From owner-chemistry@ccl.net Mon Jan 18 03:02:01 2010 From: "Prasenjit Seal prasenjit.seal|crm2.uhp-nancy.fr" To: CCL Subject: CCL: Atomic density problem Message-Id: <-41060-100118014320-14844-uLAfa8/Ed+2r4nKKDGE4NQ-*-server.ccl.net> X-Original-From: "Prasenjit Seal" Date: Mon, 18 Jan 2010 01:43:16 -0500 Sent to CCL by: "Prasenjit Seal" [prasenjit.seal]|[crm2.uhp-nancy.fr] Hello, Recently, I am involved in some calculations where I have to calculate the free atomic density (or the density of an isolated atom) using a cube file through a grid-based approach. Actually, I am not habituated with these kind of techniques/approaches and hence seek kind help in this regard. I mean is there any such fortran program where we can calculate the free atomic density of an atom via grdi based approach? Looking forward for a kind reply and cooperation. Cheers, Prasenjit From owner-chemistry@ccl.net Mon Jan 18 04:47:00 2010 From: "San fabian Emilio sanfa-*-ua.es" To: CCL Subject: CCL:G: Spin projected HF Message-Id: <-41061-100118043742-25416-SgOtoplVBBcb3k/rwMjEJg\a/server.ccl.net> X-Original-From: "San fabian Emilio" Date: Mon, 18 Jan 2010 04:37:38 -0500 Sent to CCL by: "San fabian Emilio" [sanfa=ua.es] I mean is there any program where we can calculate the energy and the population analysis of a spin projected UHF wavefunction. I think that the Gaussian only make these using the UHF wf after single annihilation. From owner-chemistry@ccl.net Mon Jan 18 08:09:01 2010 From: "Prasenjit SEAL prasenjit.seal#crm2.uhp-nancy.fr" To: CCL Subject: CCL: Atomic Density Problem Message-Id: <-41062-100118080708-29381-rpfo0i6oGUDjiletMQWm9A=-=server.ccl.net> X-Original-From: Prasenjit SEAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Jan 2010 13:23:11 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] Hello, Thanks for the reply... However, that is not what I meant. I mean to say that suppose I have a cube file of 'water' molecule containing the charge densities at each grid point. Obviously, one has to specify the number of grid points along with the grid spacing. Now I want to calculate the free atomic densities (which has to be spherical in nature irrespective of the atom) of the two H atoms and one O atom present in H2O using that molecular cube file. If any Fortran code is available which can read the molecular cube file of a system and can calculate the spherically averaged free atomic densities for the constituent atoms, then it would be very helpful. Cheers, Prasenjit From owner-chemistry@ccl.net Mon Jan 18 09:21:01 2010 From: "Prasenjit SEAL prasenjit.seal^^crm2.uhp-nancy.fr" To: CCL Subject: CCL: Problem in reading and writting a 3-dimensional matrix Message-Id: <-41063-100118091912-31992-a2w7CLyZGNSYvIJ4aplLeg###server.ccl.net> X-Original-From: Prasenjit SEAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Jan 2010 15:18:46 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] Hello, I am trying to read and write a simple 3-dimensional matrix of the order 2 x 2 x 2. However, although it takes 8 values but the values are not arranged in a proper order. Suppose, when I give the following values: 2.73484E-04 2.79487E-04 2.84006E-04 2.90279E-04 2.78942E-04 2.85085E-04 2.89712E-04 2.96132E-04 I want them to read as 2.73484E-04 2.79487E-04 2.84006E-04 2.90279E-04 2.78942E-04 2.85085E-04 2.89712E-04 2.96132E-04 However, it reads as 2.89712E-04 2.89712E-04 2.89712E-04 2.89712E-04 2.96132E-04 2.96132E-04 2.96132E-04 2.96132E-04 I have used the following fortran code (the do loop part is given) for reading and writting the 3-dimensional array read*, "Write the elements of the 3-D matrix row-wise" do n1=1,2 do n2=1,2 read*, (rho(n1,n2,n3), n3=1,2) enddo enddo print*,"Wrte the matrix elements row-wise" do n1=1,2 do n2=1,2 print*, (rho(n1,n2,n3), n3=1,2) enddo enddo I have also tried with 3 x 3 x 3 matrix and the result is the same. Could somebody help me out. Cheers, Prasenjit From owner-chemistry@ccl.net Mon Jan 18 10:16:01 2010 From: "Ciaran Murray ciaran.a.murray^-^nuim.ie" To: CCL Subject: CCL:G: Improving TD-DFT Results Message-Id: <-41064-100118101256-28741-Pn/20sOIH/5Lzl7SEFR2oQ|*|server.ccl.net> X-Original-From: "Ciaran Murray" Date: Mon, 18 Jan 2010 10:12:52 -0500 Sent to CCL by: "Ciaran Murray" [ciaran.a.murray%nuim.ie] Hi All, I've been calculating the spectroscopic properties of a suite of large heterocyclic aromatic compounds using DFT and TD-DFT and large Pople basis sets with loads of diffuse and polarised orbitals using Gaussian 03. The vibrational frequencies are nearly a perfect match to matrix-isolated experimental data (with some scaling of course) but the TD-DFT electronic spectra are a bit off from the experimental data. The error is between 0.1-0.2 eV, which is pretty good, but this corresponds to up to a 75 nm difference to experiment. I've tried different functionals and different Pople and Dunning basis sets but there is not much of an improvement. Is there anyway to improve these results? Is there some correction to be made to the excited state energies like Zero Point Energy correction in the ground state? Yours Gratefully, Ciaran Murray ciaran.a.murray--at--nuim.ie Dept. of Chemistry, NUI Maynooth, Co. Kildare, Ireland From owner-chemistry@ccl.net Mon Jan 18 10:54:01 2010 From: "Xiaohu Li xiaohuli914]|[gmail.com" To: CCL Subject: CCL: Problem in reading and writting a 3-dimensional matrix Message-Id: <-41065-100118105148-21447-rrEaF90sNQl/QqND2fmxUg{=}server.ccl.net> X-Original-From: Xiaohu Li Content-Type: multipart/alternative; boundary=0016e6d77d0303ecdd047d72408d Date: Mon, 18 Jan 2010 10:46:00 -0500 MIME-Version: 1.0 Sent to CCL by: Xiaohu Li [xiaohuli914|-|gmail.com] --0016e6d77d0303ecdd047d72408d Content-Type: text/plain; charset=ISO-8859-1 in fortran the fast index in the first index, so you need to loop n1 first instend of n3 which is the slowest varing index in fortran. this convention is different from C. On Mon, Jan 18, 2010 at 9:18 AM, Prasenjit SEAL prasenjit.seal^^ crm2.uhp-nancy.fr wrote: > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] > Hello, > > I am trying to read and write a simple 3-dimensional matrix of the order 2 > x 2 x 2. However, although it takes 8 values but the values are not arranged > in a proper order. > > Suppose, when I give the following values: > > 2.73484E-04 2.79487E-04 > 2.84006E-04 2.90279E-04 > 2.78942E-04 2.85085E-04 > 2.89712E-04 2.96132E-04 > > I want them to read as > > 2.73484E-04 2.79487E-04 > 2.84006E-04 2.90279E-04 > 2.78942E-04 2.85085E-04 > 2.89712E-04 2.96132E-04 > > However, it reads as > > 2.89712E-04 2.89712E-04 > 2.89712E-04 2.89712E-04 > 2.96132E-04 2.96132E-04 > 2.96132E-04 2.96132E-04 > > > I have used the following fortran code (the do loop part is given) for > reading and writting the 3-dimensional array > > read*, "Write the elements of the 3-D matrix row-wise" > do n1=1,2 > do n2=1,2 > read*, (rho(n1,n2,n3), n3=1,2) > enddo > enddo > print*,"Wrte the matrix elements row-wise" > do n1=1,2 > do n2=1,2 > print*, (rho(n1,n2,n3), n3=1,2) > enddo > enddo > > I have also tried with 3 x 3 x 3 matrix and the result is the same. > > Could somebody help me out. > > Cheers, > > Prasenjithttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e6d77d0303ecdd047d72408d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable in fortran the fast index in the first index, so you need to loop n1 first = instend of n3 which is the slowest varing index in fortran. this convention= is different from C.

On Mon, Jan 18, 201= 0 at 9:18 AM, Prasenjit SEAL prasenjit.seal^^crm2.uhp-nancy.fr <owner-chemistry.{=}.ccl.net> wrote:

Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr]
Hello,

I am trying to read and write a simple 3-dimensional matrix of the order 2 = x 2 x 2. However, although it takes 8 values but the values are not arrange= d in a proper order.

Suppose, when I give the following values:

=A02.73484E-04 =A02.79487E-04
=A02.84006E-04 =A02.90279E-04
=A02.78942E-04 =A02.85085E-04
=A02.89712E-04 =A02.96132E-04

I want them to read as

=A02.73484E-04 =A02.79487E-04
=A02.84006E-04 =A02.90279E-04
=A02.78942E-04 =A02.85085E-04
=A02.89712E-04 =A02.96132E-04

However, it reads as

2.89712E-04 =A02.89712E-04
2.89712E-04 =A02.89712E-04
2.96132E-04 =A02.96132E-04
2.96132E-04 =A02.96132E-04


I have used the following fortran code (the do loop part is given) for read= ing and writting the 3-dimensional array

read*, "Write the elements of the 3-D matrix row-wise"
do n1=3D1,2
=A0 =A0 =A0do n2=3D1,2
=A0 =A0 =A0 =A0 read*, (rho(n1,n2,n3), n3=3D1,2)
=A0 =A0 =A0enddo
enddo
=A0 =A0 print*,"Wrte the matrix elements row-wise"
do n1=3D1,2
=A0 =A0 =A0do n2=3D1,2
=A0 =A0 =A0 =A0 print*, (rho(n1,n2,n3), n3=3D1,2)
=A0 =A0 =A0enddo
enddo

I have also tried with 3 x 3 x 3 matrix and the result is the same.

Could somebody help me out.

Cheers,

Prasenjit



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016e6d77d0303ecdd047d72408d-- From owner-chemistry@ccl.net Mon Jan 18 12:15:00 2010 From: "Michel Petitjean petitjean.chiral]=[gmail.com" To: CCL Subject: CCL: Problem in reading and writting a 3-dimensional matrix Message-Id: <-41066-100118115254-20171-E0q8qCdrFQFobsmUgWleHQ{}server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 18 Jan 2010 16:50:58 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral{:}gmail.com] I compiled: real rho(2,2,2) do n1=3D1,2 do n2=3D1,2 read*, (rho(n1,n2,n3), n3=3D1,2) enddo enddo print*,"Wrte the matrix elements row-wise" do n1=3D1,2 do n2=3D1,2 print*, (rho(n1,n2,n3), n3=3D1,2) enddo enddo stop end I run with the following input: 2.73484E-04 2.79487E-04 2.84006E-04 2.90279E-04 2.78942E-04 2.85085E-04 2.89712E-04 2.96132E-04 and I indeed got the following output: Wrte the matrix elements row-wise 2.7348401E-04 2.7948699E-04 2.8400600E-04 2.9027899E-04 2.7894200E-04 2.8508500E-04 2.8971201E-04 2.9613200E-04 So it works. How did you declare rho ? Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral^^^gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.html ---------- Forwarded message ---------- > From: Prasenjit SEAL prasenjit.seal^^crm2.uhp-nancy.fr Date: 2010/1/18 Subject: CCL: Problem in reading and writting a 3-dimensional matrix To: "Petitjean, Michel " Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] Hello, I am trying to read and write a simple 3-dimensional matrix of the order 2 x 2 x 2. However, although it takes 8 values but the values are not arranged in a proper order. Suppose, when I give the following values: =A02.73484E-04 =A02.79487E-04 =A02.84006E-04 =A02.90279E-04 =A02.78942E-04 =A02.85085E-04 =A02.89712E-04 =A02.96132E-04 I want them to read as =A02.73484E-04 =A02.79487E-04 =A02.84006E-04 =A02.90279E-04 =A02.78942E-04 =A02.85085E-04 =A02.89712E-04 =A02.96132E-04 However, it reads as 2.89712E-04 =A02.89712E-04 2.89712E-04 =A02.89712E-04 2.96132E-04 =A02.96132E-04 2.96132E-04 =A02.96132E-04 I have used the following fortran code (the do loop part is given) for reading and writting the 3-dimensional array read*, "Write the elements of the 3-D matrix row-wise" do n1=3D1,2 =A0 =A0 =A0do n2=3D1,2 =A0 =A0 =A0 =A0 read*, (rho(n1,n2,n3), n3=3D1,2) =A0 =A0 =A0enddo enddo =A0 =A0 print*,"Wrte the matrix elements row-wise" do n1=3D1,2 =A0 =A0 =A0do n2=3D1,2 =A0 =A0 =A0 =A0 print*, (rho(n1,n2,n3), n3=3D1,2) =A0 =A0 =A0enddo enddo I have also tried with 3 x 3 x 3 matrix and the result is the same. Could somebody help me out. Cheers, Prasenjit -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0 =A0=A0 =A0=A0 =A0 From owner-chemistry@ccl.net Mon Jan 18 13:39:01 2010 From: "R Chowdhury crajib2009_+_yahoo.com" To: CCL Subject: CCL:G: Regarding Gaussian 09w Message-Id: <-41067-100118062706-1419-9gvB+HqdVaQcSl2ZX35r1Q_+_server.ccl.net> X-Original-From: "R Chowdhury" Date: Mon, 18 Jan 2010 06:27:01 -0500 Sent to CCL by: "R Chowdhury" [crajib2009!A!yahoo.com] Dear All, I would like to get some expert feedback on 3 questions regarding analysis in Gaussian 09w & Gaussview 1. Vibration analysis: Is there any way to fix (or constraint) some of the atoms of a nanotube ends, so that while vibration the constrained atoms will not change their position in animation. 2. I would like to extract the eigenvalues and eigenvectors of any system from Gaussian 09. Please could anybody give some hints on this. 3. Is there any way to apply external force on some of the atoms of a nanotube ends, so that after doing energy/ analysis the whole system will reach a buckled configuration. It would great, if any of the CCL experts provide some hints. Many thanks, Rajib From owner-chemistry@ccl.net Mon Jan 18 14:14:01 2010 From: "Sai Duan duansai[#]gmail.com" To: CCL Subject: CCL: Problem in reading and writting a 3-dimensional matrix Message-Id: <-41068-100118122823-32541-/qjuxz438JHSL5SdDog6YQ(_)server.ccl.net> X-Original-From: Sai Duan Content-Type: multipart/alternative; boundary="------------010406050605070604090400" Date: Mon, 18 Jan 2010 18:30:22 +0100 MIME-Version: 1.0 Sent to CCL by: Sai Duan [duansai:-:gmail.com] This is a multi-part message in MIME format. --------------010406050605070604090400 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I don't think this is the reason of wrong reads. Following is my test code. It work correctly. Code: Program main Real*8 rho(2,2,2) do n1=1,2 do n2=1,2 read (*,*) (rho(n1,n2,n3), n3=1,2) enddo enddo print*,"Wrte the matrix elements row-wise" do n1=1,2 do n2=1,2 print*, (rho(n1,n2,n3), n3=1,2) enddo enddo End Running: $ ./a.out 2.73484E-04 2.79487E-04 2.84006E-04 2.90279E-04 2.78942E-04 2.85085E-04 2.89712E-04 2.96132E-04 Wrte the matrix elements row-wise 2.734840000000000E-004 2.794870000000000E-004 2.840060000000000E-004 2.902790000000000E-004 2.789420000000000E-004 2.850850000000000E-004 2.897120000000000E-004 2.961320000000000E-004 Xiaohu Li xiaohuli914]|[gmail.com wrote: > in fortran the fast index in the first index, so you need to loop n1 > first instend of n3 which is the slowest varing index in fortran. this > convention is different from C. > > On Mon, Jan 18, 2010 at 9:18 AM, Prasenjit SEAL > prasenjit.seal^^crm2.uhp-nancy.fr > > wrote: > > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr > ] > Hello, > > I am trying to read and write a simple 3-dimensional matrix of the > order 2 x 2 x 2. However, although it takes 8 values but the > values are not arranged in a proper order. > > Suppose, when I give the following values: > > 2.73484E-04 2.79487E-04 > 2.84006E-04 2.90279E-04 > 2.78942E-04 2.85085E-04 > 2.89712E-04 2.96132E-04 > > I want them to read as > > 2.73484E-04 2.79487E-04 > 2.84006E-04 2.90279E-04 > 2.78942E-04 2.85085E-04 > 2.89712E-04 2.96132E-04 > > However, it reads as > > 2.89712E-04 2.89712E-04 > 2.89712E-04 2.89712E-04 > 2.96132E-04 2.96132E-04 > 2.96132E-04 2.96132E-04 > > > I have used the following fortran code (the do loop part is given) > for reading and writting the 3-dimensional array > > read*, "Write the elements of the 3-D matrix row-wise" > do n1=1,2 > do n2=1,2 > read*, (rho(n1,n2,n3), n3=1,2) > enddo > enddo > print*,"Wrte the matrix elements row-wise" > do n1=1,2 > do n2=1,2 > print*, (rho(n1,n2,n3), n3=1,2) > enddo > enddo > > I have also tried with 3 x 3 x 3 matrix and the result is the same. > > Could somebody help me out. > > Cheers, > > Prasenjit > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY ~~ ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST ~~ ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --------------010406050605070604090400 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I don't think this is the reason of wrong reads. Following is my test code. It work correctly.

Code:
      Program main
      Real*8 rho(2,2,2)
      do n1=1,2
           do n2=1,2
              read (*,*)  (rho(n1,n2,n3), n3=1,2)
           enddo
      enddo
          print*,"Wrte the matrix elements row-wise"
      do n1=1,2
           do n2=1,2
              print*, (rho(n1,n2,n3), n3=1,2)
           enddo
      enddo
      End

Running:
$ ./a.out
2.73484E-04  2.79487E-04
2.84006E-04  2.90279E-04
2.78942E-04  2.85085E-04
2.89712E-04  2.96132E-04
 Wrte the matrix elements row-wise
  2.734840000000000E-004  2.794870000000000E-004
  2.840060000000000E-004  2.902790000000000E-004
  2.789420000000000E-004  2.850850000000000E-004
  2.897120000000000E-004  2.961320000000000E-004


Xiaohu Li xiaohuli914]|[gmail.com wrote:
in fortran the fast index in the first index, so you need to loop n1 first instend of n3 which is the slowest varing index in fortran. this convention is different from C.

On Mon, Jan 18, 2010 at 9:18 AM, Prasenjit SEAL prasenjit.seal^^crm2.uhp-nancy.fr <owner-chemistry ~~ ccl.net> wrote:

Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr]
Hello,

I am trying to read and write a simple 3-dimensional matrix of the order 2 x 2 x 2. However, although it takes 8 values but the values are not arranged in a proper order.

Suppose, when I give the following values:

 2.73484E-04  2.79487E-04
 2.84006E-04  2.90279E-04
 2.78942E-04  2.85085E-04
 2.89712E-04  2.96132E-04

I want them to read as

 2.73484E-04  2.79487E-04
 2.84006E-04  2.90279E-04
 2.78942E-04  2.85085E-04
 2.89712E-04  2.96132E-04

However, it reads as

2.89712E-04  2.89712E-04
2.89712E-04  2.89712E-04
2.96132E-04  2.96132E-04
2.96132E-04  2.96132E-04


I have used the following fortran code (the do loop part is given) for reading and writting the 3-dimensional array

read*, "Write the elements of the 3-D matrix row-wise"
do n1=1,2
     do n2=1,2
        read*, (rho(n1,n2,n3), n3=1,2)
     enddo
enddo
    print*,"Wrte the matrix elements row-wise"
do n1=1,2
     do n2=1,2
        print*, (rho(n1,n2,n3), n3=1,2)
     enddo
enddo

I have also tried with 3 x 3 x 3 matrix and the result is the same.

Could somebody help me out.

Cheers,

Prasenjit





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--------------010406050605070604090400-- From owner-chemistry@ccl.net Mon Jan 18 14:49:01 2010 From: "Jens Spanget-Larsen spanget^ruc.dk" To: CCL Subject: CCL:G: question Message-Id: <-41069-100118062854-1635-jGbjy0dc6nQ7fnf+gCRD1A:_:server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Jan 2010 11:57:32 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget a ruc.dk] Dear Marjan Abedi! If I understand your question correctly, you wonder why the transition energy predicted with TD-DFT does not correspond to the prediction based on orbital energy differences. But the transition energy associated with promotion of en electron from an occupied MO (1) to an unoccupied MO (2) is not equal to the difference in energy between the two MOs, E2 - E1. In the simplest, qualitative formulation, we can write the transition energy as E2 - E1 - g(1,2), where g(1,2) represents the interaction between an electron in MO1 and an electron in MO2. Hence, the transition energy depends explicitly on electron interaction terms. So your observation may be explained by the different electron interaction terms involved in the transitions. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget++ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ marjan abedi marjan_abedi2004++yahoo.com wrote: > Sent to CCL by: "marjan abedi" [marjan_abedi2004(!)yahoo.com] > Hi > I am doing DFT calculations on copper complex with organic molecule with Gaussian 98 I could calculate the electronic structure with DFT method that the HOMO-LUMO gap is about 3 ev and the LUMO orbital is characterized by dx2-y2 with spin b. In the experimental data the electronic spectra for complex show a band as a shoulder in the visible region 650nm that ascribed to d-d transition (dxz, yz dx2-y2 ) of Cu(II) ion in similar complexes. I want to discuss on this band and calculate the spin-allowed doublet-doublet electronic transitions of the compound. So I use TDDFT method to calculation with > #p td=(nstates=6) ub3lyp/gen in route section and same basis sets that used for DFT. The TDDFT calculation show that the experimental band at 650 nm (1.9074 eV) originates in the HOMO-20(B) to LUMO(B). But in DFT calculation the HOMO-LUMO gap is about 3 ev and the HOMO-20(B) - LUMO(B) gap is 5.8 ev . Therefore I have hit to this problem and I can't understand and discuss this. Therefore I wonder if you mind calculating the compound.> > > From owner-chemistry@ccl.net Mon Jan 18 15:24:01 2010 From: "Prasenjit SEAL prasenjit.seal__crm2.uhp-nancy.fr" To: CCL Subject: CCL: How to calculate molecular density from charge density cube file Message-Id: <-41070-100118145631-21031-8DFBD935raF2BchqoJ9flA(a)server.ccl.net> X-Original-From: Prasenjit SEAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Jan 2010 20:56:20 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal[#]crm2.uhp-nancy.fr] Hello, Can any one tell me how I will get the molecular density of a particular molecule from the charge density cube file of the molecule? Cheers, Prasenjit From owner-chemistry@ccl.net Mon Jan 18 19:24:01 2010 From: "Brian Salter-Duke Brian.James.Duke..gmail.com" To: CCL Subject: CCL: Atomic Density Problem Message-Id: <-41071-100118165917-25216-cbV0rbiQ1m7TA+HWI8aHlA{:}server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 19 Jan 2010 07:29:32 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [Brian.James.Duke^-^gmail.com] On Mon, Jan 18, 2010 at 01:23:11PM +0100, Prasenjit SEAL prasenjit.seal#crm2.uhp-nancy.fr wrote: > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal**crm2.uhp-nancy.fr] > Hello, > > Thanks for the reply... > > However, that is not what I meant. I mean to say that suppose I have a > cube file of 'water' molecule containing the charge densities at each > grid point. Obviously, one has to specify the number of grid points > along with the grid spacing. Now I want to calculate the free atomic > densities (which has to be spherical in nature irrespective of the atom) > of the two H atoms and one O atom present in H2O using that molecular > cube file. How do you define the free atomic densities? These are for the "free" atoms and therefore have nothing to do with the results you have for the density of the water molecule, so you can not use that molecular cube file. You may have to do separate calculations for each atom. What do you want them for? Brian. > If any Fortran code is available which can read the molecular cube file > of a system and can calculate the spherically averaged free atomic > densities for the constituent atoms, then it would be very helpful. > > Cheers, > > Prasenjithttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke()bigbond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Mon Jan 18 21:33:00 2010 From: "xunlei ding dingxunlei%gmail.com" To: CCL Subject: CCL:G: coordinates in Gaussian Message-Id: <-41072-100115215319-15119-U3MnvKgIE5kfDo/sgxV0zQ : server.ccl.net> X-Original-From: xunlei ding Content-Type: multipart/alternative; boundary=001485f0acd017419f047d3e6f8f Date: Sat, 16 Jan 2010 09:56:52 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei##gmail.com] --001485f0acd017419f047d3e6f8f Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hi, You may try to find the " Standard orientation" in the Gaussian output file to see whether the coordinates below it is what you want. Ding 2010/1/15 yahoo.com > Dear All, > I have a molecular system consist of a number of molecules. When I do the > geometrical optimization in Gaussian, the molecule is also symmetrized an= d > the coordinates are changed when viewing in Gausview; however, when savin= g > the result as a new jgf file(in Gaiusview) the coordinates are saved the > same as the input (not symmetrized). I can use the symmetrization option= in > Gausview and use the reconnected Zmatrix but its a little time consuming= . > How can I directly do it in Gaussian? > > Thank you > > --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) Associate Research Professor of Physical Chemistry, Ph.D State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 --001485f0acd017419f047d3e6f8f Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Hi,
 
You may try to find the " Standard orientation" in the = Gaussian output file to see whether the coordinates below it is what you wa= nt.
 
Ding

 
2010/1/15 yahoo.com <owner-chemistry:_:ccl.net>
Dear All,
I have a molecular system consist of a numb= er of molecules. When I do the geometrical optimization in Gaussian, the mo= lecule is also symmetrized and the coordinates are changed when viewing in = Gausview; however, when saving the result as a new jgf  file(in Gaiusv= iew) the coordinates are saved the same as the input (not symmetrized). I c= an  use the symmetrization option in Gausview and  use the reconn= ected Zmatrix but its a little time consuming. How can I directly do it in = Gaussian?

Thank you




--
---------------------------------------------------= ---
Xun-Lei Ding (=B6=A1=D1=B8=C0=D7)
Associate Research Professor of= Physical Chemistry, Ph.D
State Key Lab for Struct. Chem. of Unstable and Stable Species
Institute= of Chemistry, Chinese Academy of Sciences
Zhongguancun North First Stre= et 2=A3=AC
Beijing 100190, P. R. China
Phone 86-10-62568330
Fax &n= bsp; 86-10-62559373
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