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.
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.
Implemented get_atom_coords and vect_avg
Designed structure of screening.py
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.
Updated documentation
When clustering does not converge return every point as exemplar.
When a SDF mol file has no explicit hydrogen atoms it adds them before converting it to the adequate format.
Correct indentation for all submitted jobs
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
Moved check_bak from calculation.py to utilities.py and try_command from dos_input.py to utilities.py
Implemented function to read energies of a set of finished calculations. Implemented auxiliary function equivalent to bash tail. Reformat blank spaces and add TODO lines
Carry out the screening of adsorbate coordinates on a surface
Moved get_rmsd from isolated.py to clustering.py and changed its functionality, now it expects a list of mol objects instead of a single mol object with multiple conformers in it.
Added read_coords function to read coordinates resulting from finished calculations.
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).
Allow to convert, to rdkit.Mol object, xyz files containing multiple geometries, taking into consideration only the last one.
Reorganized job submission, every batch_q_sys submitting function is directly called from run_calc. Updated requirements.txt
Add hydrogen atoms before the conformer generation.
check_bak function checks if the target file_name is a directory or a file instead of checking if the name is present on the cwd. prep_cp2k works with the filename instead of the whole absolute filepath. Changed the warning message accordingly
Added hidden files to .gitignore and Changed Information displayed on the log for the MMFF Opt.
Unified all run_types inside the same function
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.
Fix: the number of the submitted jobs now matches the number of conforemer id.
Wait for all jobs to finish.
Changed get_queued_jobs_sge to get_jobs_status_sge which now returns a list of job status instead of a list that were in qw status.
Added init_dir variable
Changed the number of conformers for which to warn the user to be greater than 1 and not 0
Check if 'COORD_FILE_NAME' is defined in CP2K input file, and if not set to a default value. Fixed forgotten change of directory back to the initial directory.
Added a warning when a mol object with more than one conformer is parsed to the rdkit_mol_to_ase_atoms function. Extended confs_to_mol_list documentation
Removed 'project_name' from the mandatory options
The former create_bak_calc_dir function, now called check_bak, has generalized its behavior by checking if a file or directory exists and if so backs it up to a .bakX where X is a number such that bakX does not already exist.
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
Moved confs_to_mol_list function from isolated.py to formats.py module and generalised the calculations functions to be able to work with no matter which kind of calculation
Changed logging of formats.py from info to debug severity level.
Corrected argument of prep_iso and improved code documentation
Raise an error if clustering does not converge
Created calculation.py module and moved prep_run from isolated.py to it
Included printing the number of conformers generated and reformat documentation in isolated.py
Removed redundant UFF optimization, corrected type on conformer index in the writing of XYZ file and added debugging functionality for clustering.
Changed import statements and added shebang to increase portability
Extended documentation of run_isolated and prep_run
Implemented function to prepare the runs and reorganized the checks for using or not energy minima as conformers
Implemented clustering for Affinity matrices
Moved adapt_format to be available in all module and catching an error on get_rmsd when its argument is not valid.
Retrieve relevant magnitudes for clustering by calling the relative functions
mmff_opt_confs function allows to carry out single point energy calculations if max_iters is set to 0.
Split the generation of conformers and computation of their rmsd in two different functions. Added new functions to obtain the conformers moment of inertia and to optimize them using MMFF force field.
Changes rms to rmsd of new files
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 the way RMS between two conformers gets calculated. Now the RMS is performed by not considering hydrogens bonded to carbons but it does consider hydrogens bonded to all other atoms or not bonded at all.
Disabled the removal of hydrogens when using rdkit sdl mol file reader. Now, rdkit mol object contain hydrogens explicitly.
Moved logger to a global variable
Changed rmsd for rms
Created a module for each stage of DockOnSurf and started developing the isolated one
Improved the documentation of the consequent docstrings
Included, the necessity to specify the molecule file to be adsorbed, in the input.
Changed the read_coords.py module name to formats.py which states more clearly the purpose of the module.
Moved the printing of input variables from dockonsurf.py to dos_input.py
Created specific module for the reading of command-line arguments and transferred the relevant commands into it
Included tests to the implemented functions to check new commits don't mess things up
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.
Added empty init file to ease importing modules
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.
Include errors in the log, improved error handling by catching new errors.
Written the docstrings to document the code following the PEP 257 conventions
Commented out useless print statement
Reformat and cleaning the code for improved readability and adequate it to PEP 8 conventions.
Possible errors are now printed in both the screen and the log file. More errors are now handled properly.
Implemented the read coordinates module working to read xyz and mol files and obtain rdkit and ase objects to work with
Added error handling functionality to input str2lst function
Refactoring code by creating modules directory and moving dos_input.py into it.
Start v2 from scratch
In the case of launching dockOnSurf.sh with the only-refinement flag and that an analyse / relaunched_calculation directories already exists, the user is asked whether to delete or not these directories before the script puts itself to run in background; Solves #2729
Merge branch 'master' of http://forge.cbp.ens-lyon.fr/git/dockonsurf
Now modules/fe_change.sh works even if the surface file ends with blank lines; fixes #2727
Removed the possibility to remove hydrogens from the RMSD check. Changed also the RMSD check to not include atom permutations. This should speed up the RMSD check process, while distinguishing different H spatial position when important like hydrogen bond formation
Added the possibility to control the rmsd threshold in the check of different conformers
Added the possibility to remove hydrogens during the calculation of RMSD of generated structures
Sets the initial step number of the refinment calculation not to be conserved from the lower precision stage (ie. it starts always at 1); Fixes #2706
Added the possibility to carry out coadsorption. By adding the -b option, when the surface file already contains an adsorbed molecule, it creates a box around it to prevent the second adsorbate to overlap the first.
Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676
Corrected a typo in the comments
Now it is possible to call dockonsurf.sh script with options. These include: Usage: dockonsurf [OPTION]=PATTERN -h, --help display this help text and exit. -q=NUM, --max-qw=NUM allows a maximum of NUM jobs on 'qw' status. -a, --only-ads carry out only adsorption part. -i, --only-isolated carry out only isolated molecules part. -r, --only-refinement carry out only refinement of adsorbed structure.
The check for running jobs has changed from checking the job name to checking the job num id.
fe_change.sh now expects a surface xyz file ended with a carriage return character
Initial files