ASE Tutorials

  1. Introduction to ASE
  2. Getting Started
  3. Adsorption
  4. Transition States
  5. Error Estimation and Density of States

Error Estimation and Density of States

Contents

  1. Error Estimation Using BEEF
  2. Projected Density of States

Required Files

Obtain the required files by running:

on Sherlock:

cd $SCRATCH
wget http://chemeng444.github.io/ASE/BEEF_DOS/beef_dos_sherlock.tar
tar -xvf beef_dos_sherlock.tar

or on CEES:

cd ~/$USER
wget http://chemeng444.github.io/ASE/BEEF_DOS/beef_dos_cees.tar
tar -xvf beef_dos_cees.tar

This will create a folder called BEEF_DOS. Make a post on Piazza if you run into trouble.

Error Estimation Using BEEF

An example is provided in error_est.py. To obtain the error on a quantity, such as the adsorption energy, you must first load in the results from the .bee files for each calculation. For N2 dissociation that would be the calculations for N2 (g), the cluster, and the 2N*.

E_N2, E_ens_N2 = read_beef('folder_name/N2.bee')
E_cluster, E_ens_cluster = read_beef('folder_name/cluster.bee')
E_2N_cluster, E_ens_2N_cluster = read_beef('folder_name/2N_cluster.bee')

Simply take the standard deviation of the ensemble values to get the “error” on the adsorption energy. For example, the adsorption energy can be obtained using

E_2N = E_2N_cluster - E_cluster - E_N2

and then the standard deviation of the ensemble of 2N* adsorption energies can be obtained using

dE_2N = np.std(E_ens_2N_cluster - E_ens_cluster - E_ens_N2)

You may need to recalculate gas phase H2 and NH3 to obtain the associated .bee files.

Projected Density of States

To obtain the projected density of states, first submit the pdos.py script after changing the settings to match your system. Then follow the instructions here.