From owner-chemistry@ccl.net Wed Jul 4 15:17:01 2012 From: "Hao-Bo Guo guohaobo[A]gmail.com" To: CCL Subject: CCL:G: molecular orbitals using NWChem Message-Id: <-47170-120704151544-6885-yi6IhHwscVvNPO0Ls3UQNw*|*server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=f46d0438958d08719204c405db95 Date: Wed, 4 Jul 2012 15:15:35 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo:-:gmail.com] --f46d0438958d08719204c405db95 Content-Type: text/plain; charset=ISO-8859-1 Use "isosurface" instead of "orbital" in drawing method. The iso values could be set as, e.g., 0.02 for alpha and -0.02 for beta, etc. good luck! H.B. On Wed, Jul 4, 2012 at 1:48 PM, Ramachandran Chelat rcchelat,gmail.com < owner-chemistry _ ccl.net> wrote: > Dear Guo, > Thank you for your kind reply. > I changed the input as you suggested and I got the .cube file and loaded > this file in VMD. > However, when I select the orbital in the Drawing method, the molecule in > the main window disappears. > It never retained even after changing the various options like isosurface > value, range, orbitals etc. > Could you please help me to solve the problem. > > Thanks > Ramachandran > > > On Tue, Jul 3, 2012 at 4:04 PM, Hao-Bo Guo guohaobo(_)gmail.com < > owner-chemistry%x%ccl.net > wrote: > >> Hi Ramachandran, >> You can write the cube files, e.g., >> ###### >> # calculate the movecs file >> scf >> vectors output O2.movecs >> end >> # write cube files >> dplot >> TITLE HOMO >> vectors O2.movecs >> LimitXYZ >> -3.0 3.0 10 >> -3.0 3.0 10 >> -3.0 3.0 10 >> spin total # or alpha only as you did >> orbitals view; 1;8 >> output homo.cube >> end >> task scf >> task dplot >> ###### >> The Gaussian format cubes can then be visualized and plotted, e.g., with >> VMD. >> >> Hao-Bo Guo >> >> On Tue, Jul 3, 2012 at 2:30 PM, Ramachandran Chelat rcchelat|gmail.com < >> owner-chemistry:ccl.net> wrote: >> >>> >>> Sent to CCL by: "Ramachandran Chelat" [rcchelat a gmail.com] >>> Dear CCL friends, >>> Could you please explain how to plot the molecular orbitals using NWChem. >>> I used the following input for O2 molecule: >>> >>> start M06L-O2 >>> geometry >>> O 0.000000 0.000000 0.000000 >>> O 0.000000 0.000000 1.300000 >>> end >>> basis spherical >>> O library STO-3g >>> end >>> >>> scf >>> vectors output O2.movecs >>> end >>> >>> dplot >>> TITLE HOMO >>> vectors O2.movecs >>> LimitXYZ >>> -3.0 3.0 10 >>> -3.0 3.0 10 >>> -3.0 3.0 10 >>> spin alpha >>> orbitals view; 1;8 >>> output homo.grd >>> end >>> >>> task scf >>> task dplot >>> >>> I have the .grd and .movecs files after the calculation. Which software >>> (freely available) can plot the orbitals using these files? >>> >>> Thanks >>> Ramachandran* >>> * >>> E-mail to subscribers: CHEMISTRY:ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or use>>> **>>> >>> >>> >> > --f46d0438958d08719204c405db95 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Use "isosurface" instead of "orbital" in drawing method= .
The iso values could be set as, e.g., 0.02 for alpha and -0.02 for be= ta, etc.
good luck!
H.B.

On Wed, Jul 4, 2012 at 1:48 PM, Ramachandran Chelat rcchelat,gmail.com <owner-chemistry _ ccl.net>= wrote:
Dear Guo,
Thank you for your kind reply.<= br>I changed the input as you suggested and I got the .cube file and loaded= this file in VMD.
However, when I select the orbital in the Drawing method, the molecule in t= he main window disappears.
It never retained even after changing the various options like=A0 isosurfac= e value, range, orbitals=A0 etc.
Could you please help me to solve the p= roblem.=A0

Thanks
Ramachandran


On Tue, Jul 3, 2012 at 4:04 PM, Hao-Bo Guo guohaobo(_)gmail.com <owner-chemistry%x%ccl.n= et> wrote:
Hi Ramachandran,
You can write the cube f= iles, e.g.,
######
# calculate the movecs file
scf
vectors output O2.movecs
end
# write cube files
dplot
=A0TITLE HOMO
=A0 vectors O2.movecs
=A0 LimitXYZ
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0 spin total=A0 # or alpha only as you did
=A0 orbitals view; 1;8
=A0 output homo.cube
end
task scf
task dplot
######
The Gaussian format cubes can th= en be visualized and plotted, e.g., with VMD.

Hao-Bo Guo

On Tue, Jul 3, 2012 at 2:30 PM, Ramachandran Chelat = rcchelat|gmail.com <owner-chemistry:ccl.net> wrote:

Sent to CCL by: "Ramachandran =A0Chelat" [rcchelat a gmail.com]
Dear CCL friends,
Could you please explain how to plot the molecular orbitals using NWChem. I used the following input for O2 molecule:

start M06L-O2
geometry
O =A0 =A0 0.000000 =A0 =A0 0.000000 =A0 =A0 0.000000
O =A0 =A0 0.000000 =A0 =A0 0.000000 =A0 =A0 1.300000
end
basis spherical
=A0O library STO-3g
end

scf
vectors output O2.movecs
end

dplot
=A0TITLE HOMO
=A0 vectors O2.movecs
=A0 LimitXYZ
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0-3.0 3.0 10
=A0 spin alpha
=A0 orbitals view; 1;8
=A0 output homo.grd
end

task scf
task dplot

I have the .grd and .movecs files after the calculation. =A0Which software = (freely available) can plot the orbitals using these files?

Thanks
Ramachandran



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