Quantumchemistry, NWI-MOL406, Computer exercises, week 4

Hartree-Fock calculation of methane using NWCHEM and the MOPAC and MOLDEN pre and post processing tools

You can make NWCHEM (.nw) input files using: These tools are particularly useful for building the initial structure of your molecules. Of course, you can also make them by hand with an editor like nano. You may still have to edit the NWCHEM (.nw) input by hand to tailor them to your specific own needs.

The output of the calculation can be viewed with MOLDEN (orbitals, optimization history, etc.). It uses the file "ecce.out". To have NWCHEM generate this file, add a line: 

ecce_print ecce.out
to your NWCHEM input file (see a molden-generate input file).

The aim of this exercise is to familiarize with input generation, running of NWCHEM and output processing/viewing.

To this end, make a CH4 molecule in three different ways:

  1. Use the library in the MOPAC tool.
  2. Use the library in the Z-matrix editor of MOLDEN ("Substitute atom by Fragment" in Z-mat editor).
  3. Use the Z-matrix editor of MOLDEN (see the MOLDEN documentation for an explantion of the Z-matrix and its editor, e.g. select a fragment and adapt to make it into a CH4).
(BEWARE: outfile might end up on your home instead of your subdir.)

Just use a simple "STO-3G" basis. Run a geometry optimimization for all three cases, and compare the SCF energies that come out (How much do they differ?). You can find these energies (and much more) in the standard output, that you can redirect as: 
nwchem <INPUTFILE>.nw > <OUTPUTFILE>
Also find the orbital energies in the OUTPUTFILE, and for one of the three calculations, view the orbitals with MOLDEN.

Beware: Make the nwchem input file and run the calculation in a separate directory for each case. E.g., 

mkdir <DIR1>
cd <DIR1>
... do something ...
cd ..
mkdir <DIR2>
... etc.

During a geometry optimization the program will output a line that starts with "@" every iteration of the geometry optimization. You can read these lines without starting an editor with the command: 

grep @ nwch.nwout
This should give something like: 
grep @ water.output
@ Step       Energy      Delta E   Gmax     Grms     Xrms     Xmax   Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@    0     -74.96500275  0.0D+00  0.01192  0.00755  0.00000  0.00000      0.7
@    1     -74.96588623 -8.8D-04  0.00289  0.00237  0.02733  0.05095      0.8
@    2     -74.96590119 -1.5D-05  0.00002  0.00002  0.00169  0.00362      0.8
@    3     -74.96590119 -2.6D-09  0.00000  0.00000  0.00005  0.00010      0.9
@    3     -74.96590119 -2.6D-09  0.00000  0.00000  0.00005  0.00010      0.9
Try this with your output files. Also look in the OUTPUTFILE for the optimized geomtry (bond lengths, angles, dihedral angles) and explore what information you can extract with MOLDEN. Also find the Mulliken charges.

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