From owner-chemistry@ccl.net Fri Jul 22 00:27:01 2016 From: "Yingqi Tian sapientx(_)zju.edu.cn" To: CCL Subject: CCL: How to solve the HF dependence of TDDFT excitation energy ? Message-Id: <-52326-160722000023-23576-lB3JELSF8jyfk3Vt6Ym+IA:server.ccl.net> X-Original-From: "Yingqi Tian" Date: Fri, 22 Jul 2016 00:00:22 -0400 Sent to CCL by: "Yingqi Tian" [sapientx-#-zju.edu.cn] Hello everyone. It is well known that the TDDFT results are greatly dependent on the hatree-fork ratio in hybrid-functionals. One usually has to test several functionals before finding a appropriate one. I'd like to consult you that is there any promising strategy to solve this problem ? If there is, please list the representative papers. Many thanks ! sapientx . zju.edu.cn From owner-chemistry@ccl.net Fri Jul 22 04:45:01 2016 From: "Tandon Swetanshu tandons_+_tcd.ie" To: CCL Subject: CCL:G: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52327-160722044152-6925-TcJFuqP0PcSvU/lz8Qz/Xw * server.ccl.net> X-Original-From: Tandon Swetanshu Content-Type: multipart/alternative; boundary=94eb2c12324c8539000538356793 Date: Fri, 22 Jul 2016 09:41:44 +0100 MIME-Version: 1.0 Sent to CCL by: Tandon Swetanshu [tandons__tcd.ie] --94eb2c12324c8539000538356793 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Indrajit, If you want to decrease the SCF convergence criteria then you can look at the keyword 'Conver=3DN'. If you want to decrease the optimization convergence criteria, you can look at the keyword 'Opt=3DLoose'. If the displacement parameter is not convergi= ng you can also try increasing the integration grid size using the keyword' Int=3Dgrid=3DXXXYYY'. Sometimes this works. Hope that helps. Swetanshu. On 22 July 2016 at 00:01, V=C3=ADctor Lua=C3=B1a Cabal victor[-] fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor*|= * > fluor.quimica.uniovi.es] > On Thu, Jul 21, 2016 at 09:49:19PM +0200, Indrajit Deb biky2004indra(a) > gmail.com wrote: > > Finally I solved the problem. And fortunately the problem was with > > the input file. I am trying to explain. May be it will help others. > > Indrajit, > > An excellent iniciative that was common years ago but it is disappearing > in our days. I hope other follow this path. > > > 4. Solve: I removed all the blank lines from the end of the external > basis > > set file, but kept one blank line at end of Gaussian09 input file (as a > > general rule). Its running. > > 5. Another point to be noted----do not keep any blank lines at the > > beginning of the external basis set file. > > There are many differences in the mode programs get their input data > > from the external file. Gaussian keeps a very old format since the very > beginnings, and it is very important to examine carefully the rules in > the manual, which can be a bit obscure at some times. > > There are many different traditions in this respect. One that comes from > the tradition of compilers is using keywords to document the meaning > of each input line. This is a format that is gaining impetus: see the > format for nwchem: > > title "Nitrogen cc-pvdz SCF geometry optimization" > geometry > n 0 0 0 > n 0 0 1.08 > end > basis > n library cc-pvdz > end > task scf optimize > > Something even a non expert with some knowledge of the field can read as > a text. This format must be parsed and executed by the software. Creating > this type of soft requires some knowledge on lexical analysis and > parsing, but today is relatively simple to use a scripting language > (oldies: bash, perl, awk, ...; modern: python, php, lua, ...) for driving > the interpreting part and let fortran, c or any compiled language to > do the numerical part. > > Orca, also a relatively recent code, follow gaussian tradition, but > includes significant goodies in the format: > > # Comment lines can be added if the line begins with a #. > ! BP86 def2-SVP Opt > # BP86 is here the method (DFT functional), def2-SVP the basis set and Op= t > is the jobtype (geometry optimization). > # Order of the keywords is not important. > *xyz 0 1 > H 0.0 0.0 0.0 > H 0.0 0.0 1.0 > * > > Lesson to take home: Be very careful with the input of gaussian. You can > use a modeller to create the input or a first version for it (gaussvies, > avogadro, ...). And finally: there are many more q-chem codes apart > > from gaussian. It is a good practice to get used to several of them > > from the beginning. In fact, we theoretitians should check that a > particular result can be reproduced on more than a code to avoid > disturbing mistakes. > > Thanks for your summary of your experiences, > V=C3=ADctor > -- > . . "Patriotism is the last refuge of a scoundrel." > / `' \ -- Samuel Johnson (UK, 1755) > /(o)(o)\ > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peo= r > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +--------------------------------------------+ > GroupPage: > Articles: > git-hub: > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --94eb2c12324c8539000538356793 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Indrajit,

If you want to de= crease the SCF convergence criteria then you can look at the keyword 'C= onver=3DN'.
If you want to decrease the optimization convergen= ce criteria, you can look at the keyword 'Opt=3DLoose'. If the disp= lacement parameter is not converging you can also try increasing the integr= ation grid size using the keyword' Int=3Dgrid=3DXXXYYY'. Sometimes = this works.
Hope that helps.

Swetanshu.
=

On 22= July 2016 at 00:01, V=C3=ADctor Lua=C3=B1a Cabal victor[-]fluor.quimica.uniovi.es &l= t;owner-chemis= try|,|ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor*|*<= a href=3D"http://fluor.quimica.uniovi.es" rel=3D"noreferrer" target=3D"_bla= nk">fluor.quimica.uniovi.es]
On Thu, Jul 21, 2016 at 09:49:19PM +0200, Indrajit Deb bik= y2004indra(a)gmail.com wrote:
> Finally I solved the problem. And fortunately the problem was with
> the input file. I am trying to explain.=C2=A0 May be it will help othe= rs.

Indrajit,

An excellent iniciative that was common years ago but it is disappearing in our days. I hope other follow this path.

> 4. Solve: I removed all the blank lines from the end of the external b= asis
> set file, but kept one blank line at end of Gaussian09 input file (as = a
> general rule). Its running.
> 5. Another point to be noted----do not keep any blank lines at the
> beginning of the external basis set file.

There are many differences in the mode programs get their input data=
> from the external file. Gaussian keeps a very old format since the ver= y
beginnings, and it is very important to examine carefully the rules in
the manual, which can be a bit obscure at some times.

There are many different traditions in this respect. One that comes from the tradition of compilers is using keywords to document the meaning
of each input line. This is a format that is gaining impetus: see the
format for nwchem:

=C2=A0title "Nitrogen cc-pvdz SCF geometry optimization"
=C2=A0geometry
=C2=A0 =C2=A0n 0 0 0
=C2=A0 =C2=A0n 0 0 1.08
=C2=A0end
=C2=A0basis
=C2=A0 =C2=A0n library cc-pvdz
=C2=A0end
=C2=A0task scf optimize

Something even a non expert with some knowledge of the field can read as a text. This format must be parsed and executed by the software. Creating this type of soft requires some knowledge on lexical analysis and
parsing, but today is relatively simple to use a scripting language
(oldies: bash, perl, awk, ...; modern: python, php, lua, ...) for driving the interpreting part and let fortran, c or any compiled language to
do the numerical part.

Orca, also a relatively recent code, follow gaussian tradition, but
includes significant goodies in the format:

# Comment lines can be added if the line begins with a #.
! BP86 def2-SVP Opt
# BP86 is here the method (DFT functional), def2-SVP the basis set and Opt = is the jobtype (geometry optimization).
# Order of the keywords is not important.
*xyz 0 1
H 0.0 0.0 0.0
H 0.0 0.0 1.0
*

Lesson to take home: Be very careful with the input of gaussian. You can use a modeller to create the input or a first version for it (gaussvies, avogadro, ...). And finally: there are many more q-chem codes apart
> from gaussian. It is a good practice to get used to several of them > from the beginning. In fact, we theoretitians should check that a
particular result can be reproduced on more than a code to avoid
disturbing mistakes.

Thanks for your summary of your experiences,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 V=C3=ADctor
--
=C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "Patriotism is the last ref= uge of a scoundrel."
=C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0-- Samuel Johnson (UK, 1755)
=C2=A0 =C2=A0/(o)(o)\
=C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero ta= mbi=C3=A9n es peor
=C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, porque la medio= cridad no es un grado, es una
=C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015=
=C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it i= s also worse than
=C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade,= it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:=C2=A0 <victor*fluor.quimica.uniovi.es>=C2=A0 ! ! phone: +34-985-10= 3491=C2=A0 fax: +34-985-103125 !
+--------------------------------------------+
=C2=A0GroupPage: <http://azufre.quimica.uniovi.es/>
=C2=A0Articles:=C2=A0 <http://= scholar.google.com/citations?user=3DIbl1BWAAAAAJ&hl=3Des>
=C2=A0git-hub:=C2=A0 =C2=A0<https://github.com/aoterodelaroza>



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--94eb2c12324c8539000538356793-- From owner-chemistry@ccl.net Fri Jul 22 16:54:01 2016 From: "Emin Cinar e.m.i.n]~[hotmail.de" To: CCL Subject: CCL: DFT calculations for electrochemical reaction Message-Id: <-52328-160721102318-23949-/W6zokgh1+wZ8/FT8mSVJw%x%server.ccl.net> X-Original-From: "Emin Cinar" Date: Thu, 21 Jul 2016 10:23:17 -0400 Sent to CCL by: "Emin Cinar" [e.m.i.n[*]hotmail.de] Dear CCLers, I am dealing with the explanation of the thermal reactions by performing DFT calculations. For my new project, I am supposed to unveil the proton coupled electron transfer mechanism in electrochemistry. I have one small question regarding the calculation of the energies. How can I calculate the relative energy of the molecules in the stage of removal of one electron or proton? I would be grateful to you if you could help me in this respect. Thanking you. Regards, Emin Cinar From owner-chemistry@ccl.net Fri Jul 22 17:29:01 2016 From: "Chandan Kumar Choudhury iitdckc[#]gmail.com" To: CCL Subject: CCL:G: Dihedral potential energy scan using Gaussian Message-Id: <-52329-160722152912-26931-BOPIdhYAeU6S0dl2GF87Uw * server.ccl.net> X-Original-From: "Chandan Kumar Choudhury" Date: Fri, 22 Jul 2016 15:29:11 -0400 Sent to CCL by: "Chandan Kumar Choudhury" [iitdckc(0)gmail.com] Hi CCL users, I need to perform a dihedral scan, and the energy profile would be fitted and used for the molecular dynamics simulation. I did a relaxed potential energy scan (using Gaussian 09 software) of the molecule shown below, but after the rotation of 360 degrees, I get a different conformation and thus different energy. Can any one help me on this? The Gaussian input file is as follows: %chk=5-7-10-16.chk %nprocshared=8 # opt=modredundant 6-311g(d,p) geom=connectivity m06 5-7-10-16 0 1 C 2.67365300 -0.18104900 0.12744400 H 2.89644500 -1.17508300 -0.27943900 H 2.73205100 -0.25849500 1.22953000 H 3.46558100 0.49360800 -0.20963100 N 1.39217100 0.26857100 -0.36464100 H 1.21528200 1.22632900 -0.07579500 C 0.29776800 -0.54410500 0.11089200 H 0.40470500 -1.56207900 -0.29197100 H 0.27493800 -0.63798300 1.21787500 C -1.02497000 0.02898200 -0.33711900 H -0.98881200 0.13065200 -1.43503200 C -2.19493500 -0.83832700 0.07221000 H -3.14443100 -0.39019500 -0.24054900 H -2.13105300 -1.83333500 -0.38077800 H -2.21692900 -0.94854900 1.16174900 O -1.10990800 1.31497400 0.26284800 H -1.88280800 1.76234200 -0.08680800 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 6 1.0 7 1.0 6 7 8 1.0 9 1.0 10 1.0 8 9 10 11 1.0 12 1.0 16 1.0 11 12 13 1.0 14 1.0 15 1.0 13 14 15 16 17 1.0 17 * 7 10 * D 5 7 10 16 S 36 10.0 Chandan From owner-chemistry@ccl.net Fri Jul 22 21:45:00 2016 From: "David Shobe avidshobe..yahoo.com" To: CCL Subject: CCL:G: Dihedral potential energy scan using Gaussian Message-Id: <-52330-160722212858-25840-+4M1mwtduHio2Mp5SwvsxA(!)server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="----=_Part_3317904_619150706.1469237272667" Date: Sat, 23 Jul 2016 01:27:52 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Shobe [avidshobe###yahoo.com] ------=_Part_3317904_619150706.1469237272667 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Chandan-- If the 360-degree energy is lower than the original 0-degree energy, then t= he 0-degree energy was not optimized to the lowest possible energy for that= given dihedral angle. In that case, you can scan for another 360 degrees a= nd see if the 720-degree energy is the same as the 360-degree energy. =C2= =A0Use the second scan for your molecular dynamics simulation. Also, are there any sudden changes of energy on going from x degrees to x+1= 0 degrees? --David =20 On Friday, July 22, 2016 6:11 PM, Chandan Kumar Choudhury iitdckc[#]gma= il.com wrote: =20 =20 Sent to CCL by: "Chandan Kumar Choudhury" [iitdckc(0)gmail.com] Hi CCL users, I need to perform a dihedral scan, and the energy profile would be fitted a= nd used for the molecular dynamics simulation. I did a relaxed potential en= ergy scan (using Gaussian 09 software) of the molecule shown below, but aft= er the rotation of 360 degrees, I get a different conformation and thus dif= ferent energy. Can any one help me on this? The Gaussian input file is as follows: %chk=3D5-7-10-16.chk %nprocshared=3D8 # opt=3Dmodredundant 6-311g(d,p) geom=3Dconnectivity m06 5-7-10-16 0 1 C 2.67365300 -0.18104900 0.12744400 H 2.89644500 -1.17508300 -0.27943900 H 2.73205100 -0.25849500 1.22953000 H 3.46558100 0.49360800 -0.20963100 N 1.39217100 0.26857100 -0.36464100 H 1.21528200 1.22632900 -0.07579500 C 0.29776800 -0.54410500 0.11089200 H 0.40470500 -1.56207900 -0.29197100 H 0.27493800 -0.63798300 1.21787500 C -1.02497000 0.02898200 -0.33711900 H -0.98881200 0.13065200 -1.43503200 C -2.19493500 -0.83832700 0.07221000 H -3.14443100 -0.39019500 -0.24054900 H -2.13105300 -1.83333500 -0.38077800 H -2.21692900 -0.94854900 1.16174900 O -1.10990800 1.31497400 0.26284800 H -1.88280800 1.76234200 -0.08680800 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 6 1.0 7 1.0 6 7 8 1.0 9 1.0 10 1.0 8 9 10 11 1.0 12 1.0 16 1.0 11 12 13 1.0 14 1.0 15 1.0 13 14 15 16 17 1.0 17 * 7 10 * D 5 7 10 16 S 36 10.0 Chandan -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------=_Part_3317904_619150706.1469237272667 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Chandan--

=
If the 360-deg= ree energy is lower than the original 0-degree energy, then the 0-degree en= ergy was not optimized to the lowest possible energy for that given dihedra= l angle. In that case, you can scan for another 360 degrees and see if the = 720-degree energy is the same as the 360-degree energy.  Use the secon= d scan for your molecular dynamics simulation.

Also, are there any sudden changes of ene= rgy on going from x degrees to x+10 degrees?

--David




=
On Friday, July 22, = 2016 6:11 PM, Chandan Kumar Choudhury iitdckc[#]gmail.com <owner-chemist= ry~~ccl.net> wrote:



Sent to CCL by: "Chandan Kumar Choudhury" [iitdckc(0)gmail.com]Hi CCL users,

I need to perform a dihedral scan, and the energy pro= file would be fitted and used for the molecular dynamics simulation. I did = a relaxed potential energy scan (using Gaussian 09 software) of the molecul= e shown below, but after the rotation of 360 degrees, I get a different con= formation and thus different energy. Can any one help me on this?

The Gaussian input file is as follows:

%chk=3D5-7-10-16.chk
%np= rocshared=3D8
# opt=3Dmodredundant 6-311g(d,p) geom=3Dconnectivity m06
5-7-10-16

0 1
C 2.67365300 -0.18104900 0.12744400
H 2.89= 644500 -1.17508300 -0.27943900
H 2.73205100 -0.25849500 1.22953000
H = 3.46558100 0.49360800 -0.20963100
N 1.39217100 0.26857100 -0.36464100H 1.21528200 1.22632900 -0.07579500
C 0.29776800 -0.54410500 0.11089200=
H 0.40470500 -1.56207900 -0.29197100
H 0.27493800 -0.63798300 1.2178= 7500
C -1.02497000 0.02898200 -0.33711900
H -0.98881200 0.13065200 -1= .43503200
C -2.19493500 -0.83832700 0.07221000
H -3.14443100 -0.39019= 500 -0.24054900
H -2.13105300 -1.83333500 -0.38077800
H -2.21692900 -= 0.94854900 1.16174900
O -1.10990800 1.31497400 0.26284800
H -1.882808= 00 1.76234200 -0.08680800

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
45 6 1.0 7 1.0
6
7 8 1.0 9 1.0 10 1.0
8
9
10 11 1.0 12 1.0 = 16 1.0
11
12 13 1.0 14 1.0 15 1.0
13
14
15
16 17 1.0
1= 7

* 7 10 *
D 5 7 10 16 S 36 10.0

Chandan



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