add RESP script with nogui version
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script/RESP_ORCA.sh
Executable file
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script/RESP_ORCA.sh
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# A script to calculate RESP charge based on ORCA and Multiwfn
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# Written by Tian Lu (sobereva@sina.com), last update: 2022-Mar-8
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# Examples:
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# Calculating neutral singlet molecule in water: RESP_ORCA.sh H2O.xyz
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# Calculating anionic singlet molecule in water: RESP_ORCA.sh ani.pdb -1 1
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# Calculating neutral triplet molecule in ethanol: RESP_ORCA.sh nico.xyz 0 3 ethanol
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# Calculating neutral singlet molecule in ETHYL ETHANOATE: RESP_ORCA.sh nico.xyz 0 1 "ETHYL ETHANOATE"
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# Calculating cation doublet molecule in vacuum: RESP_ORCA.sh maki.xyz 0 2 gas
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#!/bin/bash
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#Set actual paths of ORCA and orca_2mkl utility here
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ORCA="/root/orca_6_0_0_shared_openmpi416_avx2/orca"
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orca_2mkl="/root/orca_6_0_0_shared_openmpi416_avx2/orca_2mkl"
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#Set number of CPU cores used in calculation here
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nprocs=12
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maxcore=1000
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keyword_opt="! B97-3c opt"
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keyword_SP="! B3LYP/G D3 def2-TZVP def2/J RIJCOSX"
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export inname=$1
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filename=${inname%.*}
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suffix=${inname##*.}
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### Parse arguments
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if [ $2 ];then
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echo "Net charge = $2"
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chg=$2
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else
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echo "Net charge was not defined. Default to 0"
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chg=0
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fi
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if [ $3 ];then
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echo "Spin multiplicity = $3"
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multi=$3
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else
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echo "Spin multiplicity was not defined. Default to 1"
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multi=1
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fi
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if [ "$4" ];then
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if [[ $4 == gas ]] ; then
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echo Calculations will be done in vacuum
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solvent=""
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else
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echo Solvent is $4
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solvent=$4
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fi
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else
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echo "Solvent name was not defined. Default to water"
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solvent="Water"
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fi
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### Convert current file to tmp.xyz
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Multiwfn_noGUI $1 > /dev/null << EOF
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100
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2
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2
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tmp.xyz
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0
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q
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EOF
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### Create input file for optimization (opt.inp)
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cat << EOF > opt.inp
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$keyword_opt
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%maxcore $maxcore
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%pal nprocs $nprocs end
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%geom Convergence loose end
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EOF
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if [[ $solvent != "" ]] ; then
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cat << EOF >> opt.inp
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%cpcm
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smd true
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SMDsolvent "$solvent"
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end
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EOF
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fi
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echo "* xyz $chg $multi" >> opt.inp
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awk '{if (NR>2) print }' tmp.xyz >> opt.inp
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echo "*" >> opt.inp
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rm tmp.xyz
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### Run optimization
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echo Running optimization task via ORCA...
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$ORCA opt.inp > opt.out
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if grep -Fq "ORCA TERMINATED NORMALLY" opt.out
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then
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echo Done!
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mv opt.xyz tmp.xyz
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rm opt.* opt_*
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else
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echo The optimization task has failed! Please check content of opt.out to find reason
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echo The script is terminated
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mv opt.out tmp.out
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rm opt.* opt_*
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mv tmp.out opt.out
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exit 1
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fi
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### Create input file for single point (SP.inp)
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cat << EOF > SP.inp
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$keyword_SP
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%maxcore $maxcore
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%pal nprocs $nprocs end
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EOF
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if [[ $solvent != "" ]] ; then
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cat << EOF >> SP.inp
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%cpcm
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smd true
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SMDsolvent "$solvent"
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end
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EOF
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fi
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echo "* xyz $chg $multi" >> SP.inp
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awk '{if (NR>2) print }' tmp.xyz >> SP.inp
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echo "*" >> SP.inp
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rm tmp.xyz
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### Run single point
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echo Running single point task via ORCA...
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$ORCA SP.inp > SP.out
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if grep -Fq "ORCA TERMINATED NORMALLY" SP.out
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then
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echo Done!
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else
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echo The single point task has failed! Please check content of SP.out to find reason
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echo The script is terminated
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mv SP.out tmp.out
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rm SP.* SP_*
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mv tmp.out SP.out
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exit 1
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fi
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### Convert to .molden file
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echo Running orca_2mkl...
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$orca_2mkl SP -molden > /dev/null
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#Field containing number of valence electrons of def2 pseudopotential basis set
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cat << EOF > Nval.txt
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[Nval]
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Rb 9
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Sr 10
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Y 11
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Zr 12
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Nb 13
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Mo 14
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Tc 15
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Ru 16
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Rh 17
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Pd 18
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Ag 19
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Cd 20
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In 21
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Sn 22
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Sb 23
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Te 24
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I 25
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Xe 26
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Cs 9
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Ba 10
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La 11
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Ce 30
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Pr 31
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Nd 32
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Pm 33
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Sm 34
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Eu 35
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Gd 36
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Tb 37
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Dy 38
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Ho 39
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Er 40
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Tm 41
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Yb 42
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Lu 43
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Hf 12
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Ta 13
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W 14
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Re 15
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Os 16
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Ir 17
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Pt 18
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Au 19
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Hg 20
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Tl 21
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Pb 22
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Bi 23
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Po 24
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At 25
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Rn 26
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EOF
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cat Nval.txt SP.molden.input > SP.molden
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### Calculate RESP charges
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echo Running Multiwfn_noGUI...
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Multiwfn_noGUI SP.molden -ispecial 1 > /dev/null << EOF
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7
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18
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1
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y
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0
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0
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q
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EOF
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### Finalize
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chgname=${1//$suffix/chg}
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mv SP.chg $chgname
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rm SP.* SP_* Nval.txt
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echo Finished! The optimized atomic coordinates with RESP charges \(the last column\) have been exported to $chgname in current folder
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echo Please properly cite Multiwfn_noGUI in your publication according to \"How to cite Multiwfn.pdf\" in Multiwfn package
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