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1. Prepare a new detector using the results of a previous alignment.
2. Rerun the reconstruction over the data sets using this new detector. I suggest creating a new directory for each detector and alignment pass to keep things clean
   

   1.  For development and testing you may want to run over a single file just to test things.

      No Format
      java -server -jar hps-distribution-4.5-SNAPSHOT-bin.jar PhysicsRun2019ReReconForAlignment.lcsim -i <inputFileName> -DoutputFile=DetectorNamePassX/<outputFileName> -d <detectorName> -R 10103

   2.  For production at SLAC you can use the following for 10103:  

      No Format

      for i in {000..191}; do bsub -W 4:00 -R rhel60 -o outputs/HPS-PhysicsRun2019-v2-4pt5_Pass0/logs/hps_010103.evio.00"$i".log java -server -jar hps-distribution-4.5-SNAPSHOT-bin.jar PhysicsRun2019ReReconForAlignment_multiFiles.lcsim -DinputFileList=inputs/hps_010103.evio.00"$i"_InputFileList.txt -DoutputFile=outputs/HPS-PhysicsRun2019-v2-4pt5_Pass0/hps_010103.evio.00"$i" -d HPS-PhysicsRun2019-v2-4pt5 -R 10103 -e 1000; done

      and similarly for 10104: 

      No Format

      for i in {000..206}; do bsub -W 4:00 -R rhel60 -o outputs/HPS-PhysicsRun2019-v2-4pt5_Pass0/logs/hps_010104.evio.00"$i".log java -server -jar hps-distribution-4.5-SNAPSHOT-bin.jar PhysicsRun2019ReReconForAlignment_multiFiles.lcsim -DinputFileList=inputs/hps_010104.evio.00"$i"_InputFileList.txt -DoutputFile=outputs/HPS-PhysicsRun2019-v2-4pt5_Pass0/hps_010104.evio.00"$i" -d HPS-PhysicsRun2019-v2-4pt5 -R 10104 -e 1000; done

      Each set of jobs normally finishes within 6 minutes, so 600k events can be processed in slightly over 10 minutes.
      
      

3.  The resulting root files can be concatenated using the command-line utility: 

   No Format
   hadd HPS-PhysicsRun2019-v2-4pt5_Pass0.root outputs/HPS-PhysicsRun2019-v2-4pt5_Pass0/*.root

   and can be analyzed using a standard set of analysis macros to produce a series of canonical plots.

4.  millepede is able to accept multiple input binary files, so there is no need to concatenate them at this time.
   
   
5. Analysis proceeds as described on the SVT Detector Alignment page.
   
   
6. Once a new detector is built incorporating the new alignment proceed to the first step to iterate the procedure or test and validate a final detector. 

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