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Added the possibility to carry out screening on a single conformer specified in a file. Rename variables.
Avoid to compare an array with a str leading to a warning.
Corrected bug: Due to molecule prealignment the molecule adsorption center coordinates were not anymore in there right position.
corrected bug: wrong assignement of norm_vect when set to 'auto'.
corrected bug: wrong import statement.
Raise FileNotFoundError when no calculations finished normally.
In align_molec, when the alignment center is at the baricenter of its neighbors, it uses the perpendicular vector to the nearest neighbor as target vector to align.
Made the deletion of dummy atom more robust
When sampling over euler angles, prealign molecules so that the neighbors to the adsorption point face the opposite direction to the surface.
Added log register to output the normal vector to the surface at the given site when calculated with asann. Added TODOs
Implemented automatic detection of normal vector to the adsorption site with ASANN.
Corrected bug when comparing np.array with a list. Added TODO
Implemented the possibility to check adsorbate-surface overlap with both methods at the same time, height and sphere collision. Changed function order.
Implemented the possibility to chose the surface H acceptors
Adapted error messages, reformat code for readability, removed TODO, refactor variables, updated docstrings.
Implemented Periodic Boundary Conditions.
user definition of the maximum value of the helicopter rotation angle in chemcat angles
Implemented Chemcat Angles
Added TODOS
Added the possibility to return the angle with the symbol if the normal vector to the other two is parsed as optional argument
Changed logger calls.
Corrected bug: Coordinates were not stored in the list in formats.py. Refactored screening.py file.
Changes in the logger warnings and info.
Added arguments due to the changes in collect_energies in formats.py
Change on function names and documentation.
Implemented check_finished_calcs which checks whether calculations are finished normally or not.
Simplified and made more pythonic the random selection of configurations when the number of generated ones is larger than the 'max_structures' value.
Included extra arguments for the proper working of special atoms.
Added logging entries at the beginning and end of each section.
Modified documentation
Add a warning when identical structures appear as a bug tester.
Prevent identical configurations in Euler rotations
Allow the user to choose a maximum number of structures to generate for the screening.
Moved adorption height to be a function argument.
Implemented the possibility to dissociatie H atoms
Corrected bug, evaluation of surface alone neighbors and molecule alone neighbors is done when no collision height is specified.
Added punctuation marks at the end of every log messages.
Corrected bug: When the same coordinate of the surface normal vector and the position of the atom had different signs was leading to no collision while it should.
Implemented function to select conformers according to the value of passed magnitudes. Acceptable magnitudes are 'moi' and 'energy'. Added log register for the number of generated structures.
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