From owner-chemistry@ccl.net Thu May 8 08:58:00 2014 From: "Sebastian Lilienthal sebastian.lilienthal^^^acb.uni-hannover.de" To: CCL Subject: CCL: MCCCS Towhee vs. Materials Studio Sorption (Isotherms) Message-Id: <-50050-140507184729-8409-yKiin7jDsxV+2vDY7VhgTw%x%server.ccl.net> X-Original-From: Sebastian Lilienthal Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 08 May 2014 00:47:19 +0200 MIME-Version: 1.0 Sent to CCL by: Sebastian Lilienthal [sebastian.lilienthal+*+acb.uni-hannover.de] Dear CCL readers, i'm currently performing MC calculations (Argon as adsoptive, T=87.45 K) to investigate the adsorption mechanism in a MOF with large pores close to the mesopore region (around 18 Angstroms). The experimental isotherm shows a type I region up to 0.05 p/p0 followed by a sudden volume jump/step and the volume reaching the saturation value around 0.15 p/p0. The region up to 0.05 p/p0 can be attributed to the formation of a "pseudo" monolayer followed by the jump/step which is the result of multilayer adsorption filling up the large pores. I performed calculations in the grand canonical (uvt) ensemble with Materials Studios Sorption module and in isothermal-isobaric (npt) ensemble with MCCCS Towhee (2 simulation boxes: adsorbent and adsorptive reservoir) with the same setups/LJ-potentials. Both programs yield isotherms which show the same shape as the experimental one and adsorpted volumes of each of both regions close to the experimental ones. What is puzzling me for quite a while is that the volume jump/step which can be attributed to the multilayer adsorption is shifted by 2-3 kPa to lower pressures in Towhee. The shape of both isotherms and even the slopes of both steps are almost identical. Its only the second step which is shifted. I tried various different setups (MC move probabilities, cut-offs, step sizes, longer equilibration times (up to 10^7 MC steps) etc.) but the difference concerning the second step remains. I took a closer look at the pressure oscillations in the adsorbtive box during the Towhee calculations, as well: They are (in my opinion) too small to be responsible for the shift of the second step. I tried GCMC simulations in Towhee, as well. But i turned out that the calculated chemical potential during prior nvt/npt calculations (again with various setups), especially in the low pressure region up to 5 kPa, has a standart deviation around 30% (which is obviously way to high). So GCMC in Towhee is not an option as it yields isotherms which look way different than the experimental one and aren't even close to the other simulated isotherms. Has anyone else experienced such a difference in isotherm calculations for MS Sorption/Towhee or an idea what might be responsible for this behaviour? Thank you in advance, Sebastian From owner-chemistry@ccl.net Thu May 8 09:33:00 2014 From: "Denis Rychkov rychkov.dennis%gmail.com" To: CCL Subject: CCL:G: Gaussian 2 dimensional scan plots Message-Id: <-50051-140508021402-4616-uvxcG1ZVMV9qHghhrqZhEQ{=}server.ccl.net> X-Original-From: Denis Rychkov Content-Type: multipart/alternative; boundary=047d7bd76d1ed9d38004f8dd62aa Date: Thu, 8 May 2014 13:13:36 +0700 MIME-Version: 1.0 Sent to CCL by: Denis Rychkov [rychkov.dennis---gmail.com] --047d7bd76d1ed9d38004f8dd62aa Content-Type: text/plain; charset=UTF-8 Hi, I'm quite new to Gaussian and struggle with several difficulties with data plotting. The task is - to create potential energy surface (PES) of a molecule with 2 angles scan. It looks like this: D61_12_13 = 61.46117939 s 72 5. D14_12_13_16 = 18.31423473 s 72 5. In fact I can obtain correct .out file and can visualize it with GaussView. But properties of this graph are very poor (for example it is impossible to show isolines only or change colours and fonts). Is it possible to extract data of angles and energies somehow to plot them with Origin or Excel or smth. else? Thanks! Denis. --047d7bd76d1ed9d38004f8dd62aa Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

I'm quite new to Gaussian and s= truggle with several difficulties with data plotting.
The task is= - to create potential energy surface (PES) of a molecule with 2 angles sca= n.
It looks like this:
D61_12_13 =C2=A0 =C2=A0 =3D =C2=A0 =C2=A0 =C2=A0 =C2= =A061.46117939 s 72 5.
D14_12_13_16 =C2=A0=3D =C2=A0 =C2=A0 =C2=A018.314= 23473 s 72 5.

In fact I can obtain correct .ou= t file and can visualize it with GaussView. But properties of this graph ar= e very poor (for example it is impossible to show isolines only or change c= olours and fonts). Is it possible to extract data of angles and energies so= mehow to plot them with Origin or Excel or smth. else?

Thanks!
Denis.
--047d7bd76d1ed9d38004f8dd62aa-- From owner-chemistry@ccl.net Thu May 8 10:21:00 2014 From: "Jean Jules Fifen julesfifen[*]gmail.com" To: CCL Subject: CCL:G: Gaussian 2 dimensional scan plots Message-Id: <-50052-140508101918-24197-Y+dZXlzaw/ecsJLLHJWbQQ||server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=20cf3079b90854753f04f8e42afb Date: Thu, 8 May 2014 15:19:13 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen-x-gmail.com] --20cf3079b90854753f04f8e42afb Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Denis, Of course, it is possible. You only need to perform the following tasks: 1. open the window displaying your surface using gaussview; 2. right click on this windows and choose save data; 3. An name your file (.txt or .dat) and save it where you want; You are now able to plot the saved file using origin or ant other plot software. Regards, On Thu, May 8, 2014 at 7:13 AM, Denis Rychkov rychkov.dennis%gmail.com < owner-chemistry[A]ccl.net> wrote: > Hi, > > I'm quite new to Gaussian and struggle with several difficulties with dat= a > plotting. > The task is - to create potential energy surface (PES) of a molecule with > 2 angles scan. > It looks like this: > D61_12_13 =3D 61.46117939 s 72 5. > D14_12_13_16 =3D 18.31423473 s 72 5. > > In fact I can obtain correct .out file and can visualize it with > GaussView. But properties of this graph are very poor (for example it is > impossible to show isolines only or change colours and fonts). Is it > possible to extract data of angles and energies somehow to plot them with > Origin or Excel or smth. else? > > Thanks! > Denis. > --=20 --------------------------------------------------------------------------- *Jean Jules FIFEN*, Ph.D. in Atomic & Molecular Physics Senior Lecturer, =E2=80=8BDepartment of Physics, Faculty of Science, University of Ngaoundere, Cameroon. P.O. BOX 454 Ngaoundere Private: P.O. BOX 547 Ngaoundere Phone number: +972 55 8961001/ +237 75 21 61 39 ---------------------------------------------------------------------------= -------------------------------------- --20cf3079b90854753f04f8e42afb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Denis,
Of course= , it is possible.
You only need to perform the following tasks:
=
1. open the window displaying your surface using gaussview;
2. right click on this windows and choose save data;
3. An name your file (.txt or .dat) and save it where you want;
You are now able to plot the saved file using origin or ant oth= er plot software.

Regards,
=

On Thu, May 8, 2014 at 7:13 AM, Denis Ry= chkov rychkov.dennis%gmail.com <o= wner-chemistry[A]ccl.net> wrote:
Hi,

I= 9;m quite new to Gaussian and struggle with several difficulties with data = plotting.
The task is - to create potential energy surface (PES) of a molecule w= ith 2 angles scan.
It looks like this:
D61_12_13 =C2=A0 =C2=A0 =3D =C2=A0 =C2=A0 =C2=A0 =C2= =A061.46117939 s 72 5.
D14_12_13_16 =C2=A0=3D =C2=A0 =C2=A0 =C2=A018.314= 23473 s 72 5.

In fact I can obtain correct .ou= t file and can visualize it with GaussView. But properties of this graph ar= e very poor (for example it is impossible to show isolines only or change c= olours and fonts). Is it possible to extract data of angles and energies so= mehow to plot them with Origin or Excel or smth. else?

Thanks!
Denis.



--
<= span style=3D"color:rgb(0,0,255)">--------------------------------------------------------------------= -------
Jean Jules FIFEN,
Ph.D. in= Atomic & Molecular Physics
Senior Lecturer,
=
=E2= =80=8BDepartment of Physics,
<= span style=3D"font-family:courier new,monospace">Faculty of Science,
Uni= versity of Ngaoundere, Cameroon.
P.O. BOX 454 Ngaounder= e
Private: P.O. BOX 547 Ngaoundere
Phone= number: +972 55 8961001/ +237 75 21 61 39 <= span style=3D"font-family:courier new,monospace">
---= ---------------------------------------------------------------------------= -----------------------------------
=C2=A0
--20cf3079b90854753f04f8e42afb-- From owner-chemistry@ccl.net Thu May 8 11:53:00 2014 From: "Subrahmanyam Sappati subrahmanyamsappati a gmail.com" To: CCL Subject: CCL:G: Gaussian 2 dimensional scan plots Message-Id: <-50053-140508115203-30704-KaY3O9JjCUb0BClTSpjHFw,,server.ccl.net> X-Original-From: Subrahmanyam Sappati Content-Type: multipart/alternative; boundary=001a11c2db14f0785004f8e575cf Date: Thu, 8 May 2014 21:21:56 +0530 MIME-Version: 1.0 Sent to CCL by: Subrahmanyam Sappati [subrahmanyamsappati{}gmail.com] --001a11c2db14f0785004f8e575cf Content-Type: text/plain; charset=ISO-8859-1 Dear sir I am not getting that option for 2-d scanning (where as I am getting for 1-d scanning). May I change any settings in visualizer or any thing else. Could you please suggest me in this issue? Thanking you Best Subrahmanyam On Thu, May 8, 2014 at 7:49 PM, Jean Jules Fifen julesfifen[*]gmail.com < owner-chemistry[-]ccl.net> wrote: > Dear Denis, > Of course, it is possible. > You only need to perform the following tasks: > 1. open the window displaying your surface using gaussview; > 2. right click on this windows and choose save data; > 3. An name your file (.txt or .dat) and save it where you want; > You are now able to plot the saved file using origin or ant other plot > software. > > Regards, > > > On Thu, May 8, 2014 at 7:13 AM, Denis Rychkov rychkov.dennis%gmail.com < > owner-chemistry:ccl.net> wrote: > >> Hi, >> >> I'm quite new to Gaussian and struggle with several difficulties with >> data plotting. >> The task is - to create potential energy surface (PES) of a molecule with >> 2 angles scan. >> It looks like this: >> D61_12_13 = 61.46117939 s 72 5. >> D14_12_13_16 = 18.31423473 s 72 5. >> >> In fact I can obtain correct .out file and can visualize it with >> GaussView. But properties of this graph are very poor (for example it is >> impossible to show isolines only or change colours and fonts). Is it >> possible to extract data of angles and energies somehow to plot them with >> Origin or Excel or smth. else? >> >> Thanks! >> Denis. >> > > > > -- > --------------------------------------------------------------------------- > *Jean Jules FIFEN*, > Ph.D. in Atomic & Molecular Physics > Senior Lecturer, > Department of Physics, > Faculty of Science, > University of Ngaoundere, Cameroon. > P.O. BOX 454 Ngaoundere > Private: P.O. BOX 547 Ngaoundere > Phone number: +972 55 8961001/ +237 75 21 61 39 > > ----------------------------------------------------------------------------------------------------------------- > > -- Subrahmanyam.Sappati C/o Dr. Prasenjit Ghosh IISER PUNE Pin code : 411 008 Phone : +91 94 03 59 35 18 --001a11c2db14f0785004f8e575cf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear sir

I am not getting that option for 2-d sca= nning (where as I am getting for 1-d scanning). May I change any settings i= n visualizer or any thing else.
Could you please suggest me in this issue?

Thanking you
<= br>
Be= st
Subrahmanyam



On Thu, May 8, 2014 at 7:49 PM, Jean Jules Fifen julesfifen[*]gmail.com <owner-chemistry[-]ccl.net> wrote:
Dear Denis,
Of course, it is possible.
You only need to perform the following tasks:
=
1. open the window displaying your surface using gaussview;
2. right click on this windows and choose save data;
3. An name your file (.txt or .dat) and save it where you want;
You are now able to plot the saved file using origin or ant oth= er plot software.

Regards,
=


On Thu, May 8, 2014 at 7= :13 AM, Denis Rychkov rychkov.dennis%gmail.com <owner-chemistry:ccl.net> wrote= :
Hi,

I= 9;m quite new to Gaussian and struggle with several difficulties with data = plotting.
The task is - to create potential energy surface (PES) of a molecule w= ith 2 angles scan.
It looks like this:
D61_12_13 =A0 =A0 =3D =A0 =A0 =A0 =A061.46117939 s 7= 2 5.
D14_12_13_16 =A0=3D =A0 =A0 =A018.31423473 s 72 5.
In fact I can obtain correct .out file and can visualize it wi= th GaussView. But properties of this graph are very poor (for example it is= impossible to show isolines only or change colours and fonts). Is it possi= ble to extract data of angles and energies somehow to plot them with Origin= or Excel or smth. else?

Thanks!
Denis.<= /div>



--
=
--------------------------------------------------------------= -------------
Jean Jules FIFEN,
Ph.D. in= Atomic & Molecular Physics
Senior Lecturer,
=
Dep= artment of Physics,
Faculty of Science,
Uni= versity of Ngaoundere, Cameroon.
P.O. BOX 454 Ngaounder= e
Private: P.O. BOX 547 Ngaoundere
Phone= number: +972 55 8961001/ +237 75 21 61 39 <= span style=3D"font-family:courier new,monospace">
---= ---------------------------------------------------------------------------= -----------------------------------
=A0



--

Subrahmanyam.Sappati
C/o Dr. Prasenjit Ghosh
IISER PUNE
Pin code : 411 008

Phone : +91 94 03 59 35 18

--001a11c2db14f0785004f8e575cf-- From owner-chemistry@ccl.net Thu May 8 15:51:00 2014 From: "Mikael Johansson mikael.johansson{=}iki.fi" To: CCL Subject: CCL: Why is the xc kernel in TD-DFT called a kernel? Message-Id: <-50054-140508131321-598-8teP1pLOtMmKbNL5aCd0IA()server.ccl.net> X-Original-From: Mikael Johansson Content-Type: multipart/mixed; BOUNDARY="-696237619-1432286818-1399569192=:4933" Date: Thu, 8 May 2014 20:13:11 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson##iki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696237619-1432286818-1399569192=:4933 Content-Type: text/plain; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: 8BIT Hola Victor y Todos, Thanks for that! I obvously need to brush up on my English mathematics :-) So kernel is just a very general mathematical term; and here I thought the term might contain an interesting story or something... Anyway, with the right pointers on what to google, came across this page with "Earliest Known Uses of Some of the Words of Mathematics", one among them, kernel: http://jeff560.tripod.com/k.html Cheers, Mikael J. http://www.iki.fi/~mpjohans/ On Thu, 8 May 2014, Víctor Luaña Cabal victor*|*fluor.quimica.uniovi.es wrote: >> Sent to CCL by: Mikael Johansson [mikael.johansson/a\iki.fi] >> >> Couldn't contain myself anymore, so here it goes: Why is the kernel, that >> is, the derivative of the exchange-correlation potential wrt the density, >> >> f_{xc} = \delta v_{xc} / \delta\rho >> >> called the kernel? Where/when was this term coined? > Mikael, > > The Kernel of an integral is not an strange term: > > > > Regards, > Dr. Víctor Luaña ---696237619-1432286818-1399569192=:4933-- From owner-chemistry@ccl.net Thu May 8 19:08:00 2014 From: "Nico G nicogreen6**gmail.com" To: CCL Subject: CCL:G: Resonance forms Message-Id: <-50055-140508190648-20094-LhHtfAj2o+ys7OPcWSvjKQ ~ server.ccl.net> X-Original-From: Nico G Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 May 2014 20:06:37 -0300 MIME-Version: 1.0 Sent to CCL by: Nico G [nicogreen6^gmail.com] Dear all, I have some systems that contain phenols rings. I need to get the optimized geometries of all the possible resonance forms. The problem is that i am unable to find how to tell gaussian that certain atoms, for example, must have a charge. ie: The resonance form of the phenol where the alcohol becomes a keto, so the oxigen atom still protonated carries a positive charge and there is a negative charge on one of the carbon atoms. The normal optimization on gaussian will end in the phenol. Thank you all Best Regards, Nico From owner-chemistry@ccl.net Thu May 8 20:02:01 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor-x-fluor.quimica.uniovi.es" To: CCL Subject: CCL: Why is the xc kernel in TD-DFT called a kernel? Message-Id: <-50056-140508181337-5948-ey6VUXEDFuv++f3z4s6diQ- -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: Fri, 09 May 2014 00:11:11 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor/a\fluor.quimica.uniovi.es] On Thu, May 08, 2014 at 08:13:11PM +0300, Mikael Johansson mikael.johansson{=}iki.fi wrote: > > Thanks for that! I obvously need to brush up on my English mathematics > :-) So kernel is just a very general mathematical term; and here I > thought the term might contain an interesting story or something... > Mikael, Don't worry. ¡Discovering the wheel has been done several times! In fact, the wheel was patented in Australia not so long ago just to demostrate how easy it was to do it. If you are decided to refresh maths a little don't forget to explore . There are many math programs, Mathematica is far from being the only one, but this math encyplopedia is really something. Regards, Víctor Luaña -- \|/ |^.^| +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! 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)