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dockonsurf / modules @ 2137c2de

Name Size
add_adsorbate_euler+dissociation.py 14.9 kB
ase_Fe1_Fe2.py 2.1 kB
calculate_rmsd 27.7 kB
clustering.py 962 Bytes
fe_change.sh 624 Bytes
generation_conformeres.py 4.5 kB
launch_cp2k_molecule_seule.sh 2.2 kB
launch_script+diss.sh 1.8 kB
mol_to_xyz.sh 960 Bytes
recenter_only.py 704 Bytes
recenter_periodicity.py 1.1 kB
script_add_adsorbate+diss.sh 2.8 kB
script_grandes_molecules+diss.sh 13.4 kB

Latest revisions

# Date Author Comment
2137c2de 01/20/2020 02:42 pm Carles Marti

Now modules/fe_change.sh works even if the surface file ends with blank lines; fixes #2727
76cb4d88 12/31/2019 06:17 pm 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 12/17/2019 10:05 am 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 11/27/2019 04:08 pm Carles Marti

Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676
a63e902e 11/27/2019 03:00 pm Carles Marti

Corrected a typo in the comments
459ffbcd 10/17/2019 04:43 pm 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 10/15/2019 11:58 am Marti Aliod Carles

The check for running jobs has changed from checking the job name to checking the job num id.
d3aa7749 10/09/2019 03:14 pm Marti Aliod Carles

fe_change.sh now expects a surface xyz file ended with a carriage return character
86112fec 10/02/2019 04:50 pm Marti Aliod Carles

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