Revision 3c26e233 dockOnSurf.sh

b/dockOnSurf.sh
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only_ads=false
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only_iso=false
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only_ref=false
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coads_box=false
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rmsd_threshold=0.01
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for i in $@; do
......
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      only_iso=true;;
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    -r|--only-refinement)
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      only_ref=true;;
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    -b|--coadsorption-box)
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      coads_box=true;;
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    -t=*|--rmsd-threshold=*)
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      rmsd_threshold="${i#*=}";;
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  esac
......
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  -a, --only-ads \t \t Carry out only adsorption part.
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  -i, --only-isolated \t \t Carry out only isolated molecules part.
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  -r, --only-refinement \t Carry out only refinement of adsorbed structure.
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  -b, --coadsorption-box \t When the surface file already contains an
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\t \t \t \t adsorbed molecule, it creates a box around it to
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\t \t \t \t prevent the second adsorbate to overlap the first.
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  -t=NUM, --rmsd-threshold=NUM \t Sets the threshold for the RMSD check of 
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\t \t \t \t different structures."
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  exit
......
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  	exit
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  fi
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  read -a list_atom_surf -p 'List of the atoms of the surface that can be adsorption sites '
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	if [ "$coads_box" = true ] ; then
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		read -a first_atom_ads1 -p 'Number of the adsorbate first atom in the surface file '
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	fi
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  echo '' 
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fi
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......
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if [ "$only_ref" = false ] ; then  
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  ### Adsorption de la molecule sur la surface
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  ${DockOnSurf_path}/modules/script_add_adsorbate+diss.sh $molecule $surface "${list_atom_1_mol[*]}" "${list_atom_2_mol[*]}" "${list_atom_surf[*]}" $coads_box $first_atom_ads1
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  ${DockOnSurf_path}/modules/script_add_adsorbate+diss.sh $molecule $surface "${list_atom_1_mol[*]}" "${list_atom_2_mol[*]}" "${list_atom_surf[*]}"
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  echo ' -- ADSORPTION SUTRUCTURES HAVE BEEN CALCULATED --'
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