Reaction path and TS search using NEB¶
In this tutorial we will use the climbing-image Nudge Elastic Band method (NEB) to find the minimum energy reaction path and transition state of the following reaction:
Setting up the calculation¶
- Start ADFjobs1. in the menu bar select SCM → New input
This will open a new ADFInput window.
In this tutorial we use the DFTB engine with the GFN1-xTB model. This is a computationally fast method (which is why we use it in this tutorial) but it is not so accurate in predicting reaction energies. For better precision, using DFT is recommended.
Your ADFInput window should look like this:
When setting up an NEB calculation we need to specify two systems: the initial and final states of the reaction. The NEB algorithm will then generate a set of images by interpolating between the initial and final systems. This will be the initial approximation of the reaction path, which will be optimized during the NEB calculation.
- 2. Import the coordinates of the initial system: in the menu bar, select File → Import Coordinates… and select the file NEB_initial.xyz3. Create a new molecule-tab: in the menu bar, select Edit → New Molecule…4. Import the coordinates of the final system in the newly created moleucle tab: in the menu bar, select File → Import Coordinates… and select the file NEB_final.xyz
You can switch between the two molecule tabs by clicking on the tabs named Mol-1 and Mol-2 at the bottom of the molecule drawing area.
The order of the atoms in the initial and final system should be the same (if you provide an intermediate system, you should use a consistent atom-ordering for that too). The order of the atoms should be consistent because the images-interpolation algorithm maps the n-th atom of the initial system to the n-th atom of the final system.
You can see the indices of the atoms by clicking in the menu bar on View → Atom Info → Name → Show. It is possible to change the order of the atoms in the Coordinates panel (in the panel bar: Model → Coordinates) using the Move atom(s) option.
Now, go to the NEB details panel where we will set up the NEB calculation:
Your ADFInput window should look like this:
To improve the initial approximation of the reaction path you can optionally provide an intermediate system.
You can read more about the various NEB options in the AMS manual.
One important NEB option is the number of images. In case of problematic NEB path optimization convergence, using more images might help (note that the computation time increases with the number of images used).
Running the calculation and visualizing results¶
We are now ready to run the calculation:
- In ADFInput:1. In the menu bar, click on File → Save and give it the name “NEB_tutorial”2. In the menu bar, click on File → Run . This will bring the ADFJobs window to the front3. Wait for the calculation to finish. It should take just a few seconds
In the logfile you can monitor the progress of your NEB calculation:
- In ADFJobs:1. Select the job “NEB_tutorial” and in the menu bar click on SCM → Logfile. This will open the logfile
A NEB calculation consists of several steps, which are automatically executed one after the other:
first, the two end points (the initial and final molecules) are optimized (in the logfile, look for
Optimizing initial stateand
Optimizing final state)
then the NEB reaction path will be optimized (in the logfile, look for
NEB Path Optimization). During the reaction path optimization, the highest-energy image on the path will climb to the transition state
finally, a single point calculation for the TS is performed (in the logfile:
Final calculation for highest-energy image). If the option Characterize PES point is on, then the lowest-lying normal modes will be calculated in order to validate the TS (the TS should have exactly one imaginary frequency). Some information on the reaction path is printed at the end of the logfile:
NEB found a transition state! TS barrier height from the left 0.02576078 Hartree 16.165 kcal/mol 67.635 kJ/mol TS barrier height from the right 0.08632064 Hartree 54.167 kcal/mol 226.635 kJ/mol
Now, let’s visualize the reaction path computed by NEB:
- In ADFJobs:1. Select the job “NEB_tutorial” and, in the menu bar, click on SCM → Movie. This will open the ADFMovie module
In ADFMovie, you can click on play (or drag the slide-bar) so see the reaction happening. On right-hand side, the energy and gradients of the images in the NEB reaction path are plotted.
At the transition state geometry, we expect to have one imaginary frequency. Let’s visualize the normal modes of the TS geometry with ADFSpectra:
- In ADFMovie:1. click on SCM → Spectra. This will open the ADFSpectra
Here you will see the computed normal modes for the TS geometry. Notice that there is one negative frequency (imaginary frequency are shown as negative numbers).
- In ADFSpectra:1. In the table, click on the line with the negative frequency
The corresponding normal mode will be displayed in the molecule-visualization area. This normal mode gives you an idea of how the atoms are moving as they cross the transition state.