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Allow 'surf_norm_vect' to accept the shortcut values '-x' '-y' '-z' equivalent to [-1, 0, 0] [0, -1, 0] [0, 0, -1] respectively. Changed When min_coll_height is not False collision is checked only by checking the height of the atoms.
Added log register for reading coordinates
Calculate the surface and molecule neighbors necessary for the collision check
Implemented the function that corrects collisions
Implemented the function to check for collisions between the adsorbate and the surface
Implemented the adsorption of conformers using euler angles to sample de orientational space.
Using a copy of the molecule to adsorb this way preventing successive translations when correcting adsorptions.
get_atom_coords function called without ctrs_list argument returns the coordinates of all atoms. It also allows ctrs_list to be an integer, thus returning the coordinate of index
Minor changes in variable names, order in functions, documentation and TODOS
Implemented function to compute the angle between two vectors.
Implement add_adsorbate function which extends the functionality of ase.build.add_adsorbate by enabling to change the z coordinate and the axis perpendicular to the surface.
Reformatting files, added documentation and getting rid of useless pieces of code.
Implemented get_atom_coords and vect_avg
Designed structure of screening.py
Corrected the extraction of MOI from a list of mol objects. For the plotting of graphs in clustering.py renamed boolean var debug to plot and added a check-backup on the plot file. Removed useless chunk on isolated.py.
Changed the import statement of internal libraries. Added logging to utilities.py
Carry out the screening of adsorbate coordinates on a surface
Created a module for each stage of DockOnSurf and started developing the isolated one