From owner-chemistry@ccl.net Wed Jun 27 00:11:00 2012 From: "Hao-Bo Guo guohaobo**gmail.com" To: CCL Subject: CCL:G: The aufbau principle in teaching chemistry Message-Id: <-47146-120626232318-2424-CpwzTMUwoxZHZ9wdnokStg _ server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/related; boundary=bcaec54eeaa0ea9d8804c36bbbcc Date: Tue, 26 Jun 2012 23:23:08 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo**gmail.com] --bcaec54eeaa0ea9d8804c36bbbcc Content-Type: multipart/alternative; boundary=bcaec54eeaa0ea9d8304c36bbbcb --bcaec54eeaa0ea9d8304c36bbbcb Content-Type: text/plain; charset=ISO-8859-1 That's interesting...haven't thought of this details, but I just did a quick calculation for Sc+ using ROMP2/6-31+G(d) to compare the two possible electronic configurations of {1s2, 2s2, 2p6, 3s2, 3p6, 3d1, 4s1} vs {1s2, 2s2, 2p6, 3s2, 3p6, 4s2}. The results indicated that the occupied orbitals are in this order: a). {A1g A1g T1u T1u T1u A1g T1u T1u T1u A1g Eg} for the former (3d14s1) b). {A1g A1g T1u T1u T1u A1g T1u T1u T1u A1g} for the latter. (4s2) However the energy of (4s2) is 48.3 kcal/mol higher than that of (3d14s1), therefore this calculation does support the points posted in Dr. Scerri's blog with (3d14s1) configuration for Sc+. For electronic transitions both the shape and amplitude of the molecular orbitals are the key issues that could be intuitively visualized. Hao-Bo Guo On Tue, Jun 26, 2012 at 12:02 PM, Prof. Dr. N. Sekar nethi.sekar[*]gmail.com wrote: > Dear Prof Eric Scerri, > > > > Really commendable. > > I was wondering whether such similar principles are available for filling > up electrons in molecules containing pi-conjugated electrons. We also > observe in reconciling the observation with DFT and TDDFT computations it > is not always HOMO which is the orbital involved in absorption. Many a > times a orbital lower than HOMO absorbs energy in bringing out verical > excitatios. So also it is not always a LUMO which is the excited state. > Sometimes a state higher than the LUMO. > > On Mon, Jun 25, 2012 at 8:38 PM, Eric Scerri scerri_-_chem.ucla.edu < > owner-chemistry*ccl.net> wrote: > >> >> Dear Colleagues, >> >> I have a blog on the question of using the aufbau to 'predict' and teach >> electronic configurations of atoms at, >> >> http://ericscerri.blogspot.com/ >> >> and would be interested in hearing comments on it. >> >> all the best >> eric scerri >> UCLA >> >> ______________________________________________________ >> >> >> >> >> ericscerri.com >> >> On Twitter: >> https://twitter.com/#!/ericscerri >> >> >> >> >> >> >> >> >> >> >> > > > -- > Thanks and regards > > Prof. Dr. N. Sekar CCol FSDC > Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry > Dyestuff Technology Department > Institute of Chemical Technology (formerly UDCT) > Matunga, Mumbai-400019 > > Mob +91-9867958452 > n.sekar*ictmumbai.edu.in > sekarnm*rediffmail.com > drnsekar4562000*yahoo.co.in > > website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 > > --bcaec54eeaa0ea9d8304c36bbbcb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable That's interesting...haven't thought of this details, but I just di= d a quick calculation for Sc+ using ROMP2/6-31+G(d) to compare the two poss= ible electronic configurations of {1s2, 2s2, 2p6, 3s2, 3p6, 3d1, 4s1} vs {1= s2, 2s2, 2p6, 3s2, 3p6, 4s2}.
The results indicated that the occupied orbitals are in this order:
a). {A1g A1g T1u T1u T1u A1g T1u T1u T1u A1g Eg} for the former (3d14s1)=
b). {A1g A1g T1u T1u T1u A1g T1u T1u T1u A1g} for the latter. (4= s2)
However the energy of (4s2) is 48.3 kcal/mol higher than that of (3d14= s1), therefore this calculation does support the points posted in Dr. Scerr= i's blog with (3d14s1) configuration for Sc+.

For electronic transitions both the shape and amplitude of the molecular or= bitals are the key issues that could be intuitively visualized.=A0

Hao-Bo Guo =A0

On= Tue, Jun 26, 2012 at 12:02 PM, Prof. Dr. N. Sekar nethi.sekar[*]gmail.com <owner-chemistry:ccl.net> wrote:

Dear Prof Eric Scerri,<= /p>

=A0

Really commendable.=A0

I was wondering whether= such similar principles are available for filling up electrons in molecule= s containing pi-conjugated electrons.=A0 We also observe in reconciling the= observation with DFT and TDDFT computations it is not always HOMO which is= the orbital involved in absorption.=A0 Many a times a orbital lower than H= OMO absorbs energy in bringing out verical excitatios.=A0 So also it is not= always a LUMO which is the excited state.=A0 Sometimes a state higher than= the LUMO.=A0

On Mon, Jun 25, 2012 a= t 8:38 PM, Eric Scerri scerri_-_chem.ucla.edu <owner-chemistry*ccl.net><= /span> wrote:

Dear Colleagues,

I have a blog on the question of using the aufbau to 'p= redict' and teach electronic configurations of atoms at,


and would be i= nterested in hearing comments on it.

all the best
eric s= cerri
UCLA

_____________________________________= _________________
=


=A0= =A0 =A0 =A0=A0 ericsce= rri.com




--
Thanks and = regards

Prof. Dr. N. Sekar=A0=A0 CCol FSDC
Co-ordinator, UGC-CAS = and Professor in Tinctorial Chemistry
Dyestuff Technology Department
Institute of Chemical Technology (formerl= y UDCT)
Matunga, Mumbai-400019

Mob +91-9867958452
n.sekar*ictmumb= ai.edu.in
sekarnm*rediffm= ail.com
drnsekar4562000*yahoo.co.in
=A0


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rK9ZGawVFE3frgtQwaU+FbLZ9fy4xYsbIBoXi0O2x6KRlPAo3XOMhEk8qty3ord8P0DQdN1WjaTX 9UMEviOoisLQETMjWQd25wE4+7e48Za6novw3pxqNnW2lO9xp/4q/wAYCHeoah5CX/h2eLH45qBq Ndm08kIJIO32XAxxjaDtPGbnqejfC0WyWD4immWpC5MixkEOoQC158u8/wDqDxYzTNbLp11s0Ubv qIlkZY5iNviICQGr3I5r0w0xbTHGqrdiQT3PPOYdj4Rk2n6+v+M9/rkHoOw9s8OZADyK7ZVEmwZD WR3J7k5FbO9gxocGj2wGpJ+z3fO4/wBMYgAOl3ECygs/icaidgGYtQLEA/l9cDIGUhy/lHoF7jMs SBJRP389KAXWxfk/tmMR3tZ2Hg9+/v7YbTRszEWoHpXri+kJMrKTxtPH4ZaaHsn1xXIaEbDxxrED uCgUQOcT18YDLJJtAYeXjv8A3y1IFVXFdsqJ+YiT6MQMkzpj0B0BNRU7T86GZSMCxRJJvtWLxcul /wD3k45peYSDzW4j5YBnSMSbgdhjKLx6kX9MLRB3bCK+fJwyEkgE3TGvliupdxKQGYW/POAARydr FmYgiq9OMrpAxvdsUeg98LqiRE5vnccBCA0jWAefXGQrP//Z --bcaec54eeaa0ea9d8804c36bbbcc-- From owner-chemistry@ccl.net Wed Jun 27 08:02:00 2012 From: "EMRYS THOMAS ddolgam*live.co.uk" To: CCL Subject: CCL:G: Methyl Carbamic Acid, collinearity and relaxed PES Message-Id: <-47147-120627055516-10106-ttpvJCbchIGac3BQn+J/7g]_[server.ccl.net> X-Original-From: "EMRYS THOMAS" Date: Wed, 27 Jun 2012 05:55:15 -0400 Sent to CCL by: "EMRYS THOMAS" [ddolgam(_)live.co.uk] > "Salomon Turgman Cohen sturgman|gmail.com" wrote: > > Sent to CCL by: Salomon Turgman Cohen [sturgman**gmail.com] > --047d7b15fcffad7fa704c356482c > Content-Type: text/plain; charset=ISO-8859-1 > > Hello, > I just started using QM software in my work and I am running into a > problem when attempting optimization of molecules with carbon oxygen double > bonds. I am using Gaussian 09 software and I am attempting to obtain a > relaxed PES by scanning through a dihedral angle. My input file looks like > this: > > ======================= > > %chk=checkpoint.out > > # opt=modredundant > # MP2/3-21G > > Methyl Carbamic Acid > > -1 1 > C -1.138918 0.893653 -0.049356 > H -2.079107 0.544512 -0.478804 > H -1.021588 1.947417 -0.306449 > H -1.280611 0.865522 1.032038 > N -0.023046 0.089597 -0.511660 > H 0.244819 -0.107547 -1.462151 > C 0.759629 -0.614681 0.333273 > O 1.812834 0.147724 0.752146 > O 0.484148 -1.759325 0.621099 > > D * 5 7 * R > D 1 5 7 8 S 18 10.0 > > ========================= > > If I remove the "D * 5 7 * R" line the program runs properly, but with the > line I get the error relating to internal coordinates: > > NTrRot= -1 NTRed= 27 NAtoms= 9 NSkip= 6 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun 25 > 21:24:51 2012. > > The reason I try to remove the coordinates related to that bond is that > Gaussian manual suggests this is necessary to obtain relaxed PES (although > I do not understand exactly why and could not find the answer in Jensen's > Intro. or Lewars' book) > > Searching through your website (what seemed like the archives) I found this > paragraph that may be related: > "It is important to realize that the torsional angle is undefined if either > atoms *i*, *j* and *k*, or *j*, *k* and *l* are collinear (i.e., a straight > line is passing through three consecutive atoms) because an infinite number > of planes can pass through three collinear points. For this reason, it does > not make sense to talk about a torsional angle in acetylene. " > > Is this related to the problem I am having. While visualizing the molecule > it is not clear to me how it is becoming collinear during the optimization > and scanning. Can anyone provide a hint on what concept I am missing here? > > > -- > Salomon Turgman Cohen > Postdoctoral Associate > Cornell University > (919) 341-9650 > > --047d7b15fcffad7fa704c356482c > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hello,
=A0=A0 I just started using QM software in my work and I am runni= > ng into a problem when attempting optimization of molecules with carbon oxy= > gen double bonds. I am using Gaussian 09 software and I am attempting to ob= > tain a relaxed PES by scanning through a dihedral angle. My input file look= > s like this:
>
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D r>
%chk=3Dcheckpoint.out

# opt=3Dmodredundant
# MP2/3-21G
<= > br>Methyl Carbamic Acid

-1 1
C=A0=A0=A0=A0=A0=A0=A0=A0 -1.138918= > =A0=A0=A0=A0 0.893653=A0=A0=A0 -0.049356
H=A0=A0=A0=A0=A0=A0=A0=A0 -2.07= > 9107=A0=A0=A0=A0 0.544512=A0=A0=A0 -0.478804
> H=A0=A0=A0=A0=A0=A0=A0=A0 -1.021588=A0=A0=A0=A0 1.947417=A0=A0=A0 -0.306449= >
H=A0=A0=A0=A0=A0=A0=A0=A0 -1.280611=A0=A0=A0=A0 0.865522=A0=A0=A0=A0 1.= > 032038
N=A0=A0=A0=A0=A0=A0=A0=A0 -0.023046=A0=A0=A0=A0 0.089597=A0=A0=A0= > -0.511660
H=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.244819=A0=A0=A0 -0.107547=A0= > =A0=A0 -1.462151
C=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.759629=A0=A0=A0 -0.61468= > 1=A0=A0=A0=A0 0.333273
> O=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.812834=A0=A0=A0=A0 0.147724=A0=A0=A0=A0 0.75= > 2146
O=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.484148=A0=A0=A0 -1.759325=A0=A0=A0= > =A0 0.621099

D * 5 7 * R
D 1 5 7 8 S 18 10.0

>=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

If I remove the "D *=A0 5 7 * R" line the program runs= > properly, but with the line I get the error relating to internal coordinat= > es:
>
=A0NTrRot=3D=A0=A0=A0 -1 NTRed=3D=A0=A0=A0 27 NAtoms=3D=A0=A0=A0=A0 9 N= > Skip=3D=A0=A0=A0=A0 6 IsLin=3DF
=A0Error in internal coordinate system.<= > br>=A0Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun= > 25 21:24:51 2012.

The reason I try to remove the coordinates relate= > d to that bond is that Gaussian manual suggests this is necessary to obtain= > relaxed PES (although I do not understand exactly why and could not find t= > he answer in Jensen's Intro. or Lewars' book)
>
Searching through your website (what seemed like the archives) I found = > this paragraph that may be related:
"It is important to realize tha= > t the torsional angle is undefined if either > atoms i, j and k, or j, k and l a= > re collinear (i.e., a straight > line is passing through three consecutive atoms) because an infinite number > of planes > can pass through three collinear points. For this reason, it does not > make sense to talk about a torsional angle in acetylene. > "

Is this related to the problem I am having. While visualizing= > the molecule it is not clear to me how it is becoming collinear during the= > optimization and scanning. Can anyone provide a hint on what concept I am = > missing here?
>

--
Salomon Turgman Cohen
Postdoctoral Associate
Cornell U= > niversity
rget=3D"_blank">(919) 341-9650
> > --047d7b15fcffad7fa704c356482c-- > > If you work with an internal coordinate input file(Gaussview)as below you will see the relevant dihedral for scanning listed(D5).Removing D5 using * 5 7 * R simply confuses Gaussian-colinearity is not the problem.For this molecule opt=z-matrix,(with D5 directly labelled S 18 10.00) would also work. -1 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 N 1 B4 4 A3 2 D2 H 5 B5 1 A4 4 D3 C 5 B6 1 A5 4 D4 O 7 B7 5 A6 1 D5 O 7 B8 5 A7 1 D6 B1 1.09099994 B2 1.09099980 B3 1.09099956 B4 1.45100035 B5 1.00700094 B6 1.34999981 B7 1.36600046 B8 1.21199949 A1 107.99995438 A2 105.80991795 A3 113.66540106 A4 127.86353928 A5 122.38005985 A6 110.34994685 A7 120.63402531 D1 -112.77096125 D2 -122.07837956 D3 173.68882023 D4 -0.33914046 D5 0.00000000 (preadjusted to 0 in GView for a clearer scan) D6 179.97998495 D 1 5 7 8 S 18 10.000000 Regards Emrys Thomas From owner-chemistry@ccl.net Wed Jun 27 09:57:00 2012 From: "Andrew Yeung andrew.yeung=chem.tamu.edu" To: CCL Subject: CCL: CBS-4M Warning Message-Id: <-47148-120627095245-16498-jShlJeYtnjKXGtLCg6zBpQ(0)server.ccl.net> X-Original-From: "Andrew Yeung" Date: Wed, 27 Jun 2012 09:52:43 -0400 Sent to CCL by: "Andrew Yeung" [andrew.yeung-$-chem.tamu.edu] Hi All I get frequent warning messages like the following for CBS-4M calculations on fairly large systems (~50 heavy atoms): "Warning! The extrapolated energy is higher than the direct energy for pair ( 18 17 1)" I am using 4 processors, 4-6 gb of memory, and each calculation should have about 0.4 terabytes of disk available to it (maxdisk not set). The HOMO-LUMO gap for this example is 0.6 eV, for what it's worth. For some calculations, I only get a few of these warning messages, and the job concludes properly. For several others, I get a few screenfulls of this error message, before I run out of walltime before the job terminates. Any idea what this means? Thanks. Andrew Yeung Dept. of Chemistry Texas A&M University From owner-chemistry@ccl.net Wed Jun 27 12:23:00 2012 From: "Salomon Turgman Cohen sturgman-,-gmail.com" To: CCL Subject: CCL:G: Methyl Carbamic Acid, collinearity and relaxed PES Message-Id: <-47149-120627095728-1664-XV5wdXsDCkIDZ8cul3EJaQ:_:server.ccl.net> X-Original-From: Salomon Turgman Cohen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 27 Jun 2012 09:57:19 -0400 MIME-Version: 1.0 Sent to CCL by: Salomon Turgman Cohen [sturgman##gmail.com] Dear Emrys,     There is still some confusion for me. According to the Gaussian manual a relaxed pes may be obtained by: ==== Wildcards in the ModRedundant input may also be useful in setting up relaxed PES scans. For example, the following input is appropriate for a potential energy surface scan involving the N1-N2-N3-N4 dihedral angle. Note that all other dihedrals around the bond should be removed: * N2 N3 * R           !Remove all dihedrals involving the N2-N3 bond N1 N2 N3 N4 S 20 2.0  !Specify a relaxed PES scan of 20 steps in 2° increments ==== I have also learned that Gaussian creates its own set of redundant coordinates. Furthermore, when I apply the example in the manual to a molecule like the methylammonium ion in which all 9 dihedrals along the central bond of interest are equivalent, the procedure works. Does this perhaps have something to do with the dihedrals along the bond of interest not being equivalent? For example if I do a regular optimization for methylcarbamic acid ion I get the following redundant coordinate dihedrals: ! D7 D(1,5,7,8) -179.98 estimate D2E/DX2 ! ! D8 D(1,5,7,9) 0.0 estimate D2E/DX2 ! ! D9 D(6,5,7,8) 0.0 estimate D2E/DX2 ! ! D10 D(6,5,7,9) 179.98 estimate D2E/DX2 ! For methylammonium I get: ! D1 D(2,1,5,6) -179.0062 estimate D2E/DX2 ! ! D2 D(2,1,5,7) 58.5607 estimate D2E/DX2 ! ! D3 D(2,1,5,8) -70.8255 estimate D2E/DX2 ! ! D4 D(3,1,5,6) 60.0 estimate D2E/DX2 ! ! D5 D(3,1,5,7) -62.4331 estimate D2E/DX2 ! ! D6 D(3,1,5,8) 168.1807 estimate D2E/DX2 ! ! D7 D(4,1,5,6) -59.9898 estimate D2E/DX2 ! ! D8 D(4,1,5,7) 177.5771 estimate D2E/DX2 ! ! D9 D(4,1,5,8) 48.1909 estimate D2E/DX2 ! Why does this work for methylammonium but not for the methyl carbamic acid? I am missing some important, perhaps obvious detail here. Salomon On Wed, Jun 27, 2012 at 5:55 AM, EMRYS THOMAS ddolgam*live.co.uk wrote: > > > Sent to CCL by: "EMRYS  THOMAS" [ddolgam(_)live.co.uk] > > > "Salomon Turgman Cohen sturgman|gmail.com"  wrote: > > > > Sent to CCL by: Salomon Turgman Cohen [sturgman**gmail.com] > > --047d7b15fcffad7fa704c356482c > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hello, > >    I just started using QM software in my work and I am running into a > > problem when attempting optimization of molecules with carbon oxygen double > > bonds. I am using Gaussian 09 software and I am attempting to obtain a > > relaxed PES by scanning through a dihedral angle. My input file looks like > > this: > > > > ======================= > > > > %chk=checkpoint.out > > > > # opt=modredundant > > # MP2/3-21G > > > > Methyl Carbamic Acid > > > > -1 1 > > C         -1.138918     0.893653    -0.049356 > > H         -2.079107     0.544512    -0.478804 > > H         -1.021588     1.947417    -0.306449 > > H         -1.280611     0.865522     1.032038 > > N         -0.023046     0.089597    -0.511660 > > H          0.244819    -0.107547    -1.462151 > > C          0.759629    -0.614681     0.333273 > > O          1.812834     0.147724     0.752146 > > O          0.484148    -1.759325     0.621099 > > > > D * 5 7 * R > > D 1 5 7 8 S 18 10.0 > > > > ========================= > > > > If I remove the "D *  5 7 * R" line the program runs properly, but with the > > line I get the error relating to internal coordinates: > > > >  NTrRot=    -1 NTRed=    27 NAtoms=     9 NSkip=     6 IsLin=F > >  Error in internal coordinate system. > >  Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun 25 > > 21:24:51 2012. > > > > The reason I try to remove the coordinates related to that bond is that > > Gaussian manual suggests this is necessary to obtain relaxed PES (although > > I do not understand exactly why and could not find the answer in Jensen's > > Intro. or Lewars' book) > > > > Searching through your website (what seemed like the archives) I found this > > paragraph that may be related: > > "It is important to realize that the torsional angle is undefined if either > > atoms *i*, *j* and *k*, or *j*, *k* and *l* are collinear (i.e., a straight > > line is passing through three consecutive atoms) because an infinite number > > of planes can pass through three collinear points. For this reason, it does > > not make sense to talk about a torsional angle in acetylene. " > > > > Is this related to the problem I am having. While visualizing the molecule > > it is not clear to me how it is becoming collinear during the optimization > > and scanning. Can anyone provide a hint on what concept I am missing here? > > > > > > -- > > Salomon Turgman Cohen > > Postdoctoral Associate > > Cornell University > > (919) 341-9650 > > > > --047d7b15fcffad7fa704c356482c > > Content-Type: text/html; charset=ISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Hello,
=A0=A0 I just started using QM software in my work and I am runni= > > ng into a problem when attempting optimization of molecules with carbon oxy= > > gen double bonds. I am using Gaussian 09 software and I am attempting to ob= > > tain a relaxed PES by scanning through a dihedral angle. My input file look= > > s like this:
> >
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > r>
%chk=3Dcheckpoint.out

# opt=3Dmodredundant
# MP2/3-21G
<= > > br>Methyl Carbamic Acid

-1 1
C=A0=A0=A0=A0=A0=A0=A0=A0 -1.138918= > > =A0=A0=A0=A0 0.893653=A0=A0=A0 -0.049356
H=A0=A0=A0=A0=A0=A0=A0=A0 -2.07= > > 9107=A0=A0=A0=A0 0.544512=A0=A0=A0 -0.478804
> > H=A0=A0=A0=A0=A0=A0=A0=A0 -1.021588=A0=A0=A0=A0 1.947417=A0=A0=A0 -0.306449= > >
H=A0=A0=A0=A0=A0=A0=A0=A0 -1.280611=A0=A0=A0=A0 0.865522=A0=A0=A0=A0 1.= > > 032038
N=A0=A0=A0=A0=A0=A0=A0=A0 -0.023046=A0=A0=A0=A0 0.089597=A0=A0=A0= > >  -0.511660
H=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.244819=A0=A0=A0 -0.107547=A0= > > =A0=A0 -1.462151
C=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.759629=A0=A0=A0 -0.61468= > > 1=A0=A0=A0=A0 0.333273
> > O=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.812834=A0=A0=A0=A0 0.147724=A0=A0=A0=A0 0.75= > > 2146
O=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.484148=A0=A0=A0 -1.759325=A0=A0=A0= > > =A0 0.621099

D * 5 7 * R
D 1 5 7 8 S 18 10.0

> >=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

If I remove the "D *=A0 5 7 * R" line the program runs= > >  properly, but with the line I get the error relating to internal coordinat= > > es:
> >
=A0NTrRot=3D=A0=A0=A0 -1 NTRed=3D=A0=A0=A0 27 NAtoms=3D=A0=A0=A0=A0 9 N= > > Skip=3D=A0=A0=A0=A0 6 IsLin=3DF
=A0Error in internal coordinate system.<= > > br>=A0Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun= > >  25 21:24:51 2012.

The reason I try to remove the coordinates relate= > > d to that bond is that Gaussian manual suggests this is necessary to obtain= > >  relaxed PES (although I do not understand exactly why and could not find t= > > he answer in Jensen's Intro. or Lewars' book)
> >
Searching through your website (what seemed like the archives) I found = > > this paragraph that may be related:
"It is important to realize tha= > > t the torsional angle is undefined if either > > atoms i, j and k, or j, k and l a= > > re collinear (i.e., a straight > > line is passing through three consecutive atoms) because an infinite number > > of planes > > can pass through three collinear points. For this reason, it does not > > make sense to talk about a torsional angle in acetylene. > > "

Is this related to the problem I am having. While visualizing= > >  the molecule it is not clear to me how it is becoming collinear during the= > >  optimization and scanning. Can anyone provide a hint on what concept I am = > > missing here?
> >

--
Salomon Turgman Cohen
Postdoctoral Associate
Cornell U= > > niversity
> rget=3D"_blank">(919) 341-9650
> > > > --047d7b15fcffad7fa704c356482c-- > > > > > If you work with an internal coordinate input file(Gaussview)as below you will > see the relevant dihedral for scanning listed(D5).Removing > D5 using * 5 7 * R simply confuses Gaussian-colinearity is not the problem.For this molecule opt=z-matrix,(with D5 directly labelled S 18 10.00) would also work. > -1 1 >  C >  H                  1              B1 >  H                  1              B2    2              A1 >  H                  1              B3    3              A2    2              D1 >  N                  1              B4    4              A3    2              D2 >  H                  5              B5    1              A4    4              D3 >  C                  5              B6    1              A5    4              D4 >  O                  7              B7    5              A6    1              D5 >  O                  7              B8    5              A7    1              D6 > >   B1             1.09099994 >   B2             1.09099980 >   B3             1.09099956 >   B4             1.45100035 >   B5             1.00700094 >   B6             1.34999981 >   B7             1.36600046 >   B8             1.21199949 >   A1           107.99995438 >   A2           105.80991795 >   A3           113.66540106 >   A4           127.86353928 >   A5           122.38005985 >   A6           110.34994685 >   A7           120.63402531 >   D1          -112.77096125 >   D2          -122.07837956 >   D3           173.68882023 >   D4            -0.33914046 >   D5             0.00000000 (preadjusted to 0 in GView for a clearer scan) >   D6           179.97998495 > > > D 1 5 7 8 S 18 10.000000 > Regards > Emrys Thomas>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > -- Salomon Turgman Cohen Postdoctoral Associate Cornell University (919) 341-9650 From owner-chemistry@ccl.net Wed Jun 27 15:38:00 2012 From: "Billy McCann bwm0005-x-tigermail.auburn.edu" To: CCL Subject: CCL:G: Using read-write file to distribute time allocation Message-Id: <-47150-120627143255-29959-fcIp3GgMp+OCm9qOfA95ZA()server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Jun 2012 18:32:38 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005]*[tigermail.auburn.edu] Hi David. Here's a bash script which may suite your needs. You and I communicated privately but I felt this script may be useful in the future, should someone search CCL for such a use case. Also, I'd like to post this script should anyone else on CCL have criticisms or comments regarding it. Billy ## BEGIN SCRIPT ## #!/bin/bash # About ------------------------- # # Script to resubmit an incompleted Gaussian job through the use of the rwf # file. # # The Guassian job file needs to have the directive %nosave after identifying # the name of the rwf, e.g.: # %rwf=/path/to/myjob/myjob.rwf # %nosave # %chk=/path/to/myjobs/myjob.chk # # # hf/3-21g opt freq # # Note that absolute pathnames ought to be given for the names of the rwf and # the chk file. # # The %nosave directive _must_ be placed after the %rwf directive. This tells # Gaussian to save the rwf only if the job doesn't complete. If the job does in # fact complete, Gaussian will not save the rwf. Note that rwf files may # become very, very large. # # The fact that Gaussian will save the rwf (per our directive) is crucial to # this script, as the script will check for the existene of the rwf and then # restart the calculation based on whether or not the file exists. Once the # file is no longer there once the calculation is completed, the script will # exit. # # The script will use the original job file in order to create a restart job # file. It will create a new job file with the same name as the original but # with 'restart' appended before the suffix. It will also change the route line # to just the word 'Restart', as that's all that is need to restart the job if # the rwf and chk files are in place. # # See the website http://www.gaussian.com/g_tech/g_ur/k_restart.htm for more # details. # # Invocation ---------------------- # ./restart_calc.sh # Comment: only use after initial job has been submitted! # ---------------------------------- # # Script written by Billy Wayne McCann. # Contact: bwm0005{=}auburn.edu # # --------------------------------- # Begin Script ------------ # WHAT IS THE COMMAND TO SUBMIT THE JOB? # ENTER IT BETWEEN THE TWO DOUBLE QUOTES BELOW!! SUBMIT="" # test to see that the submit command has been filled in [ -z $SUBMIT ] && echo "SUBMIT command not filled in. Please edit the script" \ && exit -1 # find the gaussian job file: must have suffic either gjf or com GJF=$( find . -maxdepth 1 -type f -name "*.gjf" -o -name "*.com" ) # rename the gjfname file to include 'restart' in the filename. GJF_RESTART=${GJF%.*}.restart.${GJF##*.} # copy the GJF file to the $GJF_RESTART file. Do this in order to preserve the # existance of the original GJF file. cp $GJF $GJF_RESTART # substitue the route line of the $GJF_RESTART file to 'Restart' sed -i "s/^#.*/# Restart/" $GJF_RESTART # test to see if the initial rwf exists. If not, tell the user and exit the # script. [ -f *rwf ] || echo "Initial rwf doesn't exist" && exit -1 # enter the while loop which will restart the job every 24 hours and 30 minutes # first, test to see if the rwf still exists. if it does, proceed. while [ -f *rwf ] ; do # submit the restart job $SUBMIT $GJF_RESTART || echo "Job not submitted successfully" && exit -1 # sleep 24 hours and 30 minutes sleep 24h 30m done # tell the user that the job is done and exit with success (0) status echo "The job appears appears to have completed. Congratulations!" echo "Script $0 completed." exit 0 +++++++++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Reseach Auburn University, Alabama Office # = 334.844.6948 bwayne on irc.freenode.net +++++++++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu{=}ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu{=}ccl.net] On Behalf Of Davee McCloud davemccloud886:yahoo.com Sent: Saturday, June 16, 2012 3:38 PM To: Billy McCann Subject: CCL: Using read-write file to distribute time allocation Sent to CCL by: "Davee McCloud" [davemccloud886::yahoo.com] Dear All: I am aware that rwf can be used to segment memory allocation. However, I will like to know if this can also be used in time allocation/distribution on a server e.g. I am submitting a job to a server that only allows 24 hour allocation,I am sure my job will require more than 24 hours, can i write a rwf for time allocation so my job does not automatically stop after 24 hours? Thanks Dave McCloudhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt