Geometry Scan
Sometimes when studying a reaction mechanism is necessary to optimize all atoms except a
pair or more atoms. For example in a decarboxylation, the O-H distance elongates
--meanwhile a C-C elongates to--, due to an energy input (experimentaly heat), so all the
molecule reconfigures.
For this problem ORCA has enable a Geometry Scan utility. Let's perform a decarboxylation of a simple molecule:
First perform a geometry optimization for the malonic acid molecule.
Second with the relaxed geometry transform from cartesian coordinates to internal ones.
This can be done with
wxMacMolplt software.
Hint: with vim order the atoms.
In your xyz file put in order the atoms. This will allow wxMacMolplt to put in order the z-matrix.
2 H 0.981 0.014 0.484
3 C -0.436 -1.253 0.283
4 O -1.579 -1.546 0.017
In your xyz file put in order the atoms. This will allow wxMacMolplt to put in order the z-matrix.
2 H 0.981 0.014 0.484
3 C -0.436 -1.253 0.283
4 O -1.579 -1.546 0.017
Third run a Geometry Scan indicating the atoms that will stretch. In this case, we will start with the O-H relaxed distance 0.99 Å and finish with 1.99 Å. You can use either internal cordinates or gzmat that is the gaussian internal coordinates nomenclature.
Fourth generate the energy vs geometry step plot by using the output file *.relaxscanact.dat and the gnuplot software.
[emma@pople]$ vi geom_scan.inp
#ORCA Geometry Scan DFT calculation
! RKS PBE TZVP
! PMODEL TightSCF
! PAL8
! Opt
%method
Grid 2
FinalGrid 4
end
#Streching the O-H atom from 0.99 to 1.99
#7 steps all with geometry optimizations
%Geom Scan
B 0 1 = 0.99, 1.99, 7
# B - Bond between atom 0 and 1
end
end
#Type Charge Multiplicity
* int 0 1
O 0 0 0 0.000 0.0000 0.0000
H 1 0 0 0.997 0.0000 0.0000
C 1 2 0 1.345 108.51 0.0000
O 3 1 2 1.210 122.69 -175.57
C 3 1 2 1.542 116.74 7.1870
H 5 3 4 1.104 106.23 -81.437
H 5 6 3 1.096 106.23 -115.64
C 5 3 1 1.506 116.88 -23.401
O 8 5 3 1.226 124.77 26.252
O 8 5 3 1.348 112.78 -154.72
H 10 8 9 0.981 106.95 0.0000
*
! RKS PBE TZVP
! PMODEL TightSCF
! PAL8
! Opt
%method
Grid 2
FinalGrid 4
end
#Streching the O-H atom from 0.99 to 1.99
#7 steps all with geometry optimizations
%Geom Scan
B 0 1 = 0.99, 1.99, 7
# B - Bond between atom 0 and 1
end
end
#Type Charge Multiplicity
* int 0 1
O 0 0 0 0.000 0.0000 0.0000
H 1 0 0 0.997 0.0000 0.0000
C 1 2 0 1.345 108.51 0.0000
O 3 1 2 1.210 122.69 -175.57
C 3 1 2 1.542 116.74 7.1870
H 5 3 4 1.104 106.23 -81.437
H 5 6 3 1.096 106.23 -115.64
C 5 3 1 1.506 116.88 -23.401
O 8 5 3 1.226 124.77 26.252
O 8 5 3 1.348 112.78 -154.72
H 10 8 9 0.981 106.95 0.0000
*
[emma@pople]$/path/to/orca geom_scan.inp
Alternative for torque users
[emma@pople]$qsub orca-4.2.0.pbs
Generate the plot with the gnuplot script
[emma@pople]$gnuplot geom_scan.p
[emma@pople]$shotwell geom_scan.png
[emma@pople]$shotwell geom_scan.png
