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.
Changed collision_bottom option name to min_coll_height
Enabled the creation of calculation subdirectories and files when carrying out a dry run (batch_q_sys = None)
Read the number of conformers per magnitude from input file
Restructured 'get_surf_norm_vect' function to prevent recording an error to the log when 'x', 'y' or 'z' is passed as option value.
Added TODO. Added comments for visually separating functions belonging to different sections inside code.
Added 'euler' as default value for the ads_algo option in input.
Reordered the calling of functions.
Moved cluster_magns from Isolated to Screening section
Merge remote-tracking branch 'origin/v2' into v2 caused by ammending a commit which was already pushed. Taking local version.
Updated tests for reading norm_vect
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.
Included the ads_algo option in the input file. Fixed the default value of surface normal vector.
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
Check for options 'code', 'subm_script' is consistent with dry runs and running locally.
Minor changes in variable names, order in functions, documentation and TODOS
Implemented function to compute the angle between two vectors.
Function get_surf_norm_vect returns a numpy.ndarray instead of a list. Function get_pts_per_angle checks that the number of points per angle to be positive. Added TODO on get_moments_of_inertia
Changed input option from collision_bottom_z to collision_bottom
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.
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