Sample directory: band/Frags_COCu/
This example illustrates the usage of fragments in a BAND
calculation for analysis purposes. It takes two runs to do the DOS analysis in a fragment basis, and an extra two runs to get the deformation density with respect
to the fragment densities.
The setup involves first the computation of the free CO overlayer, which is to be absorbed on a Cu surface. To suppress (most of the) interactions between the CO molecules, i.e. to effectively get the molecular CO, the KSpace parameter is set to 1 (= no dispersion), and the lattice parameters are set so large that the CO molecules are far apart. The standard result file RUNKF is saved under the name 'CO.runkf'.
# ----------------------------- CO molecule -------------------------- $ADFBIN/band << eor Title The CO fragment Comment Technical Zero order k space integration Good real space integration accuracy Definitions of variables Features Lattice : 2D, large lattice vectors Unit cell : 2 atoms, 1x1, quasi molecular Basis : NO+STO w/ core End PRINT EIGENS Kspace 1 ! neglect dispersion Accuracy 4 Define bond=2.18 far=25 End Lattice ! CO molecules far apart far 0.0 0.0 far End Atoms C 0 0 0 End Atoms O 0 0 bond End BasisDefaults BasisType DZ Core Large End End Input eor mv RUNKF CO.runkf
Now we can use the result file to do a DOS analysis for CO on a copper surface treating the molecule as a fragment. With Fragment%Labels we assign names to the different symmetry orbitals. The Density-of-States analysis details are given with the keys DOS (energy grid, result file with DOS data) and, optionally, GrossPopulations and OverlapPopulations.
# ----------------------------- CO + Cu slab --------------------------
$ADFBIN/band << eor
Title Cu slab with CO adsorbed
Comment
Technical
Quadratic K space integration (low)
Good real space integration accuracy
Definitions of variables
Features
Lattice : 2D
Unit cell : 3 atoms, 1x1
Basis : NO+STO w/ core
Options : Molecular fragment
Analysis: DOS, PDOS, COOP
End
KSpace 3
Accuracy 4
! fragment specification
Fragment CO.runkf
1 1
2 2
Labels ! let us give them some labels
2Sigma
2Sigma*
1Pi_x
1Pi_y
3Sigma
1Pi_x*
1Pi_y*
3Sigma*
SubEnd
End
! use fragment basis in dos
DosBas
Fragment 1
End
DOS ! Analysis
File pdos.CO_Cu
Energies 500
Min -0.750
Max 0.300
End
GrossPopulations
3 2 ! All metal d states
Sum ! ALl metal sp states
3 0
3 1
EndSum
Frag 1 ! All CO states
Sum ! CO 1pi
FragFun 1 5
FragFun 1 6
EndSum
FragFun 1 7 ! CO 5-sigma
End
OverlapPopulations
Left ! Metal d with CO
3 2
Right
Frag 1
End
Define
dist=3.44
bond=2.18
End
Lattice
4.822 0.0
0.0 4.822
End
Atoms C
0 0 dist
End
Atoms O
0 0 dist+bond
End
Atoms CU
0.0 0.0 0.0
End
BasisDefaults
BasisType DZ
Core Large
End
End Input
eor
After this run we copy the computed DOS data from the DOS result file to standard output. We also save the restart file for later use.
echo Contents of DOS file cat pdos.CO_Cu mv RUNKF COCu.runkf
Next we want to know the deformation density with respect to the two fragments: 1) The CO molecule and 2) the bare Cu surface. We haven't done the bare Cu surface yet, so that is what happens next.
# ----------------------------- Cu slab -------------------------- $ADFBIN/band << eor Title Cu slab Comment Technical Quadratic K space integration (low) Good real space integration accuracy Definitions of variables Features Lattice : 2D Unit cell : 3 atoms, 1x1 Basis : NO+STO w/ core Options : End Kspace 3 Accuracy 4 Define dist=3.44 bond=2.18 End Lattice 4.822 0.0 0.0 4.822 End Atoms CU 0.0 0.0 0.0 End BasisDefaults BasisType DZ Core Large End End Input eor mv RUNKF Cu.runkf
Now we are all set to do our final calculation. We have the two fragment files CO.runkf and Cu.runkf, and the restart file COCu.runkf. Next we want to know the deformation density with respect to the two fragments: 1) The CO molecule and 2) the bare Cu surface. The visualization options like OrbitalPlot and Densityplot require a regular set of points (a grid). Here is how it works
# ----------------------------- CO + Cu slab restart -------------------------- $ADFBIN/band -n 1 << eor Title Cu slab with CO adsorbed (restart density plot) Kspace 3 Accuracy 4 Restart COCu.runkf & DensityPlot End Grid Type Coarse End DensityPlot scf End ! fragment specification Fragment CO.runkf 1 1 2 2 End Fragment Cu.runkf 1 3 End Define dist=3.44 bond=2.18 End Lattice 4.822 0.0 0.0 4.822 End Atoms C 0 0 dist End Atoms O 0 0 dist+bond End Atoms CU 0.0 0.0 0.0 End BasisDefaults BasisType DZ Core Large End End Input eor
This particular restart options does not work in parallel, hence the "-n 1" on the first line.The result of the last run is a file named TAPE41. Normally you would save that to COCu.t41
mv TAPE41 COCu.t41
and view it with adfview. On the TAPE41 file are now three fields shown in adfview as
being the deformation density of CO+Cu with
respect to the atoms, and the same for the two fragments CO and the Cu slab. In adfview you can add the fields of the two fragments, and then create another
field that holds the difference.
