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dockonsurf / modules @ a02c931d

# Date Auteur Commentaire
a02c931d 07/04/2020 20:40 Carles Marti

Added error handling functionality to input str2lst function
ec35a9b4 07/04/2020 15:19 Carles Marti

Refactoring code by creating modules directory and moving dos_input.py into it.
bf219e2b 01/04/2020 16:47 Carles Marti

Start v2 from scratch
3ba3c134 21/01/2020 15:14 Carles Marti

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
aa4d21b6 20/01/2020 14:43 Carles Marti

Merge branch 'master' of http://forge.cbp.ens-lyon.fr/git/dockonsurf
2137c2de 20/01/2020 14:42 Carles Marti

Now modules/fe_change.sh works even if the surface file ends with blank lines; fixes #2727
e75a54af 16/01/2020 11:32 Carles Marti

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
088cfdb3 07/01/2020 16:09 Carles Marti

Added the possibility to control the rmsd threshold in the check of different conformers
afd5ca03 06/01/2020 16:58 Carles Marti

Added the possibility to remove hydrogens during the calculation of RMSD of generated structures
76cb4d88 31/12/2019 18:17 Carles Marti

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
36f722bc 17/12/2019 10:05 Carles Marti

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.
454be75d 27/11/2019 16:08 Carles Marti

Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676
a63e902e 27/11/2019 15:00 Carles Marti

Corrected a typo in the comments
459ffbcd 17/10/2019 16:43 Marti Aliod Carles

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.
f43a1b4c 15/10/2019 11:58 Marti Aliod Carles

The check for running jobs has changed from checking the job name to checking the job num id.
d3aa7749 09/10/2019 15:14 Marti Aliod Carles

fe_change.sh now expects a surface xyz file ended with a carriage return character
86112fec 02/10/2019 16:50 Marti Aliod Carles

Initial files