From owner-chemistry@ccl.net Wed Jul 4 13:50:00 2012 From: "Ramachandran Chelat rcchelat,gmail.com" To: CCL Subject: CCL:G: molecular orbitals using NWChem Message-Id: <-47169-120704134844-28269-FFEWHUDsv8cjOHpKyb6cug[]server.ccl.net> X-Original-From: Ramachandran Chelat Content-Type: multipart/alternative; boundary=bcaec54c5392f9023104c404a328 Date: Wed, 4 Jul 2012 13:48:36 -0400 MIME-Version: 1.0 Sent to CCL by: Ramachandran Chelat [rcchelat]-[gmail.com] --bcaec54c5392f9023104c404a328 Content-Type: text/plain; charset=UTF-8 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|,|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>> **>> >> >> > --bcaec54c5392f9023104c404a328 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Guo,
Thank you for your kind reply.
I changed the input as you s= uggested 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 w= indow disappears.
It never retained even after changing the various options like=C2=A0 isosur= face value, range, orbitals=C2=A0 etc.
Could you please help me to solve= the problem.=C2=A0

Thanks
Ramachandran


On Tue, Jul 3, 2012 at 4:04 PM, Hao-Bo Guo guohaobo(_)gmail.com <owner-chemistry|,|ccl.net> 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
=C2=A0TITLE HOMO
=C2=A0 vectors O2.movecs
=C2=A0 LimitXYZ
=C2=A0-3.0 3.0 10
=C2=A0-3.0 3.0 10
=C2=A0-3.0 3.0 10
=C2=A0 spin total=C2=A0 # or alpha only as you did
=C2=A0 orbitals view; 1;8
=C2=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 =C2=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 =C2=A0 =C2=A0 0.000000 =C2=A0 =C2=A0 0.000000 =C2=A0 =C2=A0 0.000000
O =C2=A0 =C2=A0 0.000000 =C2=A0 =C2=A0 0.000000 =C2=A0 =C2=A0 1.300000
end
basis spherical
=C2=A0O library STO-3g
end

scf
vectors output O2.movecs
end

dplot
=C2=A0TITLE HOMO
=C2=A0 vectors O2.movecs
=C2=A0 LimitXYZ
=C2=A0-3.0 3.0 10
=C2=A0-3.0 3.0 10
=C2=A0-3.0 3.0 10
=C2=A0 spin alpha
=C2=A0 orbitals view; 1;8
=C2=A0 output homo.grd
end

task scf
task dplot

I have the .grd and .movecs files after the calculation. =C2=A0Which softwa= re (freely available) can plot the orbitals using these files?

Thanks
Ramachandran



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--bcaec54c5392f9023104c404a328-- 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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