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 #!/bin/bash
 
 # This file is part of the ACTS project.
 #
 # Copyright (C) 2016 CERN for the benefit of the ACTS project
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
 # Absolute path of detray git root directory
 root_dir="$(git rev-parse --show-toplevel)"
 
 # Number of threads
 n_threads=1
 
 # Number of tracks per thread
 n_tracks_per_thread=1000
 
 # Min and Max log10 rk tolerance to iterate
 log10_min_rk_tol=-6
 log10_max_rk_tol=2
 
 # log10 rk tolerance for displaced track
 log10_rk_tol_dis=-6
 
 # log10 rk tolerance for jacobian comparison
 log10_rk_tol_jac=${log10_min_rk_tol}
 
 # log10 rk tolerance for covariance transport
 log10_rk_tol_cov=-4
 
 # Helix intersector tolerance [log10 in mm]
 log10_helix_tol=-3
 # Surface tolerance [log10 in mm]
 log10_on_surface_tol=-3
 
 # Monte-Carlo seed
 mc_seed=0
 
 # Skip the first phase
 skip_first_phase=false
 
 # Skip the second phase
 skip_second_phase=false
 
 # Verbose level
 verbose_level=1
 
 while getopts "hd:n:t:m:c:p:q:i:s:f:r:v:" arg; do
     case $arg in
         h)
             echo ""
             echo "Mandatory arguments"
             echo "-d <Directory of detray_integration_test_jacobian_validation>"
             echo ""
             echo "Optional arguments"
             echo "-n <Number of threads>"
             echo "-t <Number of tracks per thread>"
             echo "-m <log10(rk_error_tolerance_in_mm_for_displaced_tracks)>"
             echo "-c <log10(rk_error_tolerance_in_mm_for_covariance_transport)>"
             echo "-p <log10(min_rk_error_tolerance_in_mm)>"
             echo "-q <log10(max_rk_error_tolerance_in_mm)>"
             echo "-i <log10(intersection_tolerance_in_mm)>"
             echo "-s <Monte-Carlo seed>"
             echo "-f <Skip the first phase>"
             echo "-r <Skip the second phase>"
             echo "-v <Verbose level>"
             echo ""
             exit 0
         ;;
         d)
             dir=$OPTARG
         ;;
         n)
             n_threads=$OPTARG
         ;;
         t)
             n_tracks_per_thread=$OPTARG
         ;;
         m)
             log10_rk_tol_dis=$OPTARG
             echo "log10(rk_error_tolerance_in_mm_for_displaced_tracks): ${log10_rk_tol_dis}"
         ;;
         c)
             log10_rk_tol_cov=$OPTARG
         ;;
         p)
             log10_min_rk_tol=$OPTARG
             log10_rk_tol_jac=${log10_min_rk_tol}
         ;;
         q)
             log10_max_rk_tol=$OPTARG
         ;;
         i)
             log10_helix_tol=$OPTARG
             log10_on_surface_tol=$OPTARG
         ;;
         s)
             mc_seed=$OPTARG
         ;;
         f)
             skip_first_phase=$OPTARG
         ;;
         r)
             skip_second_phase=$OPTARG
         ;;
         v)
             verbose_level=$OPTARG
         ;;
         *)
             echo "Unknown option"
         ;;
     esac
 done
 
 echo "Directory of detray_integration_test_jacobian_validation: ${dir}"
 echo "Number of threads: ${n_threads}"
 echo "Number of tracks per thread: ${n_tracks_per_thread}"
 echo "log10(rk_error_tolerance_in_mm_for_covariance_transport): ${log10_rk_tol_cov}"
 echo "log10(min_rk_error_tolerance_in_mm): ${log10_min_rk_tol}"
 echo "log10(max_rk_error_tolerance_in_mm): ${log10_max_rk_tol}"
 echo "log10(intersection_tolerance_in_mm): ${log10_helix_tol}"
 echo "Monte-Carlo seed: ${mc_seed}"
 echo "Skip the first phase: ${skip_first_phase}"
 echo "Skip the second phase: ${skip_second_phase}"
 echo "Set the verbose level: ${verbose_level}"
 
 echo ""
 
 if [[ -z "${dir}" ]]; then
     echo "Option -d is missing"
     exit 1
 fi
 
 ##########################
 # RK tolerance iteration #
 ##########################
 
 if [[ "$skip_first_phase" = false ]] ; then
 
     echo "Starting rk toleracne iteration..."
 
     # Remove the old directories
     for (( i=0; i < ${n_threads}; ++i ))
     do
         rm -rf ${PWD}/thread_${i}
     done
     rm -rf ${PWD}/merged
 
     for (( i=0; i < ${n_threads}; ++i ))
     do
         n_skips=`expr ${i} \* ${n_tracks_per_thread}`
 
         command_rk_tolerance="${dir}/detray_integration_test_jacobian_validation \
         --output-directory=thread_${i} \
         --rk-tolerance-iterate-mode=true \
         --n-tracks=${n_tracks_per_thread} \
         --n-skips=${n_skips} \
         --log10-rk-tolerance-dis-mm=${log10_rk_tol_dis} \
         --log10-min-rk-tolerance-mm=${log10_min_rk_tol} \
         --log10-max-rk-tolerance-mm=${log10_max_rk_tol} \
         --log10-helix-tolerance-mm=${log10_helix_tol} \
         --log10-on-surface-tolerance-mm=${log10_on_surface_tol} \
         --mc-seed=${mc_seed} \
         --verbose-level=${verbose_level}"
         ${command_rk_tolerance} &
     done
     wait
 
     echo "Finished rk toleracne iteration"
 
 fi
 
 #####################################
 # Jacobi validation & Cov transport #
 #####################################
 
 if [[ "$skip_second_phase" = false ]] ; then
 
     echo "Starting Jacobi validation & Cov transport..."
 
     for (( i=0; i < ${n_threads}; ++i ))
     do
         n_skips=`expr ${i} \* ${n_tracks_per_thread}`
 
         command_jacobi_validation="${dir}/detray_integration_test_jacobian_validation \
         --output-directory=thread_${i} \
         --rk-tolerance-iterate-mode=false \
         --n-tracks=${n_tracks_per_thread} \
         --n-skips=${n_skips} \
         --log10-rk-tolerance-dis-mm=${log10_rk_tol_dis} \
         --log10-rk-tolerance-jac-mm=${log10_rk_tol_jac} \
         --log10-rk-tolerance-cov-mm=${log10_rk_tol_cov} \
         --log10-helix-tolerance-mm=${log10_helix_tol} \
         --log10-on-surface-tolerance-mm=${log10_on_surface_tol} \
         --mc-seed=${mc_seed} \
         --verbose-level=${verbose_level}"
         ${command_jacobi_validation} &
     done
     wait
 
     echo "Finished Jacobi validation & Cov transport"
 fi
 
 ###################
 # Merge Csv files #
 ###################
 
 echo "Starting merging Csv files..."
 
 file_names=()
 
 # Get the unique file names
 echo ""
 echo "/// Merged Csv file list ///"
 for full_name in ./thread_0/*; do
     # Only take csv format files
     if [[ "$full_name" == *".csv" ]];then
         name=$(basename -- "$full_name")
         file_names+=(${name})
         echo $name
     fi
 done
 echo ""
 
 output_dir=merged
 mkdir -p ${output_dir}
 # Merge the files
 for name in "${file_names[@]}"
 do
     arr=()
     for (( i=0; i < ${n_threads}; ++i ))
     do
         arr+=(thread_${i}/${name})
     done
     awk 'FNR==1 && NR!=1{next;}{print}' ${arr[@]} > ./${output_dir}/${name}
 done
 
 echo "Finished merging Csv files"
 
 ####################
 # Run ROOT Scripts #
 ####################
 
 cd ${output_dir}
 
 if [[ "$skip_first_phase" = false ]] && [[ "$skip_second_phase" = false ]]; then
 
     # Run rk_tolerance_comparision.C
     root -q "$root_dir"'/tests/tools/root/rk_tolerance_comparison.C+O('${log10_min_rk_tol}','${log10_max_rk_tol}')'
 
     # Run jacobian_histogram.C
     root -q -l "$root_dir"'/tests/tools/root/jacobian_histogram.C+O('${log10_min_rk_tol}')'
 
     # Run jacobian_comparison.C
     root -q -l "$root_dir"/tests/tools/root/jacobian_comparison.C+O
 
     # Run covariance_validation.C
     root -q -l "$root_dir"/tests/tools/root/covariance_validation.C+O
 
     elif [[ "$skip_first_phase" = true ]] && [[ "$skip_second_phase" = false
     ]]; then
 
     # Run covariance_validation.C
     root "$root_dir"/tests/tools/root/covariance_validation.C+O
 
     elif [[ "$skip_first_phase" = false ]] && [[ "$skip_second_phase" = true ]]; then
 
     # Run rk_tolerance_comparision.C
     root "$root_dir"'/tests/tools/root/rk_tolerance_comparison.C+O('${log10_min_rk_tol}','${log10_max_rk_tol}')'
 
     # Run jacobian_histogram.C
     root "$root_dir"'/tests/tools/root/jacobian_histogram.C+O('${log10_min_rk_tol}')'
 
 fi

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