with best regards
=C2=A0=C2=A0 Niveditha Surukonti,

=C2=A0=C2=A0=C2=A0 Research Scholar,

=C2=A0=C2=A0=C2=A0 CSIR-IICT, HYD.

On Fri, Jun 20, 2014 at 7:29 PM, Cenk Se= lcuki cselcuki#,#yahoo.com <owner-c= hemistry{}ccl.net> wrote:

Dear= =C2=A0Niveditha= Reddy Surukonti,
Add Pseudo=3DRead keyw= ord to the keyword line and try again.=C2=A0
Best Regards,
Cenk

On Friday, = June 20, 2014 4:41 PM, Niveditha Reddy Surukonti nivs916(0)gmail.com <owner-chemistry : ccl.net> wrote:

Sent = to CCL by: "Niveditha=C2=A0 Reddy Surukonti" [nivs916]_[gmail.com]
Iam performing op= timization of a chemosensor molecule, which involves a
thiazole substituted ferrocene = ligand and mercury dication. At
mpw1b95/lanl2dz level of theory optimiz= ation terminated normally, placing
mercury cation at 3.6 angstroms dist= ance. but when am placing 6-311g(d,p) on
C,H atoms and 6-311+g(d,P)on S,N atoms using gen keyword in gaussian, after=
each optimization mercury is moving close to nitrogen and finally nitr= ozen is
sitting inside the Hg, missing all connectivities, finally beco= ming clumpsy,
and error terminated. i tried in other ways such as stating from other lowe= r
basis sets still it is showing same behaviour. i have no idea about w= hat is
actually going on here, so am unable to solve this problem. if a= nybody has
any idea about this, kindly let me know. here is my input file.

%mem=3D4000MB
#p opt=3Dmaxcyc=3D700= mpwb95/gen iop(3/76=3D0690003100) scf(maxcyc=3D300)
geom=3Dconnectivit= y

Title Card Required

2 1
C=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.03589400=C2=A0 -3.09448500=C2=A0 =C2= =A0 0.19674500
C=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 -1.35242600=C2= =A0 -3.27805600=C2=A0 -0.31384300
H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 -2.00984800=C2=A0 -3.66901500=C2=A0 =C2=A0 0.468499= 00
continues......

C H 0
6-311g(d,p)
******
S N 0
6-3= 11+g(d,p)
******
Hg 0
LanL2DZ
*****

Hg 0
LanL2DZ

Any help will be highly = appreciated.

=C2=A0 Thanks in advance.

-=3D This is a= utomatically added to each message by the mailing script =3D-
To recover= the email address of the author of the message, please change

the strange characters on the top line to the : sign. You can= also

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--bcaec548a7a3e39aa104fc5492db-- From owner-chemistry@ccl.net Sat Jun 21 13:51:00 2014 From: "Giuseppe Mallia g.mallia:-:imperial.ac.uk" To: CCL Subject: CCL: MSSC2014 - Ab initio Modelling in Solid State Chemistry - EARLY BIRDS Message-Id: <-50264-140621094625-12819-TLelH+xv4CTQ1FzsQAYAGQ() server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Sat, 21 Jun 2014 09:46:23 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia a imperial.ac.uk] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WORKSHOP ANNOUNCEMENT MSSC2014 - Ab initio Modelling in Solid State Chemistry ==> London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL http://www3.imperial.ac.uk/mssc2014 London (UK), September 15-19, 2014 Directors: L. Bernasconi - N.M. Harrison - G. Mallia ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL (http://www.crystal.unito.it/) and CRYSCOR (http://www.cryscor.unito.it). New tutorials are available. The programme is on-line; please visit the following link: http://www3.imperial.ac.uk/mssc2014/programme Please note: Monday 30th June - Deadline for payment of early bird fees ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Sat Jun 21 14:25:01 2014 From: "Thomas Manz thomasamanz]~[gmail.com" To: CCL Subject: CCL:G: Chargemol 3.0 released Message-Id: <-50265-140621105611-16404-PkLODzUXg3ATHhGYx8aDtg(~)server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a11c1190e216da504fc59cf8c Date: Sat, 21 Jun 2014 08:56:04 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz=-=gmail.com] --001a11c1190e216da504fc59cf8c Content-Type: text/plain; charset=UTF-8 Hi Brian, >Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can > only use HF or DFT densities as it calculated them from the MOs (KS > orbitals)? Would it need something that outputs the full density matrix > to use CASSCF results? The Chargemol program can use input from any quantum chemistry method (DFT, HF, CASSCF, MP2, coupled-cluster, etc.). Just include Density = Current, Output = WFX, Pop= NO (for spin unpolarized calculation) or NOAB (for spin polarized calculation) on the GAUSSIAN 09 route line and the name of the .wfx file at the bottom of the GAUSSIAN input (.com or .gjf) file. This directs GAUSSIAN 09 to output the fully correlated density to the .WFX file, so you will get the corresponding density when running methods like DFT, HF, CASSCF, MP2, coupled-cluster, etc. > Does anyone have any idea how it could use output from GAMESS(US) [or > indeed GAMESS(UK) or Firefly]? Best route in the long run would be for GAMESS and Firefly developers to add code to output .wfx file. The .wfx files are read by AIMALL, MultiWFN, and Chargemol programs that perform various kinds of atomic population analysis. The .wfx format specification is shown at http://aim.tkgristmill.com/wfxformat.html The .wfx file contains information about the cartesian Gaussian basis set primitives, the basis set coefficients for the natural orbitals (eigenvectors of the first-order density matrix), positions of each atom, system net charge and total number of electrons, nuclear charges, and core electrons replaced by effective core potentials (if any). For quantum chemistry calculations that used effective core potentials, the .wfx file contains Electron Density Functions (EDFs), which are normally spherically symmetric for each atom, that specify the electron density of the core electrons replaced by the atom's effective core potential. In principle, it should only take one person a few of days of programming to add the option to output a .wfx file from the GAMESS or Firefly software packages. Presumably, all of the information about the cartesian basis set primitives, natural orbital basis set coefficients, nuclear positions, etc. is already available within these programs and code just needs to be added to output them in .wfx file format. The only information that may not be already available within the GAMESS and Firefly codes is the EDFs that specify the density of the core electrons replaced by effective core potentials. I have generated a set of core electron densities for all elements atomic number 1 (H) to 109 (Mt), so if one of the GAMESS or Firefly developers is in need of that information, they can contact me and I can help them with a library of core electron densities for the purpose of generating .wfx files. I recommend that you contact the GAMESS or Firefly developers and ask if it is possible for them to add output of .wfx file format. This will certainly be the best long-term solution. Sincerely, Tom Manz assistant professor, Chemical & Materials Engineering New Mexico State University On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James brian.james.duke() gmail.com wrote: > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke(_) > gmail.com] > This seems a really useful program. > > Does anyone have any idea how it could use output from GAMESS(US) [or > indeed GAMESS(UK) or Firefly]? > > Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can > only use HF or DFT densities as it calculated them from the MOs (KS > orbitals)? Would it need something that outputs the full density matrix > to use CASSCF results? > > Brian. > > On Mon, Jun 16, 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu > wrote: > > Hi, > > > > I just wanted to let everyone know about the release of Chargemol > > version 3.0, which performs Density Derived Electrostatic and Chemical > > (DDEC) atomic population analysis. > > > > The latest version has the following features: > > > > 1) Computes net atomic charges, atomic spin moments, and now effective > > bond orders (EBOs) for nonperiodic and periodic materials. For each atom, > > the sum of effective bond orders (SEBO) is also computed and printed. The > > program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a > variety > > of other quantum chemistry programs. > > > > 2) Atomic dipole and quadrupole moments are computed for all systems. > > For nonperiodic materials, the total system dipole and quadrupole moments > > are also computed. The latest version adds the computation and printing > of > > the traceless quadrupole tensor eigenvalues. > > > > 3) A new constraint has been added to improvement the treatment in ionic > > systems containing small cations. For example, it was noticed that in > > crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too > > contracted and too positively charged. This has been fixed by > constraining > > the rate of decay of atomic weights to be no faster than exp(-3*r) in > > regions where atoms overlap. > > > > 4) To improve the speed, the program has been translated from Matlab > > into Fortran code. The Fortran code is parallelized with OpenMP allowing > it > > to run on multiple processors with a shared memory (i.e., single > > node, multiple processors). A serial version of the Fortran code is also > > available. > > > > 5) Precompiled Windows and Linux binaries and the uncompiled sourcecode > > are available. Many users can utilize the precompiled executables > > without recompiling the program. > > > > 6) The program is free to download from ddec.sourceforge.net. The > > download includes a manual explaining how to install and run the program. > > > > Sincerely, > > > > Tom Manz > > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(a)monash.edu > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia> > > --001a11c1190e216da504fc59cf8c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Brian,

>Am I correct in thinking that with GAUSS= IAN 09 using .wfx files, it can

> only use HF or DFT densities as it c= alculated them from the MOs (KS

> orbit= als)? Would it need something that outputs the full density matrix

> t= o use CASSCF results?

The Chargemol program can use input from any quantum chemistry method (D= FT, HF, CASSCF, MP2, coupled-cluster, etc.).

Just include Density =3D Current, Out= put =3D WFX, Pop=3D NO (for spin unpolarized calculation) or NOAB (for spin= polarized calculation) on the GAUSSIAN 09 route line and the name of the .= wfx file at the bottom of the GAUSSIAN input (.com or .gjf) file.=C2=A0This directs GAUSSIAN 09 to output the = fully correlated density to the .WFX file, so you will get the correspondin= g density when running methods like=C2=A0DFT, HF, CASSCF, MP2, coupled-cluster, etc= .

>= ; Does anyone have any idea how it could use output from GAMESS(US) [or

> indee= d GAMESS(UK) or Firefly]?

Best route in the long run would be for GAMESS and Firefly developers to= add code to output .wfx file.=C2=A0The .wfx files are read by AIMALL, MultiWFN, and Chargemol pro= grams that perform various kinds of atomic population analysis.=C2=A0The .wfx forma= t specification is shown at=C2=A0http://aim.tkgristmill.= com/wfxformat.html =C2=A0The .wfx file contains information about the c= artesian Gaussian basis set primitives, the basis set coefficients for the = natural orbitals (eigenvectors of the first-order density matrix), position= s of each atom, system net charge and total number of electrons, nuclear ch= arges, and core electrons replaced by effective core potentials (if any). F= or quantum chemistry calculations that used effective core potentials, the = .wfx file contains Electron Density Functions (EDFs), which are normally sp= herically symmetric for each atom, that specify the electron density of the= core electrons replaced by the atom's effective core potential.=C2=A0<= /font>

In principle, it should only take= one person a few of days of programming to add the option to output a .wfx= file from the GAMESS or Firefly software packages. Presumably, all of the = information about the cartesian basis set primitives, natural orbital basis= set coefficients, nuclear positions, etc. is already available within thes= e programs=C2=A0and cod= e just needs to be added to output them in .wfx file format. The only infor= mation that may not be already available within the GAMESS and Firefly code= s is the EDFs that specify the density of the core electrons replaced by ef= fective core potentials. I have generated a set of core electron densities = for all elements atomic number 1 (H) to 109 (Mt), so if one of the GAMESS o= r Firefly developers is in need of that information, they can contact me an= d I can help them with a library of core electron densities for the purpose= of generating .wfx files.

I recommend that you contact the = GAMESS or Firefly developers and ask if it is possible for them to add outp= ut of .wfx file format. This will certainly be the best long-term solution.= =C2=A0

Sincerely,

Tom Manz

= assistant professor, Chemical & Materials Engineering

New Mex= ico State University

On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James brian.ja= mes.duke() gmail.com <= ;owner-chemist= ry..ccl.net> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke(_)gmail.com]
This seems a really useful program.

Does anyone have any idea how it could use output from GAMESS(US) [or
indeed GAMESS(UK) or Firefly]?

Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can
only use HF or DFT densities as it calculated them from the MOs (KS
orbitals)? Would it need something that outputs the full density matrix
to use CASSCF results?

Brian.

On Mon, Jun 16, 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu wrote:
> Hi,
>
> I just wanted to let everyone know about the release of Chargemol
> version 3.0, which performs Density Derived Electrostatic and Chemical=
> (DDEC) atomic population analysis.
>
> The latest version has the following features:
>
> 1) Computes net atomic charges, atomic spin moments, and now effective=
> bond orders (EBOs) for nonperiodic and periodic materials. For each at= om,
> the sum of effective bond orders (SEBO) is also computed and printed. = The
> program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a var= iety
> of other quantum chemistry programs.
>
> 2) Atomic dipole and quadrupole moments are computed for all systems.<= br> > For nonperiodic materials, the total system dipole and quadrupole mome= nts
> are also computed. The latest version adds the computation and printin= g of
> the traceless quadrupole tensor eigenvalues.
>
> 3) A new constraint has been added to improvement the treatment in ion= ic
> systems containing small cations. For example, it was noticed that in<= br> > crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too
> contracted and too positively charged. This has been fixed by constrai= ning
> the rate of decay of atomic weights to be no faster than exp(-3*r) in<= br> > regions where atoms overlap.
>
> 4) To improve the speed, the program has been translated from Matlab > into Fortran code. The Fortran code is parallelized with OpenMP allowi= ng it
> to run on multiple processors with a shared memory (i.e., single
> node, multiple processors). A serial version of the Fortran code is al= so
> available.
>
> 5) Precompiled Windows and Linux binaries and the uncompiled sourcecod= e
> are available. Many users can utilize the precompiled executables
> without recompiling the program.
>
> 6) The program is free to download from ddec.sourceforge.net. The
> download includes a manual explaining how to install and run the progr= am.
>
> Sincerely,
>
> Tom Manz

--
=C2=A0 =C2=A0Brian Salter-Duke (Brian Duke) =C2=A0 Brian.Salter-Duke(a)monash.edu
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Adjun= ct Associate Professor
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Monash Institute of Pharmaceutica= l Sciences
=C2=A0 =C2=A0 =C2=A0 Monash University Parkville Campus, VIC 3052, Australi= a

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--001a11c1190e216da504fc59cf8c-- From owner-chemistry@ccl.net Sat Jun 21 15:00:02 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor~~fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Degenerate states of Nickel atom with Gaussian G03 program Message-Id: <-50266-140621144251-32267-pYhTgfGoItD5b5LZiOwvhQ[-]server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Sat, 21 Jun 2014 20:35:22 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor++fluor.quimica.uniovi.es] On Sat, Jun 21, 2014 at 03:32:40AM -0400, Krishna Mohan GP gpkmohan{}yahoo.com wrote: > > Sent to CCL by: "Krishna Mohan GP" [gpkmohan]=[yahoo.com] > Dear List, > > For a didactical purpose, I have been running a single-atom calculation in > G03. > The purpose is to show students the degenerate states of d-orbitals of > Nickel, [Ar] 3d8 4s2. > > Since it is a Polarized system, I used UHF, and below shows the input file: > ----------------------------------------------------------------------------- > #p UHF/6-31G(d'f) scf=(verytight,IntRep) Guess=core > UHF SCF on Ni > 0 3 > Ni 0. 0. 0. > ----------------------------------------------------------------------------- > > But familiar ground state electronic levels (3F4) are NOT obtained from this > G03 calc. > In other words, the energy level order of, > d(z^2)= d(xx-yy)= d(xy) = d(xz)= d(yz), is NOT observed. > > Actually, I expected that it will give an ordering of (t2g)<(eg) levels which > was not happened (i.e. three t2g orbitals (with same Energy) with 6 > electrons and 2, electrons at each of the eg levels which are above the t2g > levels). Interestingly, the Oh symmetry of the atomic-structure is recognized > by the ...PG=Oh... data at the end of the log file. > > Again, I have noted that for Full/Half-filled electronic systems like, [Ar] > or [Mn]++, this degenerate levels can be Perfectly obtained with G03. > > My doubt is that, using UHF whether it is possible to align electrons in > three t2g orbitals and two eg orbitals? > Does spin contamination lift the degeneracies of this system? And, If UHF is > unable to catch the degeneracies, > which method can be used to illustrate the (t2g) and (eg) pairs of the > degenerate states. > > Can any Gaussian people help me at this point? Krishnamohan, Try to surround your Ni[+2] center of an octahedron of charges at experimental geometries. Your purpose is didactical. Remember that eg and t2g are irreducible representations of the octahedral (Oh) of tetrahedral (Th) group of symmetry. Don't expect accuracy. The correlation energy is VERY large in d elements. If you want bibliografy try to read on the embedding problem. Regards, Dr. V�ctor Lua�a -- \|/a "After years working on a problem the genius exclaimed: |^.^| what an idiot I am ... the solution is trivial!' +!OO--\_/--OO!---------------------------------+----------------------- ! Dr.V�ctor Lua�a ! ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor()fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Sat Jun 21 15:35:01 2014 From: "Partha Sengupta anapspsmo(-)gmail.com" To: CCL Subject: CCL:G: problem in using gen keyword using gaussian09 Message-Id: <-50267-140621141049-1515-dzJt3c2fwOsfLWm6SuBJdw.:.server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=e89a8ff1c11a0b630d04fc5c8784 Date: Sat, 21 Jun 2014 23:40:39 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo*o*gmail.com] --e89a8ff1c11a0b630d04fc5c8784 Content-Type: text/plain; charset=UTF-8 A space is required when Gen pseudo=read is used in gjf file. Partha On Sat, Jun 21, 2014 at 2:11 PM, Niveditha Surukonti nivs916|*|gmail.com < owner-chemistry**ccl.net> wrote: > with pseudo=read optimization done successfully. thankyou very much > > with best regards > Niveditha Surukonti, > Research Scholar, > CSIR-IICT, HYD. > > > On Fri, Jun 20, 2014 at 7:29 PM, Cenk Selcuki cselcuki#,#yahoo.com < > owner-chemistry(~)ccl.net> wrote: > >> Dear Niveditha Reddy Surukonti, >> Add Pseudo=Read keyword to the keyword line and try again. >> Best Regards, >> Cenk >> >> >> On Friday, June 20, 2014 4:41 PM, Niveditha Reddy Surukonti nivs916(0) >> gmail.com wrote: >> >> >> >> Sent to CCL by: "Niveditha Reddy Surukonti" [nivs916]_[gmail.com] >> Iam performing optimization of a chemosensor molecule, which involves a >> thiazole substituted ferrocene ligand and mercury dication. At >> mpw1b95/lanl2dz level of theory optimization terminated normally, placing >> mercury cation at 3.6 angstroms distance. but when am placing 6-311g(d,p) >> on >> C,H atoms and 6-311+g(d,P)on S,N atoms using gen keyword in gaussian, >> after >> each optimization mercury is moving close to nitrogen and finally >> nitrozen is >> sitting inside the Hg, missing all connectivities, finally becoming >> clumpsy, >> and error terminated. i tried in other ways such as stating from other >> lower >> basis sets still it is showing same behaviour. i have no idea about what >> is >> actually going on here, so am unable to solve this problem. if anybody >> has >> any idea about this, kindly let me know. here is my input file. >> >> %mem=4000MB >> #p opt=maxcyc=700 mpwb95/gen iop(3/76=0690003100) scf(maxcyc=300) >> geom=connectivity >> >> Title Card Required >> >> 2 1 >> C 0.03589400 -3.09448500 0.19674500 >> C -1.35242600 -3.27805600 -0.31384300 >> H -2.00984800 -3.66901500 0.46849900 >> continues...... >> >> C H 0 >> 6-311g(d,p) >> ****** >> S N 0 >> 6-311+g(d,p) >> ****** >> Hg 0 >> LanL2DZ >> ***** >> >> Hg 0 >> LanL2DZ >> >> >> Any help will be highly appreciated. >> >> Thanks in advance.>> the strange characters on the top line to the : sign. You can also >> >> E-mail to subscribers: CHEMISTRY : ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST : ccl.net or use>> >> >> >> >> > -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --e89a8ff1c11a0b630d04fc5c8784 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

A space is required when Gen pseudo=3Dread is used in= gjf file.

Partha

On Sat, Jun 21, 2014 at 2:11 PM, Niveditha Surukonti= nivs916|*|gmail.com <= ;owner-chemist= ry**ccl.net> wrote:

with pseudo=3Dread optimiza= tion done successfully. thankyou very much
=

with best regards
=C2= =A0=C2=A0 Niveditha Surukonti,
=C2=A0=C2=A0=C2=A0 Research Scholar= ,

=C2=A0=C2=A0=C2=A0 CSIR-IICT, HYD.

On Fri, Jun 20, 2014 at 7:29 PM, C= enk Selcuki cselcuki#,#yahoo= .com <owner-chemistry(~)ccl.net> wrote:

Dear= =C2=A0Niveditha= Reddy Surukonti,
Add Pseudo=3DRead keyw= ord to the keyword line and try again.=C2=A0
Best Regards,
Cenk

On Friday, June 20, 2014= 4:41 PM, Niveditha Reddy Surukonti nivs916(0)gmail.com <owner-chemistry : ccl.net> wrote:

Sent to CCL by: "Niveditha=C2=A0 Reddy Surukonti"= ; [nivs916]_[gmail.com]<= br>Iam performing optimization of a chemosensor molecule, which involves a
thiazole substituted ferrocene = ligand and mercury dication. At
mpw1b95/lanl2dz level of theory optimiz= ation terminated normally, placing
mercury cation at 3.6 angstroms dist= ance. but when am placing 6-311g(d,p) on
C,H atoms and 6-311+g(d,P)on S,N atoms using gen keyword in gaussian, after=
each optimization mercury is moving close to nitrogen and finally nitr= ozen is
sitting inside the Hg, missing all connectivities, finally beco= ming clumpsy,
and error terminated. i tried in other ways such as stating from other lowe= r
basis sets still it is showing same behaviour. i have no idea about w= hat is
actually going on here, so am unable to solve this problem. if a= nybody has
any idea about this, kindly let me know. here is my input file.

%mem=3D4000MB
#p opt=3Dmaxcyc=3D700= mpwb95/gen iop(3/76=3D0690003100) scf(maxcyc=3D300)
geom=3Dconnectivit= y

Title Card Required

2 1
C=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.03589400=C2=A0 -3.09448500=C2=A0 =C2= =A0 0.19674500
C=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 -1.35242600=C2= =A0 -3.27805600=C2=A0 -0.31384300
H=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 -2.00984800=C2=A0 -3.66901500=C2=A0 =C2=A0 0.468499= 00
continues......

C H 0
6-311g(d,p)
******
S N 0
6-3= 11+g(d,p)
******
Hg 0
LanL2DZ
*****

Hg 0
LanL2DZ

Any help will be highly = appreciated.

=C2=A0 Thanks in advance.

-=3D This is a= utomatically added to each message by the mailing script =3D-

the strange characters on the top line to the = : sign. You can also

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Vivekananda Mahavidyalaya, Burdwan
--e89a8ff1c11a0b630d04fc5c8784-- From owner-chemistry@ccl.net Sat Jun 21 18:25:00 2014 From: "Alex A. Granovsky gran(!)classic.chem.msu.su" To: CCL Subject: CCL:G: Chargemol 3.0 released Message-Id: <-50268-140621164759-6666-iVy4L0k3XofCT/NNBFGWSQ|a|server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Type: multipart/alternative; boundary="----=_NextPart_000_166E_01CF8DB3.767DC4D0" Date: Sun, 22 Jun 2014 00:46:54 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran(~)classic.chem.msu.su] This is a multi-part message in MIME format. ------=_NextPart_000_166E_01CF8DB3.767DC4D0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Tom, Frankly I do not understand why should we incorporate EDFs into Firefly. = EDFs is an approximation which does not take into account effects due to = core-valence polarization and intimate details of the ECPs in use. It is = only useful to perform approximate AIM analysis with ECPs.=20 If one wants to use, say, Chargemol in conjunction with Firefly, it = would be logical if EDFs will be provided by Chargemol as these are not = the data computed within the particular QC run.=20 With no EDF data, .wfx format is pretty similar to .wfn and could be = implemented.=20 Kind regards, Alex Granovsky > From: Thomas Manz thomasamanz]~[gmail.com=20 Sent: Saturday, June 21, 2014 6:56 PM To: Granovsky, Alex, A. =20 Subject: CCL:G: Chargemol 3.0 released Hi Brian,=20 >Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can > only use HF or DFT densities as it calculated them from the MOs (KS > orbitals)? Would it need something that outputs the full density = matrix > to use CASSCF results? The Chargemol program can use input from any quantum chemistry method = (DFT, HF, CASSCF, MP2, coupled-cluster, etc.). Just include Density =3D Current, Output =3D WFX, Pop=3D NO (for spin = unpolarized calculation) or NOAB (for spin polarized calculation) on the = GAUSSIAN 09 route line and the name of the .wfx file at the bottom of = the GAUSSIAN input (.com or .gjf) file. This directs GAUSSIAN 09 to = output the fully correlated density to the .WFX file, so you will get = the corresponding density when running methods like DFT, HF, CASSCF, = MP2, coupled-cluster, etc. > Does anyone have any idea how it could use output from GAMESS(US) [or > indeed GAMESS(UK) or Firefly]? Best route in the long run would be for GAMESS and Firefly developers to = add code to output .wfx file. The .wfx files are read by AIMALL, = MultiWFN, and Chargemol programs that perform various kinds of atomic = population analysis. The .wfx format specification is shown at = http://aim.tkgristmill.com/wfxformat.html The .wfx file contains = information about the cartesian Gaussian basis set primitives, the basis = set coefficients for the natural orbitals (eigenvectors of the = first-order density matrix), positions of each atom, system net charge = and total number of electrons, nuclear charges, and core electrons = replaced by effective core potentials (if any). For quantum chemistry = calculations that used effective core potentials, the .wfx file contains = Electron Density Functions (EDFs), which are normally spherically = symmetric for each atom, that specify the electron density of the core = electrons replaced by the atom's effective core potential.=20 In principle, it should only take one person a few of days of = programming to add the option to output a .wfx file from the GAMESS or = Firefly software packages. Presumably, all of the information about the = cartesian basis set primitives, natural orbital basis set coefficients, = nuclear positions, etc. is already available within these programs and = code just needs to be added to output them in .wfx file format. The only = information that may not be already available within the GAMESS and = Firefly codes is the EDFs that specify the density of the core electrons = replaced by effective core potentials. I have generated a set of core = electron densities for all elements atomic number 1 (H) to 109 (Mt), so = if one of the GAMESS or Firefly developers is in need of that = information, they can contact me and I can help them with a library of = core electron densities for the purpose of generating .wfx files. I recommend that you contact the GAMESS or Firefly developers and ask if = it is possible for them to add output of .wfx file format. This will = certainly be the best long-term solution.=20 Sincerely, Tom Manz assistant professor, Chemical & Materials Engineering New Mexico State University On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James = brian.james.duke() gmail.com wrote: Sent to CCL by: "Salter-Duke, Brian James " = [brian.james.duke(_)gmail.com] This seems a really useful program. Does anyone have any idea how it could use output from GAMESS(US) [or indeed GAMESS(UK) or Firefly]? Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can only use HF or DFT densities as it calculated them from the MOs (KS orbitals)? Would it need something that outputs the full density matrix to use CASSCF results? Brian. On Mon, Jun 16, 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu = wrote: > Hi, > > I just wanted to let everyone know about the release of Chargemol > version 3.0, which performs Density Derived Electrostatic and Chemical > (DDEC) atomic population analysis. > > The latest version has the following features: > > 1) Computes net atomic charges, atomic spin moments, and now effective > bond orders (EBOs) for nonperiodic and periodic materials. For each = atom, > the sum of effective bond orders (SEBO) is also computed and printed. = The > program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a = variety > of other quantum chemistry programs. > > 2) Atomic dipole and quadrupole moments are computed for all systems. > For nonperiodic materials, the total system dipole and quadrupole = moments > are also computed. The latest version adds the computation and = printing of > the traceless quadrupole tensor eigenvalues. > > 3) A new constraint has been added to improvement the treatment in = ionic > systems containing small cations. For example, it was noticed that in > crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too > contracted and too positively charged. This has been fixed by = constraining > the rate of decay of atomic weights to be no faster than exp(-3*r) in > regions where atoms overlap. > > 4) To improve the speed, the program has been translated from Matlab > into Fortran code. The Fortran code is parallelized with OpenMP = allowing it > to run on multiple processors with a shared memory (i.e., single > node, multiple processors). A serial version of the Fortran code is = also > available. > > 5) Precompiled Windows and Linux binaries and the uncompiled = sourcecode > are available. Many users can utilize the precompiled executables > without recompiling the program. > > 6) The program is free to download from ddec.sourceforge.net. The > download includes a manual explaining how to install and run the = program. > > Sincerely, > > Tom Manz -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(a)monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia -=3D This is automatically added to each message by the mailing script = =3D- E-mail to subscribers: CHEMISTRY-$-ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_NextPart_000_166E_01CF8DB3.767DC4D0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi Tom,

Frankly I do not understand why should we incorporate EDFs into = Firefly.=20

EDFs is an approximation which does not take into account effects = due to=20 core-valence polarization and intimate details of the ECPs in use. It is = only=20 useful to perform approximate AIM analysis with ECPs.

If one wants to use, say, Chargemol in conjunction with Firefly, it = would=20 be logical if EDFs will be provided by Chargemol as these are not the = data=20 computed within the particular QC run.

With no EDF data, .wfx format is pretty similar to .wfn and = could be=20 implemented.

Kind regards,

Alex Granovsky

From: Thomas Manz = thomasamanz]~[gmail.com=20

Sent: Saturday, June 21, 2014 6:56 PM

To: Granovsky, Alex, A. =

Subject: CCL:G: Chargemol 3.0 released

Hi Brian,=20

>Am I=20 correct in thinking that with GAUSSIAN 09 using .wfx files, it = can

> = only use=20 HF or DFT densities as it calculated them from the MOs (KS

> = orbitals)? Would it need something that outputs the full density=20 matrix

> = to use=20 CASSCF results?

The = Chargemol=20 program can use input from any quantum chemistry method (DFT, HF, = CASSCF, MP2,=20 coupled-cluster, etc.).

Just include Density =3D Current, = Output =3D=20 WFX, Pop=3D NO (for spin unpolarized calculation) or NOAB (for spin = polarized=20 calculation) on the GAUSSIAN 09 route line and the name of the .wfx file = at the=20 bottom of the GAUSSIAN input (.com or .gjf) file. This directs GAUSSIAN 09 to output the fully = correlated=20 density to the .WFX file, so you will get the corresponding density when = running=20 methods like DFT, HF, = CASSCF, MP2,=20 coupled-cluster, etc.

> = Does=20 anyone have any idea how it could use output from GAMESS(US) = [or

> = indeed=20 GAMESS(UK) or Firefly]?

Best = route in=20 the long run would be for GAMESS and Firefly developers to add code to = output=20 .wfx file. The .wfx = files are=20 read by AIMALL, MultiWFN, and Chargemol programs that perform various = kinds of=20 atomic population analysis. The .wfx format = specification is shown at http://aim.tkgristmill= .com/wfxformat.html =20 The .wfx file contains information about the cartesian Gaussian basis = set=20 primitives, the basis set coefficients for the natural orbitals = (eigenvectors of=20 the first-order density matrix), positions of each atom, system net = charge and=20 total number of electrons, nuclear charges, and core electrons replaced = by=20 effective core potentials (if any). For quantum chemistry calculations = that used=20 effective core potentials, the .wfx file contains Electron Density = Functions=20 (EDFs), which are normally spherically symmetric for each atom, that = specify the=20 electron density of the core electrons replaced by the atom's effective = core=20 potential.

In principle, it = should only=20 take one person a few of days of programming to add the option to output = a .wfx=20 file from the GAMESS or Firefly software packages. Presumably, all of = the=20 information about the cartesian basis set primitives, natural orbital = basis set=20 coefficients, nuclear positions, etc. is already available within these=20 programs and code = just needs=20 to be added to output them in .wfx file format. The only information = that may=20 not be already available within the GAMESS and Firefly codes is the EDFs = that=20 specify the density of the core electrons replaced by effective core = potentials.=20 I have generated a set of core electron densities for all elements = atomic number=20 1 (H) to 109 (Mt), so if one of the GAMESS or Firefly developers is in = need of=20 that information, they can contact me and I can help them with a library = of core=20 electron densities for the purpose of generating .wfx = files.

I recommend that you = contact=20 the GAMESS or Firefly developers and ask if it is possible for them to = add=20 output of .wfx file format. This will certainly be the best long-term = solution.=20

Sincerely,

Tom Manz

assistant professor, Chemical & Materials Engineering

New Mexico State University

On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, = Brian James=20 brian.james.duke() gmail.com <owner-chemistry-$-ccl.net> = wrote:

Sent to CCL=20 by: "Salter-Duke, Brian James " [brian.james.duke(_)gmail.com]
This seems a really useful = program.

Does=20 anyone have any idea how it could use output from GAMESS(US) = [or
indeed=20 GAMESS(UK) or Firefly]?

Am I correct in thinking that with = GAUSSIAN 09=20 using .wfx files, it can
only use HF or DFT densities as it = calculated them=20 > from the MOs (KS
orbitals)? Would it need something that outputs the = full=20 density matrix
to use CASSCF results?

Brian.

On Mon, = Jun 16,=20 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu wrote:
> Hi,
>
> I just = wanted to=20 let everyone know about the release of Chargemol
> version 3.0, = which=20 performs Density Derived Electrostatic and Chemical
> (DDEC) = atomic=20 population analysis.
>
> The latest version has the = following=20 features:
>
> 1) Computes net atomic charges, atomic spin = moments,=20 and now effective
> bond orders (EBOs) for nonperiodic and = periodic=20 materials. For each atom,
> the sum of effective bond orders = (SEBO) is=20 also computed and printed. The
> program analyzes output from = GAUSSIAN 09=20 (.wfx files), VASP, and a variety
> of other quantum chemistry=20 programs.
>
> 2) Atomic dipole and quadrupole moments are = computed=20 for all systems.
> For nonperiodic materials, the total system = dipole and=20 quadrupole moments
> are also computed. The latest version adds = the=20 computation and printing of
> the traceless quadrupole tensor=20 eigenvalues.
>
> 3) A new constraint has been added to = improvement=20 the treatment in ionic
> systems containing small cations. For = example, it=20 was noticed that in
> crystals such as Na2Cl and Li-Ru-O, the Na = and Li=20 atoms become too
> contracted and too positively charged. This has = been=20 fixed by constraining
> the rate of decay of atomic weights to be = no=20 faster than exp(-3*r) in
> regions where atoms = overlap.
>
> 4)=20 To improve the speed, the program has been translated from = Matlab
> into=20 Fortran code. The Fortran code is parallelized with OpenMP allowing = it
>=20 to run on multiple processors with a shared memory (i.e., single
> = node,=20 multiple processors). A serial version of the Fortran code is = also
>=20 available.
>
> 5) Precompiled Windows and Linux binaries and = the=20 uncompiled sourcecode
> are available. Many users can utilize the=20 precompiled executables
> without recompiling the = program.
>
>=20 6) The program is free to download from ddec.sourceforge.net. The
> download includes = a manual=20 explaining how to install and run the program.
>
>=20 Sincerely,
>
> Tom Manz

--
   Brian = Salter-Duke=20 (Brian Duke)   Brian.Salter-Duke(a)monash.edu
      &nb= sp;           &nbs= p;=20 Adjunct Associate=20 Professor
          = =20 Monash Institute of Pharmaceutical = Sciences
     =20 Monash University Parkville Campus, VIC 3052, = Australia

-=3D This=20 is automatically added to each message by the mailing script =3D-

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------=_NextPart_000_166E_01CF8DB3.767DC4D0-- From owner-chemistry@ccl.net Sat Jun 21 21:26:00 2014 From: "Salter-Duke, Brian James - brian.james.duke:+:gmail.com" To: CCL Subject: CCL:G: Chargemol 3.0 released Message-Id: <-50269-140621203720-18016-KEnAhMqN32cRVzkfcOAqug]![server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sun, 22 Jun 2014 10:37:09 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke]=[gmail.com] I agree with Alex. If EDFs are included in the .wfx file, might it not cause problems if that file is used by a program other than Chargemol. I also agree that the .wfx format could be implemented in GAMESS. I am a developer of VB2000 which is included in GAMESS, so I will talk to Mike Schmidt in the Gordon Group about this. Brian. On Sun, Jun 22, 2014 at 12:46:54AM +0400, Alex A. Granovsky gran(!)classic.chem.msu.su wrote: > Hi Tom, > > Frankly I do not understand why should we incorporate EDFs into Firefly. > > EDFs is an approximation which does not take into account effects due to core-valence polarization and intimate details of the ECPs in use. It is only useful to perform approximate AIM analysis with ECPs. > > If one wants to use, say, Chargemol in conjunction with Firefly, it would be logical if EDFs will be provided by Chargemol as these are not the data computed within the particular QC run. > > With no EDF data, .wfx format is pretty similar to .wfn and could be implemented. > > Kind regards, > Alex Granovsky > > > > From: Thomas Manz thomasamanz]~[gmail.com > Sent: Saturday, June 21, 2014 6:56 PM > To: Granovsky, Alex, A. > Subject: CCL:G: Chargemol 3.0 released > > Hi Brian, > > >Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can > > only use HF or DFT densities as it calculated them from the MOs (KS > > orbitals)? Would it need something that outputs the full density matrix > > to use CASSCF results? > > > > The Chargemol program can use input from any quantum chemistry method (DFT, HF, CASSCF, MP2, coupled-cluster, etc.). > Just include Density = Current, Output = WFX, Pop= NO (for spin unpolarized calculation) or NOAB (for spin polarized calculation) on the GAUSSIAN 09 route line and the name of the .wfx file at the bottom of the GAUSSIAN input (.com or .gjf) file. This directs GAUSSIAN 09 to output the fully correlated density to the .WFX file, so you will get the corresponding density when running methods like DFT, HF, CASSCF, MP2, coupled-cluster, etc. > > > > Does anyone have any idea how it could use output from GAMESS(US) [or > > indeed GAMESS(UK) or Firefly]? > > > > Best route in the long run would be for GAMESS and Firefly developers to add code to output .wfx file. The .wfx files are read by AIMALL, MultiWFN, and Chargemol programs that perform various kinds of atomic population analysis. The .wfx format specification is shown at http://aim.tkgristmill.com/wfxformat.html The .wfx file contains information about the cartesian Gaussian basis set primitives, the basis set coefficients for the natural orbitals (eigenvectors of the first-order density matrix), positions of each atom, system net charge and total number of electrons, nuclear charges, and core electrons replaced by effective core potentials (if any). For quantum chemistry calculations that used effective core potentials, the .wfx file contains Electron Density Functions (EDFs), which are normally spherically symmetric for each atom, that specify the electron density of the core electrons replaced by the atom's effective core potential. > > > In principle, it should only take one person a few of days of programming to add the option to output a .wfx file from the GAMESS or Firefly software packages. Presumably, all of the information about the cartesian basis set primitives, natural orbital basis set coefficients, nuclear positions, etc. is already available within these programs and code just needs to be added to output them in .wfx file format. The only information that may not be already available within the GAMESS and Firefly codes is the EDFs that specify the density of the core electrons replaced by effective core potentials. I have generated a set of core electron densities for all elements atomic number 1 (H) to 109 (Mt), so if one of the GAMESS or Firefly developers is in need of that information, they can contact me and I can help them with a library of core electron densities for the purpose of generating .wfx files. > > > I recommend that you contact the GAMESS or Firefly developers and ask if it is possible for them to add output of .wfx file format. This will certainly be the best long-term solution. > > Sincerely, > > Tom Manz > assistant professor, Chemical & Materials Engineering > New Mexico State University > > > > On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James brian.james.duke() gmail.com wrote: > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke(_)gmail.com] > This seems a really useful program. > > Does anyone have any idea how it could use output from GAMESS(US) [or > indeed GAMESS(UK) or Firefly]? > > Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can > only use HF or DFT densities as it calculated them from the MOs (KS > orbitals)? Would it need something that outputs the full density matrix > to use CASSCF results? > > Brian. > > On Mon, Jun 16, 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu wrote: > > Hi, > > > > I just wanted to let everyone know about the release of Chargemol > > version 3.0, which performs Density Derived Electrostatic and Chemical > > (DDEC) atomic population analysis. > > > > The latest version has the following features: > > > > 1) Computes net atomic charges, atomic spin moments, and now effective > > bond orders (EBOs) for nonperiodic and periodic materials. For each atom, > > the sum of effective bond orders (SEBO) is also computed and printed. The > > program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a variety > > of other quantum chemistry programs. > > > > 2) Atomic dipole and quadrupole moments are computed for all systems. > > For nonperiodic materials, the total system dipole and quadrupole moments > > are also computed. The latest version adds the computation and printing of > > the traceless quadrupole tensor eigenvalues. > > > > 3) A new constraint has been added to improvement the treatment in ionic > > systems containing small cations. For example, it was noticed that in > > crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too > > contracted and too positively charged. This has been fixed by constraining > > the rate of decay of atomic weights to be no faster than exp(-3*r) in > > regions where atoms overlap. > > > > 4) To improve the speed, the program has been translated from Matlab > > into Fortran code. The Fortran code is parallelized with OpenMP allowing it > > to run on multiple processors with a shared memory (i.e., single > > node, multiple processors). A serial version of the Fortran code is also > > available. > > > > 5) Precompiled Windows and Linux binaries and the uncompiled sourcecode > > are available. Many users can utilize the precompiled executables > > without recompiling the program. > > > > 6) The program is free to download from ddec.sourceforge.net. The > > download includes a manual explaining how to install and run the program. > > > > Sincerely, > > > > Tom Manz > > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(a)monash.edu > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia> > > > E-mail to subscribers: CHEMISTRY-$-ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_NextPart_000_166E_01CF8DB3.767DC4D0 > Content-Type: text/html; > charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > > > >

Hi Tom,

Frankly I do not understand why should we incorporate EDFs into Firefly. >

EDFs is an approximation which does not take into account effects due to > core-valence polarization and intimate details of the ECPs in use. It is only > useful to perform approximate AIM analysis with ECPs.

If one wants to use, say, Chargemol in conjunction with Firefly, it would > be logical if EDFs will be provided by Chargemol as these are not the data > computed within the particular QC run.

With no EDF data, .wfx format is pretty similar to .wfn and could be > implemented.

Kind regards,

Alex Granovsky

style="FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri'; COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION: none"> >

From: href="mailto:owner-chemistry^-^ccl.net">Thomas Manz thomasamanz]~[gmail.com >

Sent: Saturday, June 21, 2014 6:56 PM

To: href="mailto:gran^-^classic.chem.msu.su">Granovsky, Alex, A.

Subject: CCL:G: Chargemol 3.0 released

style="FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri'; COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION: none"> >

Hi Brian, >

>Am I > correct in thinking that with GAUSSIAN 09 using .wfx files, it can

> only use > HF or DFT densities as it calculated them from the MOs (KS

> > orbitals)? Would it need something that outputs the full density > matrix

> to use > CASSCF results?

style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">

The Chargemol > program can use input from any quantum chemistry method (DFT, HF, CASSCF, MP2, > coupled-cluster, etc.).

Just include Density = Current, Output = > WFX, Pop= NO (for spin unpolarized calculation) or NOAB (for spin polarized > calculation) on the GAUSSIAN 09 route line and the name of the .wfx file at the > bottom of the GAUSSIAN input (.com or .gjf) file. face="arial, sans-serif">This directs GAUSSIAN 09 to output the fully correlated > density to the .WFX file, so you will get the corresponding density when running > methods like style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">DFT, HF, CASSCF, MP2, > coupled-cluster, etc.

style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">

> Does > anyone have any idea how it could use output from GAMESS(US) [or

> indeed > GAMESS(UK) or Firefly]? style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">

style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">

Best route in > the long run would be for GAMESS and Firefly developers to add code to output > .wfx file. The .wfx files are > read by AIMALL, MultiWFN, and Chargemol programs that perform various kinds of > atomic population analysis. style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">The .wfx format > specification is shown at href="http://aim.tkgristmill.com/wfxformat.html">http://aim.tkgristmill.com/wfxformat.html > The .wfx file contains information about the cartesian Gaussian basis set > primitives, the basis set coefficients for the natural orbitals (eigenvectors of > the first-order density matrix), positions of each atom, system net charge and > total number of electrons, nuclear charges, and core electrons replaced by > effective core potentials (if any). For quantum chemistry calculations that used > effective core potentials, the .wfx file contains Electron Density Functions > (EDFs), which are normally spherically symmetric for each atom, that specify the > electron density of the core electrons replaced by the atom's effective core > potential.

In principle, it should only > take one person a few of days of programming to add the option to output a .wfx > file from the GAMESS or Firefly software packages. Presumably, all of the > information about the cartesian basis set primitives, natural orbital basis set > coefficients, nuclear positions, etc. is already available within these > programs and code just needs > to be added to output them in .wfx file format. The only information that may > not be already available within the GAMESS and Firefly codes is the EDFs that > specify the density of the core electrons replaced by effective core potentials. > I have generated a set of core electron densities for all elements atomic number > 1 (H) to 109 (Mt), so if one of the GAMESS or Firefly developers is in need of > that information, they can contact me and I can help them with a library of core > electron densities for the purpose of generating .wfx files.

I recommend that you contact > the GAMESS or Firefly developers and ask if it is possible for them to add > output of .wfx file format. This will certainly be the best long-term solution. >

Sincerely,

Tom Manz

assistant professor, Chemical & Materials Engineering

New Mexico State University

On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James > brian.james.duke() gmail.com < href="mailto:owner-chemistry-$-ccl.net" > target=_blank>owner-chemistry-$-ccl.net> wrote:

Sent to CCL > by: "Salter-Duke, Brian James " [brian.james.duke(_) target=_blank>gmail.com]
This seems a really useful program.

Does > anyone have any idea how it could use output from GAMESS(US) [or
indeed > GAMESS(UK) or Firefly]?

Am I correct in thinking that with GAUSSIAN 09 > using .wfx files, it can
only use HF or DFT densities as it calculated them > > from the MOs (KS
orbitals)? Would it need something that outputs the full > density matrix
to use CASSCF results?

Brian.

On Mon, Jun 16, > 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x% target=_blank>nmsu.edu wrote:
> Hi,
>
> I just wanted to > let everyone know about the release of Chargemol
> version 3.0, which > performs Density Derived Electrostatic and Chemical
> (DDEC) atomic > population analysis.
>
> The latest version has the following > features:
>
> 1) Computes net atomic charges, atomic spin moments, > and now effective
> bond orders (EBOs) for nonperiodic and periodic > materials. For each atom,
> the sum of effective bond orders (SEBO) is > also computed and printed. The
> program analyzes output from GAUSSIAN 09 > (.wfx files), VASP, and a variety
> of other quantum chemistry > programs.
>
> 2) Atomic dipole and quadrupole moments are computed > for all systems.
> For nonperiodic materials, the total system dipole and > quadrupole moments
> are also computed. The latest version adds the > computation and printing of
> the traceless quadrupole tensor > eigenvalues.
>
> 3) A new constraint has been added to improvement > the treatment in ionic
> systems containing small cations. For example, it > was noticed that in
> crystals such as Na2Cl and Li-Ru-O, the Na and Li > atoms become too
> contracted and too positively charged. This has been > fixed by constraining
> the rate of decay of atomic weights to be no > faster than exp(-3*r) in
> regions where atoms overlap.
>
> 4) > To improve the speed, the program has been translated from Matlab
> into > Fortran code. The Fortran code is parallelized with OpenMP allowing it
> > to run on multiple processors with a shared memory (i.e., single
> node, > multiple processors). A serial version of the Fortran code is also
> > available.
>
> 5) Precompiled Windows and Linux binaries and the > uncompiled sourcecode
> are available. Many users can utilize the > precompiled executables
> without recompiling the program.
>
> > 6) The program is free to download from target=_blank>ddec.sourceforge.net. The
> download includes a manual > explaining how to install and run the program.
>
> > Sincerely,
>
> Tom Manz

--
   Brian Salter-Duke > (Brian Duke)   Brian.Salter-Duke(a) target=_blank>monash.edu
                    > Adjunct Associate > Professor
            > Monash Institute of Pharmaceutical Sciences
      > Monash University Parkville Campus, VIC 3052, Australia

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-- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke+/-monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia