Geometry Optimization

Geometry optimization
Our goal
– optimized MgO
and heptane
system
Geometry optimization - intuition
Geometry optimization =
Energy minimization
Total
energy
It is a procedure of fitting the geometry of
the system to obtain the lowest possible
energy.
Total energy of the system is the kinetic
energy of all atoms and the potential energy
of interaction between atoms.
We obtain the potential energy simply using
forcefield.
Geometrical
parameters
bond stretching
deflection out of the plane
angle bending
torsion
electrostatic interactions
Van der Waals interactions
COMPASS forcefield – what’s going on?
Cleaved MgO
surface
Cleaved MgO surface
Let’s start with the cleaved MgO surface
from previous tutorial.
The geometry of the crystal close to the
crystal’s surface is different due to the
absence of the atoms above the crystal
surface  different interactions than in
bulk crystal.
Therefore the geometry of the surface
atoms must change and we have to
optimize it.
no atoms to
interact here
Forcite module – COMPASS forcefield
The Forcite module and COMPASS forcefield
will be used during all calculations.
Before we start ANY calculations we have to
assign forcefield types to atoms:
Click the Forcite button
on
the Modules toolbar and select Calculation.
On the Setup tab select Geometry
Optimization from the Task dropdown list.
Forcite module – COMPASS forcefield
Change tab to Energy. Here
select COMPASS from the Forcefield list
and click More... button.
In a new window uncheck Calculate
automatically checkbox and click Calculate
button. Close this window.
On the Energy tab select Forcefield
assigned from the Charges drop-down list.
Forcite module – COMPASS forcefield
We have to delete bonds in Al2O3 structure
 ionic crystal  no valence terms.
Hold down the ALT key
and double-click on any
bond.
Press the DELETE key.
What have we done?
We assigned atom types and charges to
Mg and O atoms.
We removed all bonds from the surface.
By deleting the bonds we switched off the
first five terms in COMPASS forcefield.
Culombic and Van der Waals interactions
are still active (the depend on charges and
atom types).
Fix atoms
Fix atoms on the surface.
Select 4 bottom layers and click Modify |
Constrains. Then check the Fix Cartesian
Position checkbox.
Click now Run buton to optimize surface.
Select Build | Symmetry | Supercell from the menu bar to open
the Supercell dialog. Increase the Supercell range to 7 for
both U and V. Click the Create Supercell button and close the
dialog.
Changing the periodicity of cell
We will use the Build Vacuum Slab Crystal
dialog to change the periodicity from 2D to
3D.
Select Build | Crystals | Build Vacuum
Slab...,
Change the Vacuum thickness to 30.0 and
click the Build button.
3D system – surface and 30 Å vacuum slab
Our molecule
Heptane
Measure:
one lentht
one angle
one torsion
Optimizing the molecule
Before we add heptane to our surface wy need
to optimize molecule’s geometry with the
Forcite package and the COMPASS forcefield.
Click the Forcite button
on
the Modules toolbar and select Calculation.
Ensure that Geometry optimization is your Task
and COMPASS is your forcefield.
On the energy tab click More... button, check
Calculate automatically checkbox and close this
window.
Click Run button to optimize heptane’s
geometry.
Adding the molecule to the MgO surface
We can copy the optimized heptane and
simple paste it to the optimized MgO
surface supercell with a vacuum slab.
Make the optimized heptane your active
document and select whole molecule:
Copy by clicking ctrl+c and make MgO
surface an active document.
Paste by clicking ctrl+v
Locate
undecane close
to the surface
Tip: use this buttons to
navigate the molecule
easly
Optimizing the layer
Finally we have to optimize geometry of
the whole system surface + molecule.
On the Forcite Calc. choose Geometry
Optimization and click More… and change
Max iterations: to 5000 steps.
In this example we use Smart Algorithm to
perform optimization, but in case of more
advanced calculations we should use
Conjugate Gradient or Steepest Descent.
Optimizing the layer
On the energy tab click More... button, and
ensure that Calculate automatically
checkbox is uncheckd and close this
window.
Click Run button to optimize the system.
Optimized
layer