From owner-chemistry@ccl.net Tue Jul 19 08:02:01 2016 From: "Ayesha Inayat ayeshainayat9898++gmail.com" To: CCL Subject: CCL:G: DFT studies of H2O2 Message-Id: <-52311-160719043619-14080-j3OzxHNopRRcfLrNx3yGWA/a\server.ccl.net> X-Original-From: "Ayesha Inayat" Date: Tue, 19 Jul 2016 04:36:18 -0400 Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSIAN 09 software with various hybrid functions, After optimization the structure in an output file shows that the single bond between two oxygens in H2O2 is missing. Would any one please guide me why its happening??? From owner-chemistry@ccl.net Tue Jul 19 09:13:01 2016 From: "=?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= hayak ~~ ariel.ac.il" To: CCL Subject: CCL:G: DFT studies of H2O2 Message-Id: <-52312-160719091001-29252-U3plCQ6WozGKgc2ShTbHJA : server.ccl.net> X-Original-From: =?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= Content-Language: he-IL Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="windows-1255" Date: Tue, 19 Jul 2016 13:09:49 +0000 MIME-Version: 1.0 Sent to CCL by: =?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= [hayak|ariel.ac.il] I had calculated this molecule and everything was o.k. Please try to change your initial configuration. Haya -----Original Message----- > From: owner-chemistry+hayak==ariel.ac.il=ccl.net [mailto:owner-chemistry+hayak==ariel.ac.il=ccl.net] On Behalf Of Ayesha Inayat ayeshainayat9898++gmail.com Sent: Tuesday, July 19, 2016 11:36 AM To: çéä ÷åøðååéõ - ãø/Haya Kornweitz - Dr' Subject: CCL:G: DFT studies of H2O2 Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSIAN 09 software with various hybrid functions, After optimization the structure in an output file shows that the single bond between two oxygens in H2O2 is missing. Would any one please guide me why its happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 19 09:49:01 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor\a/fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: DFT studies of H2O2 Message-Id: <-52313-160719094648-14797-0g5mx2hleO7IR4CVkNFxww^-^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: Tue, 19 Jul 2016 15:28:17 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor+*+fluor.quimica.uniovi.es] On Tue, Jul 19, 2016 at 04:36:18AM -0400, Ayesha Inayat ayeshainayat9898++gmail.com wrote: > > Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] > Dear CCL members > I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSIAN 09 > software with various hybrid functions, After optimization the structure in > an output file shows that the single bond between two oxygens in H2O2 is > missing. > Would any one please guide me why its happening??? Not enough information. You assume the OO bond is missing because is not depicted by a graphical program? Did you check the OO actual distance? Is is truly large? You should provide more details of your calculation as well: basis set, DFT functional, electronic state (I asume ground state) ... Find attached a simple parser to check the most important information > from the g09 output. If you use a unix-like os you can do: extract-g09.awk g09_output and the script provides you an analysis of distances and more. Note that the script is written in gawk. Best regards, Dr. Víctor Luaña -- . . "Las mujeres suelen ser menos fanáticas que los hombres, / `' \ más prácticas y más responsables." /(o)(o)\ --John Carlin (ElPaís, 2016-07-03) /`. \/ .'\ Women USE to be less fanatical than men, more practical / '`'` \ and more responsible." | \'`'`/ | "let's hope world learns from UK what political lies and | |'`'`| | false patrioterism can comdemn a generation to suffer" \/`'`'`'\/ ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage: Articles: git-hub: From owner-chemistry@ccl.net Tue Jul 19 11:45:01 2016 From: "Victor Rosas Garcia rosas.victor,gmail.com" To: CCL Subject: CCL: DFT studies of H2O2 Message-Id: <-52314-160719114343-30344-jHZUpFao18KRbaRMeZltTA.:.server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=001a114585f2b532f90537fef2c7 Date: Tue, 19 Jul 2016 10:43:36 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor-.-gmail.com] --001a114585f2b532f90537fef2c7 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable It could be a visualization artifact, but it would be necessary to know how you found out that the bond is "missing". Did you use some visualization package? did you read a bond order from a text output file? did you do some kind of critical point analysis that shows no critical point between the oxygen atoms? Without this information, it is hard to help you. Best regards Victor 2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95= =D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' hayak ~~ ariel.ac.il : > > Sent to CCL by: > =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=3D= ?=3D > [hayak|ariel.ac.il] > I had calculated this molecule and everything was o.k. > Please try to change your initial configuration. > Haya > > > > > -----Original Message----- > > From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto: > owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Behalf Of Ayesha Inaya= t > ayeshainayat9898++gmail.com > Sent: Tuesday, July 19, 2016 11:36 AM > To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 -= =D7=93=D7=A8/Haya Kornweitz - Dr' > Subject: CCL:G: DFT studies of H2O2 > > > Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL > members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSIA= N > 09 software with various hybrid functions, After optimization the structu= re > in an output file shows that the single bond between two oxygens in H2O2 = is > missing. > Would any one please guide me why its happening???http://www.ccl.net/chemist= ry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a114585f2b532f90537fef2c7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
It could be a visualization artifact, but i= t would be necessary to know how you found out that the bond is "missi= ng". Did you use some visualization package? did you read a bond order= from a text output file? did you do some kind of critical point analysis t= hat shows no critical point between the oxygen atoms?

Without = this information, it is hard to help you.

Best regards

=
Victor

2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0= =D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' hayak ~~ <= a href=3D"http://ariel.ac.il">ariel.ac.il <owner-chemistry],[ccl.n= et>:

Sent to CCL by: =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2Vp= dHogLSBEcic=3D?=3D
=C2=A0 =C2=A0 =C2=A0 =C2=A0 [hayak|ariel.ac.il]
I had calculated this molecule and everything was o.k.
Please try to change your initial configuration.
Haya




-----Original Message-----
> From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto:owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Be= half Of Ayesha Inayat ayeshainayat9898++gmail.com
Sent: Tuesday, July 19, 2016 11:36 AM
To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - = =D7=93=D7=A8/Haya Kornweitz - Dr'
Subject: CCL:G: DFT studies of H2O2


Sent to CCL by: "Ayesha=C2=A0 Inayat" [ayeshainayat9898#gmail.com] D= ear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at G= AUSSIAN 09 software with various hybrid functions, After optimization the s= tructure in an output file shows that the single bond between two oxygens i= n H2O2 is missing.
Would any one please guide me why its happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


-=3D This is automatically added to each message by the mailing script =3D-=
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--001a114585f2b532f90537fef2c7-- From owner-chemistry@ccl.net Tue Jul 19 13:56:00 2016 From: "=?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= fpartal . ujaen.es" To: CCL Subject: CCL: DFT studies of H2O2 Message-Id: <-52315-160719133511-23804-m/p4N5SVhY+cuXXv+DDyBQ__server.ccl.net> X-Original-From: =?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= Content-Type: multipart/alternative; boundary=94eb2c0638403a15c305380081f4 Date: Tue, 19 Jul 2016 19:35:02 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Francisco_Partal_Ure=C3=B1a?= [fpartal{:}ujaen.es] --94eb2c0638403a15c305380081f4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Ayesha: I guess you are using GaussView. If so, there is no problem with your calculations, it is only that the O-O bond lengths obtained in them are higher than a single O-O bond for GaussView cutoffs. As Victor says is a visualization artifact. Just rebond using the 'bond definition' icon. If you are using another visualization software then use the proper way to do that. Best regards, Paco 2016-07-19 17:43 GMT+02:00 Victor Rosas Garcia rosas.victor,gmail.com < owner-chemistry%x%ccl.net>: > It could be a visualization artifact, but it would be necessary to know > how you found out that the bond is "missing". Did you use some > visualization package? did you read a bond order from a text output file? > did you do some kind of critical point analysis that shows no critical > point between the oxygen atoms? > > Without this information, it is hard to help you. > > Best regards > > Victor > > 2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7= =95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya Kornweitz - Dr' hayak ~~ > ariel.ac.il : > >> >> Sent to CCL by: >> =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic= =3D?=3D >> [hayak|ariel.ac.il] >> I had calculated this molecule and everything was o.k. >> Please try to change your initial configuration. >> Haya >> >> >> >> >> -----Original Message----- >> > From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto: >> owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net] On Behalf Of Ayesha Inay= at >> ayeshainayat9898++gmail.com >> Sent: Tuesday, July 19, 2016 11:36 AM >> To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 = - =D7=93=D7=A8/Haya Kornweitz - Dr' >> Subject: CCL:G: DFT studies of H2O2 >> >> >> Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] Dear CCL >> members I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSI= AN >> 09 software with various hybrid functions, After optimization the struct= ure >> in an output file shows that the single bond between two oxygens in H2O2= is >> missing. >> Would any one please guide me why its happening???http://www.ccl.net/chemis= try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >> >> >> -=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 use>> >> >> > -- --94eb2c0638403a15c305380081f4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Ayesha: I guess you are using GaussView. If so, there= is no problem with your calculations, it is only that the O-O bond lengths= obtained in them are higher than a single O-O bond for GaussView cutoffs. = As Victor says is a visualization artifact. Just rebond using the 'bond= definition' icon. If you are using another visualization software then= use the proper way to do that.

Best regards,
=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Paco


2016-07-19 17:43 GMT+02= :00 Victor Rosas Garcia rosas.victor,gmail.com= <owner-chemistry%x%ccl.net>:
It could be a visualization a= rtifact, but it would be necessary to know how you found out that the bond = is "missing". Did you use some visualization package? did you rea= d a bond order from a text output file? did you do some kind of critical po= int analysis that shows no critical point between the oxygen atoms?

=
Without this information, it is hard to help you.

Best r= egards

Victor

2016-07-19 8:09 GMT-05:00 =D7=97=D7=99=D7=94 =D7=A7=D7= =95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - =D7=93=D7=A8/Haya Kornweitz - Dr&= #39; hayak ~~ ariel.ac.il<= /a> <owner-chemistry{}ccl.net>:

Sent to CCL by: =3D?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2Vp= dHogLSBEcic=3D?=3D
=C2=A0 =C2=A0 =C2=A0 =C2=A0 [hayak|ariel.ac.il]
I had calculated this molecule and everything was o.k.
Please try to change your initial configuration.
Haya




-----Original Message-----
> From: owner-chemistry+hayak=3D=3Dariel.ac.il:ccl.net [mailto:owner-chemistry+hayak=3D=3D= ariel.ac.il:ccl.net] On Behalf Of Ayesha Inayat ayeshainayat9898++gmail.com
Sent: Tuesday, July 19, 2016 11:36 AM
To: =D7=97=D7=99=D7=94 =D7=A7=D7=95=D7=A8=D7=A0=D7=95=D7=95=D7=99=D7=A5 - = =D7=93=D7=A8/Haya Kornweitz - Dr'
Subject: CCL:G: DFT studies of H2O2


Sent to CCL by: "Ayesha=C2=A0 Inayat" [ayeshainayat9898#gmail.com] D= ear CCL members I am doing DFT calculation of H2O2(Hydrogen per oxide) at G= AUSSIAN 09 software with various hybrid functions, After optimization the s= tructure in an output file shows that the single bond between two oxygens i= n H2O2 is missing.
Would any one please guide me why its happening???http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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


<= /div>
--94eb2c0638403a15c305380081f4-- From owner-chemistry@ccl.net Tue Jul 19 14:30:00 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor]-[fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: DFT studies of H2O2 Message-Id: <-52316-160719133909-24307-USMS+DicAa0E5Kj6fYoaUg]^[server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-transfer-encoding: 8BIT Content-type: multipart/mixed; boundary="Boundary_(ID_X7fwaERpfE+dHq/sFS806Q)" Date: Tue, 19 Jul 2016 19:20:36 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor[]fluor.quimica.uniovi.es] --Boundary_(ID_X7fwaERpfE+dHq/sFS806Q) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT Content-disposition: inline On Tue, Jul 19, 2016 at 03:28:17PM +0200, Víctor Luaña Cabal victora/fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor+*+fluor.quimica.uniovi.es] > On Tue, Jul 19, 2016 at 04:36:18AM -0400, Ayesha Inayat ayeshainayat9898++gmail.com wrote: > > > > Sent to CCL by: "Ayesha Inayat" [ayeshainayat9898#gmail.com] > > Dear CCL members > > I am doing DFT calculation of H2O2(Hydrogen per oxide) at GAUSSIAN 09 > > software with various hybrid functions, After optimization the structure in > > an output file shows that the single bond between two oxygens in H2O2 is > > missing. > > Would any one please guide me why its happening??? > > Not enough information. You assume the OO bond is missing because is not > depicted by a graphical program? Did you check the OO actual distance? > Is is truly large? You should provide more details of your calculation > as well: basis set, DFT functional, electronic state (I asume ground > state) ... > > Find attached a simple parser to check the most important information > > from the g09 output. If you use a unix-like os you can do: > > extract-g09.awk g09_output > > and the script provides you an analysis of distances and more. Note > that the script is written in gawk. Sorry, I forgot to atach the awk. Here it is. Best, Víctor --Boundary_(ID_X7fwaERpfE+dHq/sFS806Q) Content-type: text/plain; charset=us-ascii; NAME=extract-g09.awk Content-transfer-encoding: 7BIT Content-disposition: attachment; filename=extract-g09.awk #! /usr/bin/awk -f # # extract-g09.awk - Analysis of the g09 output # Final geometry of an optimization and report of distances and angles # # Use as: extract-g09.awk g09_output # #----------------------------------------------------------------------- # CopyRight (c): Victor Lua~na, Feb. 23, 2000 # Departamento de Quimica Fisica y Analitica # Universidad de Oviedo, 33007-Oviedo, Spain # victor,carbono.quimica.uniovi.es # # This script is distributed as an Open Source code protected by the # GNU General Public License version 2 (GPL2) as published by the # Free Software Foundation (http://www.gnu.org). # In short: you can make and distribute copies of this script; you can # also make changes in the code and distribute the modified files; but # you should always document the introduced changes and you must distribute # or make available to others the source codes. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. #----------------------------------------------------------------------- # function isbonded(xx, yy, zz, dij){ if (xx > dij || -xx > dij) { return (0) } else if (yy > dij || -yy > dij) { return (0) } else if (zz > dij || -zz > dij ) { return (0) } else if (xx*xx+yy*yy+zz*zz > dij*dij) { return (0) } else { return (1) } } function PrintAngle(i1, i2, i3){ x21 = atxc[i2,bng] - atxc[i1,bng] y21 = atyc[i2,bng] - atyc[i1,bng] z21 = atzc[i2,bng] - atzc[i1,bng] r21 = sqrt(x21*x21 + y21*y21 + z21*z21) x23 = atxc[i2,bng] - atxc[i3,bng] y23 = atyc[i2,bng] - atyc[i3,bng] z23 = atzc[i2,bng] - atzc[i3,bng] r23 = sqrt(x23*x23 + y23*y23 + z23*z23) pesc = (x21*x23 + y21*y23 + z21*z23) x123 = y21*z23 - y23*z21 y123 = z21*x23 - z23*x21 z123 = x21*y23 - x23*y21 pvec = sqrt(x123^2 + y123^2 + z123^2) angle = atan2(pvec,pesc) angle = angle * Rad2Deg lbl0 = sprintf("%s-", atname[i1,bng]) lbl0 = lbl0 sprintf("%s-", atname[i2,bng]) lbl0 = lbl0 sprintf("%s", atname[i3,bng]) lbl1 = sprintf("%s(%d)-", atname[i1,bng], i1) lbl1 = lbl1 sprintf("%s(%d)-", atname[i2,bng], i2) lbl1 = lbl1 sprintf("%s(%d)", atname[i3,bng], i3) printf "ANGLE %12.6f %-12s %s\n", angle, lbl0, lbl1 } function PrintDihed(i1, i2, i3, i4){ # The vectorial products 12x23 and 23x34 will provide # the normal vectors of the two intersecting planes: x1 = atxc[i2,bng]-atxc[i1,bng] y1 = atyc[i2,bng]-atyc[i1,bng] z1 = atzc[i2,bng]-atzc[i1,bng] x2 = atxc[i3,bng]-atxc[i2,bng] y2 = atyc[i3,bng]-atyc[i2,bng] z2 = atzc[i3,bng]-atzc[i2,bng] ux1 = y1*z2-z1*y2 uy1 = z1*x2-x1*z2 uz1 = x1*y2-y1*x2 x3 = atxc[i4,bng]-atxc[i3,bng] y3 = atyc[i4,bng]-atyc[i3,bng] z3 = atzc[i4,bng]-atzc[i3,bng] ux2 = z3*y2-y3*z2 uy2 = x3*z2-z3*x2 uz2 = y3*x2-x3*y2 u1 = ux1*ux1+uy1*uy1+uz1*uz1 u2 = ux2*ux2+uy2*uy2+uz2*uz2 u = sqrt(u1*u2) if (u!=0.0) { cosa = (ux1*ux2+uy1*uy2+uz1*uz2) / u ux12 = uy1*uz2-uz1*uy2 uy12 = uz1*ux2-ux1*uz2 uz12 = ux1*uy2-uy1*ux2 sina = sqrt(ux12^2 + uy12^2 + uz12^2) / u dihedr = atan2(sina,cosa) * Rad2Deg } else { dihedr = -720 } # error!!! lbl0 = sprintf("%s-", atname[i1,bng]) lbl0 = lbl0 sprintf("%s-", atname[i2,bng]) lbl0 = lbl0 sprintf("%s-", atname[i3,bng]) lbl0 = lbl0 sprintf("%s", atname[i4,bng]) lbl1 = sprintf("%s(%d)-", atname[i1,bng], i1) lbl1 = lbl1 sprintf("%s(%d)-", atname[i2,bng], i2) lbl1 = lbl1 sprintf("%s(%d)-", atname[i3,bng], i3) lbl1 = lbl1 sprintf("%s(%d)", atname[i4,bng], i4) printf "DIHEDRAL %12.6f %-14s %s\n", dihedr, lbl0, lbl1 } function RingNormal(iring, normal){ # Determines the average normal vector (components: xnor..znor) # for the ring number iring, and the average angular deviation from # planarity for the ring (angle angdev). nrtmp = natr[iring] - 2 angdev = 0 xn = 0 yn = 0 zn = 0 # Decompose the ring in succesive triangles and average the normal # from all the triangles: for (itmp=1; itmp<=nrtmp; itmp++) { i1tmp = iatr[itmp,iring] i2tmp = iatr[itmp+1,iring] i3tmp = iatr[itmp+2,iring] x21tmp = atxc[i2tmp,bng] - atxc[i1tmp,bng] y21tmp = atyc[i2tmp,bng] - atyc[i1tmp,bng] z21tmp = atzc[i2tmp,bng] - atzc[i1tmp,bng] x23tmp = atxc[i2tmp,bng] - atxc[i3tmp,bng] y23tmp = atyc[i2tmp,bng] - atyc[i3tmp,bng] z23tmp = atzc[i2tmp,bng] - atzc[i3tmp,bng] x123tmp = y21tmp*z23tmp - y23tmp*z21tmp y123tmp = z21tmp*x23tmp - z23tmp*x21tmp z123tmp = x21tmp*y23tmp - x23tmp*y21tmp normtmp = sqrt(x123tmp^2 + y123tmp^2 + z123tmp^2) xntmp[itmp] = x123tmp / normtmp yntmp[itmp] = y123tmp / normtmp zntmp[itmp] = z123tmp / normtmp xn = xn + xntmp[itmp] yn = yn + yntmp[itmp] zn = zn + zntmp[itmp] } xn = xn / nrtmp yn = yn / nrtmp zn = zn / nrtmp normal[1] = xn normal[2] = yn normal[3] = zn for (itmp=1; itmp<=nrtmp; itmp++) { atmp = VecAngle(xn, yn, zn, xntmp[itmp], yntmp[itmp], zntmp[itmp]) angdev = angdev + atmp } angdev = angdev / nrtmp return (angdev) } function VecAngle(v1x, v1y, v1z, v2x, v2y, v2z){ pesctmp = v1x*v2x + v1y*v2y + v1z*v2z xtmp = v1y*v2z - v1z*v2y ytmp = v1z*v2x - v1x*v2z ztmp = v1x*v2y - v1y*v2x pvectmp = sqrt(xtmp^2 + ytmp^2 + ztmp^2) atmpp = atan2(pvectmp,pesctmp) atmpp = atmpp * Rad2Deg return (atmpp) } BEGIN{ Rad2Deg = 45 / atan2(1,1) bondmax = 1.25 atomicname[ 1] = "H" ; atomicnumber["H" ] = 1; rcov[ 1] = 53; atomicname[ 2] = "He"; atomicnumber["HE"] = 2; rcov[ 2] = 70; atomicname[ 3] = "Li"; atomicnumber["LI"] = 3; rcov[ 3] = 68; atomicname[ 4] = "Be"; atomicnumber["BE"] = 4; rcov[ 4] = 35; atomicname[ 5] = "B" ; atomicnumber["B" ] = 5; rcov[ 5] = 83; atomicname[ 6] = "C" ; atomicnumber["C" ] = 6; rcov[ 6] = 68; atomicname[ 7] = "N" ; atomicnumber["N" ] = 7; rcov[ 7] = 68; atomicname[ 8] = "O" ; atomicnumber["O" ] = 8; rcov[ 8] = 68; atomicname[ 9] = "F" ; atomicnumber["F" ] = 9; rcov[ 9] = 64; atomicname[ 10] = "Ne"; atomicnumber["NE"] = 10; rcov[ 10] = 70; atomicname[ 11] = "Na"; atomicnumber["NA"] = 11; rcov[ 11] = 97; atomicname[ 12] = "Mg"; atomicnumber["MG"] = 12; rcov[ 12] = 110; atomicname[ 13] = "Al"; atomicnumber["AL"] = 13; rcov[ 13] = 135; atomicname[ 14] = "Si"; atomicnumber["SI"] = 14; rcov[ 14] = 120; atomicname[ 15] = "P" ; atomicnumber["P" ] = 15; rcov[ 15] = 105; atomicname[ 16] = "S" ; atomicnumber["S" ] = 16; rcov[ 16] = 102; atomicname[ 17] = "Cl"; atomicnumber["CL"] = 17; rcov[ 17] = 99; atomicname[ 18] = "Ar"; atomicnumber["AR"] = 18; rcov[ 18] = 70; atomicname[ 19] = "K" ; atomicnumber["K" ] = 19; rcov[ 19] = 133; atomicname[ 20] = "Ca"; atomicnumber["CA"] = 20; rcov[ 20] = 99; atomicname[ 21] = "Sc"; atomicnumber["SC"] = 21; rcov[ 21] = 144; atomicname[ 22] = "Ti"; atomicnumber["TI"] = 22; rcov[ 22] = 147; atomicname[ 23] = "V" ; atomicnumber["V" ] = 23; rcov[ 23] = 133; atomicname[ 24] = "Cr"; atomicnumber["CR"] = 24; rcov[ 24] = 135; atomicname[ 25] = "Mn"; atomicnumber["MN"] = 25; rcov[ 25] = 135; atomicname[ 26] = "Fe"; atomicnumber["FE"] = 26; rcov[ 26] = 134; atomicname[ 27] = "Co"; atomicnumber["CO"] = 27; rcov[ 27] = 133; atomicname[ 28] = "Ni"; atomicnumber["NI"] = 28; rcov[ 28] = 150; atomicname[ 29] = "Cu"; atomicnumber["CU"] = 29; rcov[ 29] = 152; atomicname[ 30] = "Zn"; atomicnumber["ZN"] = 30; rcov[ 30] = 145; atomicname[ 31] = "Ga"; atomicnumber["GA"] = 31; rcov[ 31] = 122; atomicname[ 32] = "Ge"; atomicnumber["GE"] = 32; rcov[ 32] = 117; atomicname[ 33] = "As"; atomicnumber["AS"] = 33; rcov[ 33] = 121; atomicname[ 34] = "Se"; atomicnumber["SE"] = 34; rcov[ 34] = 122; atomicname[ 35] = "Br"; atomicnumber["BR"] = 35; rcov[ 35] = 121; atomicname[ 36] = "Kr"; atomicnumber["KR"] = 36; rcov[ 36] = 191; atomicname[ 37] = "Rb"; atomicnumber["RB"] = 37; rcov[ 37] = 147; atomicname[ 38] = "Sr"; atomicnumber["SR"] = 38; rcov[ 38] = 112; atomicname[ 39] = "Y" ; atomicnumber["Y" ] = 39; rcov[ 39] = 178; atomicname[ 40] = "Zr"; atomicnumber["ZR"] = 40; rcov[ 40] = 157; atomicname[ 41] = "Nb"; atomicnumber["NB"] = 41; rcov[ 41] = 148; atomicname[ 42] = "Mo"; atomicnumber["MO"] = 42; rcov[ 42] = 147; atomicname[ 43] = "Tc"; atomicnumber["TC"] = 43; rcov[ 43] = 135; atomicname[ 44] = "Ru"; atomicnumber["RU"] = 44; rcov[ 44] = 140; atomicname[ 45] = "Rh"; atomicnumber["RH"] = 45; rcov[ 45] = 145; atomicname[ 46] = "Pd"; atomicnumber["PD"] = 46; rcov[ 46] = 150; atomicname[ 47] = "Ag"; atomicnumber["AG"] = 47; rcov[ 47] = 159; atomicname[ 48] = "Cd"; atomicnumber["CD"] = 48; rcov[ 48] = 169; atomicname[ 49] = "In"; atomicnumber["IN"] = 49; rcov[ 49] = 163; atomicname[ 50] = "Sn"; atomicnumber["SN"] = 50; rcov[ 50] = 146; atomicname[ 51] = "Sb"; atomicnumber["SB"] = 51; rcov[ 51] = 146; atomicname[ 52] = "Te"; atomicnumber["TE"] = 52; rcov[ 52] = 147; atomicname[ 53] = "I" ; atomicnumber["I" ] = 53; rcov[ 53] = 140; atomicname[ 54] = "Xe"; atomicnumber["XE"] = 54; rcov[ 54] = 198; atomicname[ 55] = "Cs"; atomicnumber["CS"] = 55; rcov[ 55] = 167; atomicname[ 56] = "Ba"; atomicnumber["BA"] = 56; rcov[ 56] = 134; atomicname[ 57] = "La"; atomicnumber["LA"] = 57; rcov[ 57] = 187; atomicname[ 58] = "Ce"; atomicnumber["CE"] = 58; rcov[ 58] = 183; atomicname[ 59] = "Pr"; atomicnumber["PR"] = 59; rcov[ 59] = 182; atomicname[ 60] = "Nd"; atomicnumber["ND"] = 60; rcov[ 60] = 181; atomicname[ 61] = "Pm"; atomicnumber["PM"] = 61; rcov[ 61] = 180; atomicname[ 62] = "Sm"; atomicnumber["SM"] = 62; rcov[ 62] = 180; atomicname[ 63] = "Eu"; atomicnumber["EU"] = 63; rcov[ 63] = 199; atomicname[ 64] = "Gd"; atomicnumber["GD"] = 64; rcov[ 64] = 179; atomicname[ 65] = "Tb"; atomicnumber["TB"] = 65; rcov[ 65] = 176; atomicname[ 66] = "Dy"; atomicnumber["DY"] = 66; rcov[ 66] = 175; atomicname[ 67] = "Ho"; atomicnumber["HO"] = 67; rcov[ 67] = 174; atomicname[ 68] = "Er"; atomicnumber["ER"] = 68; rcov[ 68] = 173; atomicname[ 69] = "Tm"; atomicnumber["TM"] = 69; rcov[ 69] = 172; atomicname[ 70] = "Yb"; atomicnumber["YB"] = 70; rcov[ 70] = 194; atomicname[ 71] = "Lu"; atomicnumber["LU"] = 71; rcov[ 71] = 172; atomicname[ 72] = "Hf"; atomicnumber["HF"] = 72; rcov[ 72] = 157; atomicname[ 73] = "Ta"; atomicnumber["TA"] = 73; rcov[ 73] = 143; atomicname[ 74] = "W" ; atomicnumber["W" ] = 74; rcov[ 74] = 137; atomicname[ 75] = "Re"; atomicnumber["RE"] = 75; rcov[ 75] = 135; atomicname[ 76] = "Os"; atomicnumber["OS"] = 76; rcov[ 76] = 137; atomicname[ 77] = "Ir"; atomicnumber["IR"] = 77; rcov[ 77] = 132; atomicname[ 78] = "Pt"; atomicnumber["PT"] = 78; rcov[ 78] = 150; atomicname[ 79] = "Au"; atomicnumber["AU"] = 79; rcov[ 79] = 150; atomicname[ 80] = "Hg"; atomicnumber["HG"] = 80; rcov[ 80] = 170; atomicname[ 81] = "Tl"; atomicnumber["TL"] = 81; rcov[ 81] = 155; atomicname[ 82] = "Pb"; atomicnumber["PB"] = 82; rcov[ 82] = 154; atomicname[ 83] = "Bi"; atomicnumber["BI"] = 83; rcov[ 83] = 154; atomicname[ 84] = "Po"; atomicnumber["PO"] = 84; rcov[ 84] = 168; atomicname[ 85] = "At"; atomicnumber["AT"] = 85; rcov[ 85] = 170; atomicname[ 86] = "Rn"; atomicnumber["RN"] = 86; rcov[ 86] = 240; atomicname[ 87] = "Fr"; atomicnumber["FR"] = 87; rcov[ 87] = 200; atomicname[ 88] = "Ra"; atomicnumber["RA"] = 88; rcov[ 88] = 190; atomicname[ 89] = "Ac"; atomicnumber["AC"] = 89; rcov[ 89] = 188; atomicname[ 90] = "Th"; atomicnumber["TH"] = 90; rcov[ 90] = 179; atomicname[ 91] = "Pa"; atomicnumber["PA"] = 91; rcov[ 91] = 161; atomicname[ 92] = "U" ; atomicnumber["U" ] = 92; rcov[ 92] = 158; atomicname[ 93] = "Np"; atomicnumber["NP"] = 93; rcov[ 93] = 155; atomicname[ 94] = "Pu"; atomicnumber["PU"] = 94; rcov[ 94] = 153; atomicname[ 95] = "Am"; atomicnumber["AM"] = 95; rcov[ 95] = 151; atomicname[ 96] = "Cm"; atomicnumber["CM"] = 96; rcov[ 96] = 151; atomicname[ 97] = "Bk"; atomicnumber["BK"] = 97; rcov[ 97] = 151; atomicname[ 98] = "Cf"; atomicnumber["CF"] = 98; rcov[ 98] = 151; atomicname[ 99] = "Es"; atomicnumber["ES"] = 99; rcov[ 99] = 151; atomicname[100] = "Fm"; atomicnumber["FM"] = 100; rcov[100] = 151; atomicname[101] = "Md"; atomicnumber["MD"] = 101; rcov[101] = 151; atomicname[102] = "No"; atomicnumber["NO"] = 102; rcov[102] = 151; atomicname[103] = "Lw"; atomicnumber["LW"] = 103; rcov[103] = 151; esMP2 = "no" esCI = "no" NoSymm = 0 } /Default route:/ { getline; getline nroute route = "" while ($0 !~ /------*/) { nroute++ route = route $0 "\n" getline if (nroute > 5) { break } } } /l101.exe/ { getline getline runtitle = $0 } /NoSymm/ {NoSymm=1} NoSymm==1 && /Coordinates (Angstroms)/ { ng++ } NoSymm==1 && /Coordinates (Angstroms)/ { if (NF==6 && $1+0>0) { atn[ng]++ i = atn[ng] atZ[i,ng] = $2 atxc[i,ng] = $4 atyc[i,ng] = $5 atzc[i,ng] = $6 if ($2>0 && $2<104) { atname[i,ng] = atomicname[$2] } else { atname[i,ng] = "XX" } } } /Standard basis:/ { basisset = $0 } /Standard orientation/ { ng++ } /Standard orientation/,/Rotational constants/ { if (NF==6 && $1+0>0) { atn[ng]++ i = atn[ng] atZ[i,ng] = $2 atxc[i,ng] = $4 atyc[i,ng] = $5 atzc[i,ng] = $6 if ($2>0 && $2<104) { atname[i,ng] = atomicname[$2] } else { atname[i,ng] = "XX" } } } /Rotational constants/ { rotx[ng] = $4; roty[ng] = $5; rotz[ng] = $6; } /SCF Done:/ { energy[ng] = $5 cycles[ng] = $8 getline gsub("D", "E") convg[ng] = $3 virial[ng] = $6 getline spin[ng] = $3 } / EUMP2 / { gsub("D", "E"); esMP2 = "si"; energMP2[ng] = $NF } /E\(CI\)=/ { esCI = "si"; energCI[ng] = $NF } /E\(CI,SIZE\)=/ { esCI = "si"; energCIsize[ng] = $NF } /Harmonic frequencies/ { getline; getline; getline; getline; getline nfreq = 0 for (i=1; i<=NF; i++) { fsym[++nfreq] = $i } getline nfreq = 0 for (i=3; i<=NF; i++) { freq[++nfreq] = $i } } /Dipole moment/ && /Debye/ { getline; dipole = $NF } /Job cpu time:/ { $1=""; $2=""; $3=""; cpu = $0 } { lastline = $0 } END { bng = ng if (esMP2 == "si") { beneg = energMP2[ng] for (i=1; i<=ng; i++) { if (energMP2[i] < beneg) { bng = i; beneg = energMP2[i] } } } else { beneg = energy[ng] for (i=1; i<=ng; i++) { if (energy[i] < beneg) { bng = i; beneg = energy[i] } } } printf "%s\n", runtitle printf "%s\n\n", route printf "Best energy (hartree) : %18.10f\n", energy[bng] if (esMP2 == "si") { printf "MP2 energy (hartree) : %18.10f\n", energMP2[bng] } if (esCI == "si") { printf "CI energy (hartree): %18.10f\n", energCI[bng] printf "CI+size energy (hartree): %18.10f\n", energCIsize[bng] } nc = split(cpu, t); cpu_s = t[7] + 60 * (t[5] + 60 * (t[3] + 24 * t[1])) printf "Convergence : %18.10f\n", convg[bng] printf "Virial (-V/T) : %18.10f\n", virial[bng] printf "Spin S**2 : %18.10f\n", spin[bng] printf "Basis set line : %s\n", basisset printf "Number of geometries : %d\n", ng printf "Best geometries : %d\n", bng printf "Analyzed file name : %s\n", FILENAME printf "g09 cpu time : %s\n", cpu printf "g09 cpu time (s) : %.1f\n", cpu_s printf "Last output line : %s\n", lastline printf "Rotational constants GHz: %12.7f %12.7f %12.7f\n", rotx[bng], roty[bng], rotz[bng] printf "Vibration frequencies :\n" for (i=1; i<=nfreq; i++) { printf "%7s ", fsym[i] } printf "\n" for (i=1; i<=nfreq; i++) { printf "%11.4f", freq[i] } printf "\n\n" printf "Dipole moment (Debye) : %s\n", dipole if (atn[bng] <= 0) { print "---- Using initial coordinates ----------" print "---- Coordinates & distances in bohr ----" bng = 0 } else { print "---- Using final coordinates ----------------" print "---- Coordinates & distances in Angstrom ----" } printf " Atom number x y z\n" for (i=1; i<=atn[bng]; i++) { printf "%3d %-6s%4d %15.10f%15.10f%15.10f\n", i, atname[i,bng], atZ[i,bng], atxc[i,bng], atyc[i,bng], atzc[i,bng] } printf "\n" ##for (i=1; i<=atn[bng]; i++) { ## atrc[i] = sqrt(atxc[i,bng]^2 + atyc[i,bng]^2 + atzc[i,bng]^2) ## } # Determine bonded atoms and print bond distances for (i=1; i<=atn[bng]; i++) { for (j=1; j7 atoms # Unsupported here nsupring++ } } #for i7 } } #for i6 } } #for i5 } } #for i4 } } #for i3 } } #for i2 } #for i1 printf "\n" printf "Rings found in the structure : %6d\n", nring printf "Possible rings not determined: %6d\n", nsupring for (i=1; i<=nring; i++) { printf " %3d) %d-ring formed by : ", i, natr[i] for (j=1; j<=natr[i]; j++) { printf " %3d", iatr[j,i] } printf "\n" angdev = RingNormal(i, normal) printf " nonplanarity angle: %12.6f\n", angdev printf " normal vector : " printf "%12.6f %12.6f %12.6f\n", normal[1], normal[2], normal[3] rnx[i] = normal[1] rny[i] = normal[2] rnz[i] = normal[3] } if (nring > 1) { printf "\n" printf "Dihedral angles between the rings:\n", nring for (i=1; i<=nring; i++) { for (j=i+1; j<=nring; j++) { printf " Rings %3d and %3d", i, j ang = VecAngle(rnx[i], rny[i], rnz[i], rnx[j], rny[j], rnz[j]) printf " Angle %12.6f deg.\n", ang } } } } --Boundary_(ID_X7fwaERpfE+dHq/sFS806Q)-- From owner-chemistry@ccl.net Tue Jul 19 21:04:01 2016 From: "Daniel Morales Salazar danielmoralessalazar91]![gmail.com" To: CCL Subject: CCL:G: 0. Basics,1. Biradicals, Guidance. 2. Connectivity Problems Message-Id: <-52317-160719201720-16370-fp5RFkf56gJuNxkprdWLsQ(a)server.ccl.net> X-Original-From: "Daniel Morales Salazar" Date: Tue, 19 Jul 2016 20:17:19 -0400 Sent to CCL by: "Daniel Morales Salazar" [danielmoralessalazar91---gmail.com] Dear CCL Members, First of all, thank you very much for your input in my previous questions, which was always thorough and proactive. 0. This time I prepared the question by mainly glancing through: Abe, Manabu. "Diradicals." Chemical reviews 113.9 (2013): 7011-7088, Chapters 3 and 4 of, Datta, Sambhu N., Carl Trindle, and Francesc Illas. Theoretical and computational aspects of magnetic organic molecules, Imperial College Press, Hackensack, NJ;London; 2014., both a bit overwhelming for the amount of time I currently have, I also looked at some of my undergraduate textbooks and online .pdf files, but I am still struggling with some trivial and not-so trivial details. Trivial things such as terminology like the difference between a "triplet ground state" and "triplet excited state" are not very clear to me yet, what is simple and correct way of thinking about the difference of these two? it seems as if in most of my reading I keep finding that T1 is a triplet excited state, so is the "triplet ground state" a "T0"? and computationally (DFT), what is the difference? is it that one calculates a "triplet ground state" using (U)DFT and the "triplet excited state" using (R)TD-DFT? I am getting too long now so I would appreciate some feedback on the following mostly: 1. I am interested in calculating the energies and properties of neutral mesomeric systems (C, H, N, P, S) containing 25 to 60 atoms, which may or may not exist as open shell singlet biradicals in their ground state, and/or have interesting singlet triplet gaps and this type of "theoretical business" :) where can I find a good "step by step" kind of reference for an experimentalist who is learning theoretical aspects of biradicals? and which functionals do you advice me to try? I have read there may be better functionals than B3LYP for pi-conjugated systems in which the "radicals" are separated yet part of a delocalized system, in my cases they are anywhere from 7 to 13 bonds apart. 2. I am optimizing the geometry of a system (C46H43Br2PSi2) with the following input route: #p opt=tight pm6 geom=connectivity gfinput gfprint int=fine iop(6/7=3) Item Value Threshold Converged? Maximum Force 0.000001 0.000015 YES RMS Force 0.000000 0.000010 YES Maximum Displacement 0.000047 0.000060 YES RMS Displacement 0.000009 0.000040 YES Predicted change in Energy=-4.577343D-12 However, the connectivity of the final structure significantly differs > from the initial one. I see some sort of 2+2 cycloaddition product, which is definitely not what I expected since I used the "geom=connectivity" keyword as read online. I am trying to optimize this same compound using B3LYP/6-311G** from my initial ("correct") geometry, and I see the same type of "cycloaddition" or "erroneous" intermediates after a number of cycles. How can I force Gaussian to keep the bonding situation exactly as given in the input, or is this a Molden/GaussView problem? ... I doubt the latter one because some bonds I find are really longer than what they would be if they were double bonds for example. I hope the question serves to other people with similar problems. From owner-chemistry@ccl.net Tue Jul 19 22:46:00 2016 From: "Gabriele Mogni gabriele.mogni!^!gmail.com" To: CCL Subject: CCL: Free Computational Material Science Consultancy Message-Id: <-52318-160719222515-15944-7sPiFVvmRd63Dc49rb2IFw*server.ccl.net> X-Original-From: "Gabriele Mogni" Date: Tue, 19 Jul 2016 22:25:14 -0400 Sent to CCL by: "Gabriele Mogni" [gabriele.mogni^^gmail.com] If you want to collaborate with me on a computational material science project as part of your research group or company please do not hesitate to contact me at my email address: gabriele.mogni],[gmail.com or visit my website: http://gabrielemogni.wix.com/materialscience Regards, Dr. Gabriele Mogni