## page was renamed from AJMGrpOnly/teaching/electronic-structure/practical-graphical ## page was renamed from ajm/teaching/electronic-structure/practical-graphical <> = Visualising the Molecular Orbitals = Here we will use the NWChem program together with the [[http://www.avogadro.cc|Avogadro program]] to visualise the molecular orbitals. {{{#!wiki important Important You will need to have Avogadro installed on your laptop for this to work. And you will need to be able to download files from comanche to your laptop. * Avogadro is free and is cross-platform so install it on your laptop. * To download files from comanche you may use ''sftp'' from your laptop. Or use ''mobaxterm'' to do the file transfer for you. As comanche and poset share the home file system, you can just as well transfer the file from poset to your laptop. }}} == NWChem with DPLOT == {{{#!wiki important Important See the full description of the [[http://www.nwchem-sw.org/index.php/DPLOT|''DPLOT'' module on the NWChem site.]] }}} We will use the ''DPLOT'' module in NWChem to create Gaussian Cube files. These are really wasteful and simple-minded files that store graphical information on a grid of points. You set the quality of the grid, and then the code calculates the relevant quantity and stores it in the file. These files tend to be large. Worse, you will need a separate file for each orbitals! Here is an example for H$_2$O: [[attachment:H2O DPLOT example]] {{{ Memory 500 mb charge 0 Geometry units bohr O 0.0000000000 0.0000000000 0.0000000000 H1 -1.4536519600 0.0000000000 -1.1216873200 H2 1.4536519600 0.0000000000 -1.1216873200 End Basis "ao basis" spherical H library STO-3G O library STO-3G End Title "H2O STO-3G " scf Singlet vectors output h2o.movecs end dplot Title H2O vectors h2o.movecs LimitXYZ units Angstrom -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals 5 1 2 3 4 5 output density.cube end task scf energy task dplot }}} The DPLOT commands are as follows * ''Title H2O'' : this should be self-explanatory. * ''vectors h2o.movecs'': Here we have saved the molecular orbital coefficients in file ''h2o.movecs'', so these are now read in. * ''LimitXYZ'': This command is followed by three lines that specify the extent of the Cube grid as follows: [[attachment:LimitXYZ]] {{{ LimitXYZ Xmin Xmax Points_for_X Ymin Ymax Points_for_Y Zmin Zmax Points_for_Z }}} * Note that the grid does not have to be in the shape of a cube. It may be a rectangle. The important part is to make it large enough to enclose the molecular orbital and yet not too large that the spacing between points becomes too large. Units for the grid can be set using the ''units'' command. * ''Spin total'': Tells NWChem whether to include spin up or down or the sum. * ''GAUSSIAN'': Says to create a Cube file in the Gaussian format. * ''Orbitals'': Allows you to specify what to display: [[attachment:Orbitals]] {{{ ORBITALS [VIEW] For the density arising from orbitals 1 to 5 use: Orbitals 5 1 2 3 4 5 For the density arising from orbitals 4 and 5 only use: orbitals 2 4 5 For molecular orbital 3 use: Orbitals view 1 3 Note that molecular orbitals must be specified one at a time. So to visualise the first MO use: Orbitals view 1 1 }}} * ''OUTPUT'' : Specifies the name of the output file. * ''TASK DPLOT'' : Tells NWChem to run the DPLOT code. You can combine many DPLOT commands in a single file as follows: [[attachment:h2o-sto3g-dplot.nw]] {{{ Memory 500 mb charge 0 Geometry units bohr O 0.0000000000 0.0000000000 0.0000000000 H1 -1.4536519600 0.0000000000 -1.1216873200 H2 1.4536519600 0.0000000000 -1.1216873200 End Basis "ao basis" spherical H library STO-3G O library STO-3G End Title "H2O STO-3G " scf Singlet vectors output h2o.movecs end dplot Title H2O vectors h2o.movecs LimitXYZ -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals 5 1 2 3 4 5 output density.cube end task scf energy task dplot dplot Title H2O vectors h2o.movecs LimitXYZ -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals 1 5 output density-orb5.cube end task dplot dplot Title H2O vectors h2o.movecs LimitXYZ -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals view 1 5 output mo-5.cube end task dplot dplot Title H2O vectors h2o.movecs LimitXYZ -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals view 1 4 output mo-4.cube end task dplot dplot Title H2O vectors h2o.movecs LimitXYZ -4.0 4.0 40 -4.0 4.0 40 -4.0 4.0 40 spin total gaussian Orbitals view 1 3 output mo-3.cube end task dplot }}} Here we first calculate the density arising for all occupied MOs (1, 2, 3, 4 & 5), then the density from MO 5 only. This is followed by the actual MOs (3, 4 & 5). Run this as usual using: [[attachment:Run the job]] {{{ $ mpirun.mpich -np 1 nwchem h2o-sto3g-dplot.nw >& h2o-sto3g-dplot.out If it has run correctly you will have 5 Cube files in this directory. }}} = Avogadro = Now that we have the MOs, how do we display them? * Start Avogadro * File -> Open * Select Cube file: ''mo-3.cube''. * You should now see a stick figure of a water molecule. * Extensions -> Create Surfaces... * This gives you a new menu in a window. * Select: ''Surface Type'' : ''Cube file generated by NWChem'' * Select: ''Color By'' : ''Cube file generated by NWChem'' * Click on: ''Calculate'' * Do you get the following? * {{attachment:electronic-structure:avogadro-mo-3.png||width=600}} This MO is the third one and is occupied by two electrons. NWChem defines it as: [[attachment:MO 3]] {{{ Vector 3 Occ=2.000000D+00 E=-6.106389D-01 Symmetry=a' MO Center= -1.5D-01, -5.6D-16, -4.9D-32, r^2= 8.4D-01 Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function ----- ------------ --------------- ----- ------------ --------------- 4 0.605698 1 O py 6 -0.445851 2 H s 7 0.445851 3 H s }}} Can you see why this looks like the picture above?