Geometry Optimisation

Contents

Geometry Optimisation#

The geometry optimisation procedure is a standard theoretical tool used to determine molecular structure. The type of project Geometry Optimisation implemented in ASAP seeks to find the geometry of a particular arrangement of the atoms that represents a local or global minimum.
A Geometry optimisation project starts with the definition of the atomic structure. We refer the user to section Structure Modeling in ASAP for further information on ASAP structure builder/viewer interface.
After the atomic structure is defined, edit the type of project.
Workflow geom select
From the list of possible project types implemented in ASAP, select Geometry optimisation.
Workflow geom select widget

Then click on the Parameters icon to open the Geometry optimisation parameters widget.

Workflow geom param select
Workflow geom param widget

The project parameters that can be tuned are:

  • Optimisation method ASAP can make use of all the local optimisation algorithms available in ASE (https://wiki.fysik.dtu.dk/ase/ase/optimize.html): BFGS, BFGSLineSearch, LBFGS, LBFGSLineSearch, GPMin, MDMin and FIRE.

    Workflow geom param opt

    You can check the tick-box Optimise unit cell to optimise each direction of the unit cell. You can also check the tick-boxes corresponding to specific cell directions.

    Workflow geom param opt unit cell

    The Berny algorithm is currently being implemented and is not yet usable in production. It has been disabled for safety.

  • Max Force. Parameter to specify the convergence criterion. The force on all individual atoms should be less than the specified maximum force.

Click on the Calculator icon to select the computational engine to be used during geometry optimisation.

Workflow geom calc select
We refer the user to chapter Calculators for further information on ASAP available calculators.
Click on the Run icon to open Run widget. Then click on the Run button to submit the geometry optimisation calculation.
Workflow geom run select
Workflow geom run widget
We refer the user to chapter Configure ASAP runners for further information on computational resources configuration in ASAP.
After submitting a job (run), the tab Calculator output in Run widget shows the complete calculation output in real time.
Workflow geom run output calc

In addition, the tab Task output in Run widget shows relevant information of Geometry optimisation output in real-time.

Workflow geom run output task

Analysis#

When the calculation is completed, select Exit and analyse to open the analysis widget.

Workflow geom run exit analyse

Select Relaxation Analyse to visualise the energy and maximum force convergence as a function of the minimisation steps,

Workflow geom analyse widget
Workflow geom analyse energy step

Select the button View current image to visualise the converged atomic structure in any of the steps of the geometry optimisation.

Workflow geom analyse image

Select the button View all in 3D to visualise the geometry optimisation as an animation.

Workflow geom analyse animation
Contents