README.txt 1.47 KB
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The geometry of a hydrogen atom in an interstitial site in a W sample was 
obtained as follows:
1.- A pristine W sample based in a bcc unit cell is build and energy 
    optimized by using lammps with the tersoff potentials.
2.  Then a H atom was inserted in a tetrahedral site into the 
    optimized W sample.
3.- The sample with a H atoms is energy optimized with lammps and 
    tersoff potentials.
4.- The obtained W-H sample is used to compute the DVs of:
            a) bcc W atom
            b) H atom in a tetrahedral instersitial site
            c) W atom as first nearest neighbor to the H atom
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            d) W atom as second nearest neighbor to the H atom
            
Attention need to be paid to the quip command line to compute the 
DVs for the hydrogenated W sample
The command line is:
     
     quip atoms_filename=interstitial_geometry.xyz descriptor_str="soap cutoff=3.0 l_max=4 n_max=4 atom_sigma=0.5 n_Z=2 Z={74 1} n_species=2 species_Z={74 1}"

where:
    n_Z=2 is defined for 2 species in the material sample, this value can be changed
          for material with more than 2 species.
    Z={74 1} this parameter is defined according to the charge of the species, here 
             we consider that W = 74 and H = 1. The order of these number needs to be
             defined according to the list of atoms defined in the xyz file. 
    n_species=2 this is the number of species in the material
    species_Z={74 1}  the order for this parameter is defined by the xyz file.