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Raise an error if no configurations are generated at the Screening stage. Corrected fallback value of collision_threshold option in input file.
Added else clause for the scheduler/batch_quequing_system. Changed fallback values. Adjust docstrings, reformat code and other stylistic changes.
Implemented the possibility to run calculations with VASP.
Implemented the possibility to exclude the molecule adsorption center from the collision detection.
Allow to customize adsorption height. Cleaned code.
Corrected bug when reading a false value of use_molec_file.
Updated keyword for turning on internal angles, from chemcat to internal.
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.
Implemented automatic detection of normal vector to the adsorption site with ASANN.
Corrected bug when comparing np.array with a list. Added TODO
Implemented new way to specify maximum jobs on running/pending status with only one keyword in the input. Reformat files.
Reformat file. inp_vars['relaunch_err'] is not retrieved as it's not implemented yet. Warning added when both collision height and collision threshold are turned False.
When retrieving the min_coll_height value, the check of the surf_norm_vect is done within the get_min_coll_height function. Removed deprecated get_screen_rmsd function.
collision_threshold can hold False value.
get_surf_norm_vect returns a normalized vector.
check_expect_val accepts a custom message.
Allow max_structures to take False value and assign infinity
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
removed unnecessary statements
Clean unnecessary old functions.
Allowed combination of more than one run_type (eg. isolated screening)
Corrected typos and letter case errors.
Corrected bug on type_max when no value was given
Implementes support for irene custom batch queuing system.
Reformatting file.
A maximum number of jobs can be set to, not only the pending ones, but now also the running ones.
Changed min_confs option name to pre_opt which accept a turn_false_answer, uff and mmff.
Updated error message.
Corrected log messages.
Included extra arguments for the proper working of special atoms.
Allow the user to choose a maximum number of structures to generate for the screening.
Implemented the possibility to dissociatie H atoms
Added punctuation marks at the end of every log messages.
Changed variable name cart_coords to cart_axes. Simplified the check if surface normal vector is a a pure cartesian axis.
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.
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
Included the ads_algo option in the input file. Fixed the default value of surface normal vector.
Check for options 'code', 'subm_script' is consistent with dry runs and running locally.
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
Added surf_file and molec_neigh_ctrs options to the input reading. Added hematite surface file to tests.
Reformatting files, added documentation and getting rid of useless pieces of code.
Included surf_file, molec_neigh_ctrs and surf_norm_vect as input parameters
str2list accepts float numbers if it is called with the func=float argument.
Changed the import statement of internal libraries. Added logging to utilities.py
Moved check_bak from calculation.py to utilities.py and try_command from dos_input.py to utilities.py
Added 'local' and 'none' as possible batch queuing systems, to run calculations on the local computer and to not carry out the calculation at all (for debugging purposes).
Added fallback value for project_name in dos_input.py. Included log messages for submitted jobs on calculation.py, added TODO tasks and changed documentation on all three files.
Removed 'project_name' from the mandatory options
Check if the input file of the code used for calculations is readable by the relevant library. Removed project_name from the mandatory options in Global.
Removed non used options from input and added new option on tests
Included 'project_name' on global mandatory options, corrected missing parentheses on str.capitalize method.
Added the submission of jobs to the SGE batch queuing system
Revert "Changed rmsd for rms"
This reverts commit 5571316d
Extended gen_confs documentation and incorporated the possibility to choose whether molecule conformers should be minimum energy conformers or not.
Changed rmsd for rms
Improved the documentation of the consequent docstrings
Included, the necessity to specify the molecule file to be adsorbed, in the input.
Moved the printing of input variables from dockonsurf.py to dos_input.py
Refactor file dos_input.py, every option is read and checked its value with a specific function for the purpose.Included the possibility to run the file as standalone program.
Increase of the input errors that get caught by the program, change how the logger is setup, its message format and how it is organized internally.
Reformat files and extend documentation
Moved the input file option from 'Global' to each relative section and changed the values of options to non-default ones.
Reformat and cleaning the code for improved readability and adequate it to PEP 8 conventions.
Include errors in the log, improved error handling by catching new errors.
Written the docstrings to document the code following the PEP 257 conventions
Possible errors are now printed in both the screen and the log file. More errors are now handled properly.
Added error handling functionality to input str2lst function
Refactoring code by creating modules directory and moving dos_input.py into it.