Activity

From 06/11/2020 to 07/10/2020

07/01/2020

03:22 pm Revision 62a87644 (dockonsurf): Corrected log messages.
Carles Marti

06/30/2020

05:47 pm Revision ceaf7bea (dockonsurf): Reduced the molecule name length in the job_name.
Carles Marti
05:35 pm Revision 90819cc3 (dockonsurf): Included extra arguments for the proper working of special atoms.
Carles Marti
03:57 pm Revision 14f39d2a (dockonsurf): Added logging entries at the beginning and end of each section.
Carles Marti
03:15 pm Revision 91ae8d86 (dockonsurf): Modified documentation
Carles Marti
03:15 pm Revision 86cf3a38 (dockonsurf): Implemented refinement.py
Carles Marti
01:16 pm Revision d9167fea (dockonsurf): Add a warning when identical structures appear as a bug tester.
Carles Marti
01:07 pm Revision b2ffd8c5 (dockonsurf): Prevent identical configurations in Euler rotations
Carles Marti
12:01 pm Revision 7d97341d (dockonsurf): Allow the user to choose a maximum number of structures to genera...
Carles Marti
11:17 am Revision a581d3c1 (dockonsurf): Moved adorption height to be a function argument.
Carles Marti
11:08 am Revision b4b2f307 (dockonsurf): Implemented the possibility to dissociatie H atoms
Carles Marti

06/26/2020

01:47 pm Revision 3ccf0131 (dockonsurf): Corrected bug, evaluation of surface alone neighbors and molecule...
Carles Marti
01:45 pm Revision cc92f6ee (dockonsurf): Implemented add_special_atoms which Allows to use custom elements...
Carles Marti
09:19 am Revision 695dcff8 (dockonsurf): Added punctuation marks at the end of every log messages.
Carles Marti
09:08 am Revision 9c16a7e2 (dockonsurf): Changed variable name cart_coords to cart_axes. Simplified the ch...
Carles Marti
09:05 am Revision a4b57124 (dockonsurf): Corrected bug: When the same coordinate of the surface normal vec...
Carles Marti

06/25/2020

02:10 pm Revision bfe93f0d (dockonsurf): Implemented function to select conformers according to the value ...
Carles Marti
02:08 pm Revision 5fb01677 (dockonsurf): Allow 'surf_norm_vect' to accept the shortcut values '-x' '-y' '-...
Carles Marti
01:50 pm Revision 56290a13 (dockonsurf): Changed collision_bottom option name to min_coll_height
Carles Marti
01:50 pm Revision 1b54d787 (dockonsurf): Enabled the creation of calculation subdirectories and files when...
Carles Marti

06/24/2020

12:36 pm Revision af2bf62f (dockonsurf): Read the number of conformers per magnitude from input file
Carles Marti
12:20 pm Revision 3d56e566 (dockonsurf): Restructured 'get_surf_norm_vect' function to prevent recording a...
Carles Marti
12:18 pm Revision a7128ce1 (dockonsurf): Added TODO. Added comments for visually separating functions belo...
Carles Marti
11:37 am Revision ed5531ef (dockonsurf): Added 'euler' as default value for the ads_algo option in input.
Carles Marti
11:37 am Revision a765b11c (dockonsurf): Reordered the calling of functions.
Carles Marti
11:34 am Revision 8af49f6d (dockonsurf): Moved cluster_magns from Isolated to Screening section
Carles Marti
09:51 am Revision b695767e (dockonsurf): Merge remote-tracking branch 'origin/v2' into v2 caused by ammend...
Carles Marti
09:18 am Revision a3f617bc (dockonsurf): Updated tests for reading norm_vect
Carles Marti
09:17 am Revision 6430aa73 (dockonsurf): Added log register for reading coordinates
Carles Marti
08:20 am Revision bb55f47c (dockonsurf): Calculate the surface and molecule neighbors necessary for the co...
Carles Marti
08:15 am Revision a260d04d (dockonsurf): Implemented the function that corrects collisions
Carles Marti
08:13 am Revision 5f3f4b69 (dockonsurf): Implemented the function to check for collisions between the adso...
Carles Marti
08:10 am Revision 3ab0865c (dockonsurf): Implemented the adsorption of conformers using euler angles to sa...
Carles Marti

06/23/2020

11:39 am Revision 36d92f4f (dockonsurf): Using a copy of the molecule to adsorb this way preventing succes...
Carles Marti
11:35 am Revision a7c7b43e (dockonsurf): Included the ads_algo option in the input file. Fixed the default...
Carles Marti
11:32 am Revision 8fdff302 (dockonsurf): get_atom_coords function called without ctrs_list argument return...
Carles Marti
11:08 am Revision 821dca42 (dockonsurf): Check for options 'code', 'subm_script' is consistent with dry ru...
Carles Marti

06/17/2020

11:36 am Revision dadc6016 (dockonsurf): Minor changes in variable names, order in functions, documentatio...
Carles Marti
11:25 am Revision b4aef3d7 (dockonsurf): Implemented function to compute the angle between two vectors.
Carles Marti
11:18 am Revision d4bedc18 (dockonsurf): Function get_surf_norm_vect returns a numpy.ndarray instead of a ...
Carles Marti

06/16/2020

12:50 pm Revision 0dfa15ff (dockonsurf): Changed input option from collision_bottom_z to collision_bottom
Carles Marti
08:26 am Revision 1d22a086 (dockonsurf): Implement add_adsorbate function which extends the functionality ...
Carles Marti
08:23 am Revision dcc8bd46 (dockonsurf): Implement add_adsorbate function which extends the functionality ...
Carles Marti

06/15/2020

08:46 am Revision ab2d90e2 (dockonsurf): Added surf_file and molec_neigh_ctrs options to the input reading...
Carles Marti
08:44 am Revision a5cc42ff (dockonsurf): Reformatting files, added documentation and getting rid of useles...
Carles Marti

06/11/2020

07:14 pm Revision 12a12bdd (dockonsurf): Implemented get_atom_coords and vect_avg
Carles Marti
07:13 pm Revision f3d1e601 (dockonsurf): Designed structure of screening.py
Carles Marti
07:05 pm Revision c845c6f2 (dockonsurf): Included surf_file, molec_neigh_ctrs and surf_norm_vect as input ...
Carles Marti
06:20 pm Revision 4533134f (dockonsurf): str2list accepts float numbers if it is called with the func=floa...
Carles Marti
06:04 pm Revision 42fed021 (dockonsurf): Updated documentation
Carles Marti
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