3.980708083 -3.980708083 -3.980708083 Bq 3.980708083 3.980708083 3.980708083 Bq -3.980708082 3.980708083 3.980708083 Bq -3.980708083 3.980708082 -3.980708083 Bq 3.980708083 3.980708082 -3.980708083 Bq 3.980708082 -3.980708083 -3.980708083 Bq -3.980708083 -3.980708082 3.980708083 Bq 3.980708083 -3.980708082 3.980708083 Bq 11.942124248 0.000000000 0.000000000 Bq -0.000000000 -0.000000000 -11.942124248 Bq -0.000000000 -11.942124248 0.000000000 Bq 0.000000000 11.942124248 0.000000000 Bq -11.942124248 0.000000000 0.000000000 Bq 0.000000000 0.000000000 11.942124248 Bq 15.922832330 0.000000000 0.000000000 Bq -0.000000000 -0.000000000 -15.922832330 Bq -0.000000000 -15.922832330 0.000000000 Bq 0.000000000 15.922832330 0.000000000 Bq -15.922832330 0.000000000 0.000000000 Bq 0.000000000 0.000000000 15.922832330 ]~[charges_on_ecps.lat ]~[charges.lat/N 14 15 16 17 18 19 20 21 22 23 24 25 0 ]~[o.psf/N 26 27 28 29 30 31 32 33 0 ]~[mg.psf/N 34 35 36 37 38 39 0 ]~[mg.psf/N 40 41 42 43 44 45 0 ]~[o.psf/N The first 13 atoms are the QM part, and they are the only atoms on which basis set functions will be used. The -2 charge sets the correct number of electrons for the QM part. The next 32 lines are ghost atoms (of the Bq type, so you can put pseudos on them) at the position where you want the ECP+point charge. The charge_on_ecps.lat and charges.lat files contain the position and charges of the point charges. They are: > cat charges_on_ecps.lat 3.980708083 3.980708083 0.000000001 -2.000000000 [...] -3.980708083 -3.980708083 -3.980708084 2.000000000 [...] 0.000000000 0.000000000 15.922832331 -2.000000000 > cat charges.lat -7.961416165 -0.000000000 -3.980708083 2.000000000 [...] 11.942124248 -11.942124248 11.942124248 2.000000000 199.035404125 0.000000000 0.000000000 -2.748987930 0.000000000 0.000000000 199.035404125 -2.748987930 -0.000000000 -0.000000000 -199.035404125 -2.748987930 -0.000000000 -199.035404125 0.000000000 -2.748987930 0.000000000 199.035404125 0.000000000 -2.748987930 -199.035404125 0.000000000 0.000000000 -2.748987930 Note that I added 1 to the last digit in the z coordinate of the charges_on_ecps.lat point charges. This is done in order to avoid the self-energy of the charges from blowing up. In g03 this was not a problem, but in g09 I get a NaN even though there is no nuclear charge at the Bq position. The difference in self-energy introduced by this change is below the 1e-9 Hartree compared to the one I obtained with g03. The positions in charges.lat represent around 10 more shells of the crystal, and they do not correspond to any ECP so they need not be moved. The last six charges are the ghost atoms. Lastly, you assign pseudopotentials to atoms 14 through 45. The o.psf and mg.psf files contain the pseudos. They look like this (c.f. Table 1 in the article): Mg.MgO 2 0 Mg.MgO ----- d potential 5 1 287.638632100 -2.221733012 1 26.153807145 -2.205452222 1 5.954441936 -3.205282242 1 2.421788124 -1.754934219 1 1.110661394 -0.241448579 ----- s-d potential 5 2 259.834541790 202752.811410000 2 70.585531596 66180.876835000 2 29.505737538 5807.877089100 2 3.225356163 51.817572229 2 1.745584878 6.891421387 ----- p-d potential 5 2 483.582480190 1369.025952200 2 60.636758653 -1386.100267400 2 7.327324917 -29.960840154 2 1.665288736 6.396242521 3 5.627393157 62.197933908 Note that the pseudopotential replaces zero electrons (first line, third field). If you have the model potential for your metals in ECP format already, then I'd say it should be simple to adapt the above to your problem. Best, A. -- Dr. Alberto Otero de la Roza National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada * Vijay Gopal Chilkuri shadyvijay-*-gmail.com [2015-01-15 13:53:10 -0600]: > > Sent to CCL by: Vijay Gopal Chilkuri [shadyvijay/a\gmail.com] > On Thu, Jan 15, 2015 at 07:19:32AM +0000, Lars Goerigk lars.goerigk^-^unimelb.edu.au wrote: > > Hi, > > I am not sure that replacing an entire basis set with a pseudopotential is helpful, nor that Gaussian would not simply crash. > > What exactly do you try to calculate if I may ask? > > I'm trying to do embedded cluster calculations with G09. So basically there is a complex > deposited on a metal surface. The complex and the adjacent ions, treated > with B3LYP, are embedded (AIMP) in a metal. > Such calculations are routinely done, (with all electron Pseudopotentials) but > with other computational chemistry packages (MOLCAS, NWCHEM). > > What I'm looking for, is to know if it is possible to do embedded cluster > calculations with gaussian G09 (because it is parallel and fast) using all > electron (charged) pseudopotentials. > > > > > The method mentioned by Sebastian is designed for London-disperison interactions, and it still requires a basis set, of course. > > > > Between, a closer investigation of this approach is presented in > > J. Chem. Theory Comput. 2014, 10, 968. http://pubs.acs.org/doi/abs/10.1021/ct500026v > > > > Cheers, > > Lars > > > > --- > > Dr. Lars Goerigk > > ARC DECRA Fellow > > School of Chemistry > > The University of Melbourne > > VIC 3010 > > Australia > > > > Research profile: > > http://www.chemistry.unimelb.edu.au/dr-lars-goerigk > > List of my publications: > > http://www.researcherid.com/rid/D-3717-2009 > > > > On 15 Jan 2015, at 3:24 pm, Sebastian Kozuch seb.kozuch^-^gmail.com > wrote: > > > > > > Sent to CCL by: Sebastian Kozuch [seb.kozuch##gmail.com] > > Maybe this work can help you. > > > > A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP > > Edmanuel Torres and Gino A. DiLabio > > J. Phys. Chem. Lett., 2012, 3 (13), pp 1738–1744 > > > > http://pubs.acs.org/doi/abs/10.1021/jz300554y > > > > > > > > On 14/1/2015 8:52 PM, vijay CHILKURI vijay.gopal.c!A!gmail.com wrote: > > I would like to know if one could use Pseudopotentials (in gaussian G09) for > > metals/anions which are not only for core electrons. > > > > In other words, i want to know if it is possible to use Pseudopotentials (in > > G09) for the whole atom without any basis sets and a charge (+ for metal - for > > anion). > > > > > > -- > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > ..........Sebastian Kozuch........... > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > ......University of North Texas...... > > ..........Denton, Texas, USA......... > > ........ seb.kozuch[]gmail.com ....... > > http://yfaat.ch.huji.ac.il/kozuch.htm > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_E0EEC4F34ABF49BCB3E9C2459630023Eunimelbeduau_ > > Content-Type: text/html; charset="Windows-1252" > > Content-ID: > > Content-Transfer-Encoding: quoted-printable > > > > > > > > > > > > > > Hi, > >
I am not sure that replacing an entire basis set with a pseudopotential is helpful, nor that Gaussian would not simply crash.
> >
What exactly do you try to calculate if I may ask?
> >

> >
> >
The method mentioned by Sebastian is designed for London-disperison interactions, and it still requires a basis set, of course.
> >

> >
> >
Between, a closer investigation of this approach is presented in
> >
J. Chem. Theory Comput. 2014, 10, 968.  http://pubs.acs.org/doi/abs/10.1021/ct500026v
> >

> >
> >
Cheers,
> >
Lars
> >

> >
> >
> >
> > ---
> >
> > Dr. Lars Goerigk
> >
> > ARC DECRA Fellow
> >
> > School of Chemistry
> >
> > The University of Melbourne
> >
> > VIC 3010
> >
> > Australia
> >
> >
> >
> >
> > Research profile: 
> > > >
> > List of my publications:
> > > >
> >
> >
> >
> >
On 15 Jan 2015, at 3:24 pm, Sebastian Kozuch seb.kozuch^-^gmail.com <owner-chemistry~!~ccl.net> wrote:
> >
> >

> > Sent to CCL by: Sebastian Kozuch [seb.kozuch##gmail.com]
> > Maybe this work can help you.
> >
> > A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP
> > Edmanuel Torres and Gino A. DiLabio
> > J. Phys. Chem. Lett., 2012, 3 (13), pp 1738–1744
> >
> > http://pubs.acs.org/doi/abs/10.1021/jz300554y
> >
> >
> >
> > On 14/1/2015 8:52 PM, vijay CHILKURI vijay.gopal.c!A!gmail.com wrote:
> >
I would like to know if one could use Pseudopotentials (in gaussian G09) for
> > metals/anions which are not only for core electrons.
> >
> > In other words, i want to know if it is possible to use Pseudopotentials (in
> > G09) for the whole atom without any basis sets and a charge (+ for metal - for
> > anion).
> >
> >
> >
> > --
> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> > ..........Sebastian Kozuch...........
> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> > ......University of North Texas......
> > ..........Denton, Texas, USA.........
> > ........ seb.kozuch[]gmail.com .......
> > http://yfaat.ch.huji.ac.il/kozuch.htm
> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> >
> >
> > > > > >     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
> > > >     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
> > > > > > > > > > > >     http://www.ccl.net/spammers.txt
> > > >
> >
> >
> >
> >
> >
> > > >