Compare revisions

63aba3ca · 5bdf94c3 · da021c43 · 34585070 · 7e2a2331 · d7445e7e
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,10 @@ ip6

 *.swp

+fieldmaps
+
+manifest.txt
+acts.txt
+acts2.txt
+
+materials-map.cbor
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,6 +6,7 @@ workflow:
    - if: '$CI_PIPELINE_SOURCE == "web"'
    - if: '$CI_PIPELINE_SOURCE == "webide"'
    - if: '$CI_COMMIT_BRANCH == "master"'
+    - if: '$CI_COMMIT_BRANCH == "acadia"'
    - if: '$CI_COMMIT_TAG'

 default:
@@ -30,10 +31,9 @@ default:

 stages:
  - config
-  - initialize
  - build
+  - test
  - docs
-  - test 
  - collect
  - finalize 
  - deploy
@@ -47,7 +47,7 @@ common:setup:
  script:
    - export JUGGLER_DETECTOR="athena"
    - |
-      if [[ "x${CI_PIPELINE_SOURCE}" == "xmerge_request_event"  || "$CI_COMMIT_BRANCH" == "master" ]]; then
+      #      if [[ "x${CI_PIPELINE_SOURCE}" == "xmerge_request_event"  || "$CI_COMMIT_BRANCH" == "master" ]]; then
        export JUGGLER_DETECTOR_VERSION="${CI_COMMIT_REF_NAME}"
        echo "BEAMLINE_CONFIG          = ${BEAMLINE_CONFIG}"
        echo "BEAMLINE_CONFIG_VERSION  = ${BEAMLINE_CONFIG_VERSION}"
@@ -55,35 +55,42 @@ common:setup:
        echo "JUGGLER_DETECTOR_VERSION = ${CI_COMMIT_REF_NAME}"
        echo "JUGGLER_DETECTOR_VERSION=$CI_COMMIT_REF_NAME" >> juggler.env
        echo "JUGGLER_DETECTOR=$JUGGLER_DETECTOR" >> juggler.env
-      fi
+        #fi
    - source setup/bin/env.sh && ./setup/bin/install_common.sh

 common:detector:
-  stage: initialize
-  needs: ["common:setup"]
+  stage: build
+  needs: 
+    - common:setup
  script:
-    - source .local/bin/env.sh && build_detector.sh
-    - mkdir_local_data_link sim_output
+    #- source .local/bin/env.sh && build_detector.sh
+    - build_detector.sh
    - mkdir -p results
    - mkdir -p config
    - mkdir -p doc
    - mkdir -p geo
    - print_env.sh

-compile:
+build:simple:
  stage: build
-  needs:
-    - ["common:detector"]
  script:
    - mkdir -p build && cd build && cmake ../. -DCMAKE_INSTALL_PREFIX=/usr/local && make -j20 && make install  && cd ..
    - echo "Build successful."

+
 .views:
  stage: docs
+  tags:
+    - phy-scratch
+  before_script:
+    - source .local/bin/env.sh
+    - env
+    - pip3 install psutil
  needs:
    - ["common:detector"]

 include:
+  - local: 'views/generate_prim_files.yml'
  - local: 'views/view1.yml'
  - local: 'views/view2.yml'
  - local: 'views/view3.yml'
@@ -94,20 +101,67 @@ include:
  - local: 'views/view13.yml'
  - local: 'views/view14.yml'
  - local: 'views/view15.yml'
+  - local: 'views/view20.yml'

 dump_geometry:
  stage: test
  needs:
    - common:detector
  script:
-   - echo "dumping geometry"
-   - mkdir -p geo
-   ## full geo with downstream beamline
-   - dd_web_display --output geo/detector_geo_full.root ${DETECTOR_PATH}/athena.xml
-   ## only central detector geo
-   - sed -i '/forward_ion_beamline/d' ${DETECTOR_PATH}/athena.xml
-   - sed -i '/far_forward/d' ${DETECTOR_PATH}/athena.xml
-   - dd_web_display --output geo/detector_geo.root ${DETECTOR_PATH}/athena.xml
+    - echo "dumping geometry"
+    ## DEBUG
+    - echo "LD_LIBRARY_PATH - $LD_LIBRARY_PATH"
+    - echo "PATH - $PATH"
+    - print_env.sh
+    ## DEBUG
+    - mkdir -p geo
+    - |
+      sed -i -e '/<detectors>/,/<\/detectors>/d' ${DETECTOR_PATH}/compact/tracking_config*.xml
+      mv ${DETECTOR_PATH}/compact/display_geoviewer.xml ${DETECTOR_PATH}/compact/display.xml
+      for xml in ${DETECTOR_PATH}/compact/subsystem_views/*.xml; do
+        echo $xml
+        geo_name=`basename $xml .xml`_geo.root
+        cp $xml ${DETECTOR_PATH}/geo.xml
+        dd_web_display --output geo/${geo_name} ${DETECTOR_PATH}/geo.xml
+      done
+    ## Lower-resolution display of the pfRICH sensors for global views
+    - sed -i 's/_default"\/>/_lores"\/>/' ${DETECTOR_PATH}/compact/pfrich.xml
+    ## full geo with downstream beamline
+    - dd_web_display --output geo/detector_geo_full.root ${DETECTOR_PATH}/athena.xml
+    ## only central detector geo
+    - sed -i '/forward_ion_beamline/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/beampipe_hadron_B0/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/B0_/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/far_forward_offM/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/far_forward_detectors/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/roman_pots/d' ${DETECTOR_PATH}/athena.xml
+    - sed -i '/inner_vacuum_FF_magnets/d' ${DETECTOR_PATH}/athena.xml
+    - dd_web_display --output geo/detector_geo.root ${DETECTOR_PATH}/athena.xml
+    ## print some useful output
+    - |
+      echo "Geometry viewer at:"
+      echo "https://eic.phy.anl.gov/geoviewer/index.htm?file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/${CI_JOB_ID}/artifacts/raw/geo/detector_geo_full.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY290;ROTZ350;trz0;trr0;ctrl;all"
+      echo " - Central detector view at: "
+      echo "https://eic.phy.anl.gov/geoviewer/index.htm?file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/${CI_JOB_ID}/artifacts/raw/geo/detector_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom120;ROTY320;ROTZ340;trz0;trr0;ctrl;all"
+      for xml in ${DETECTOR_PATH}/compact/subsystem_views/*.xml; do
+        geo_name=`basename $xml .xml`_geo.root
+        echo " - Subsystem view for `basename $xml .xml` at:"
+        echo "   https://eic.phy.anl.gov/geoviewer/index.htm?file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/${CI_JOB_ID}/artifacts/raw/geo/${geo_name}?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY320;ROTZ340;trz0;trr0;ctrl;all"
+      done
+
+detector_documentation:
+  stage: docs
+  needs:
+    - common:detector
+  script:
+    - mkdir -p doc
+    - bash bin/build_documentation | tee doc/detector.md
+      #- |
+      #  xmllint --format --xpath '//comment/text()' ${DETECTOR_PATH}/athena.xml | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee  doc/detector.md
+      #  xmllint --format --xpath '//comment/text()' ${DETECTOR_PATH}/ip6/definitions.xml | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee -a doc/detector.md || true
+      #  for afile in ${DETECTOR_PATH}/compact/*.xml ; do
+      #    xmllint --format --xpath '//comment/text()' ${afile} | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee -a doc/detector.md || true
+      #  done

 report:
  stage: finalize
@@ -122,12 +176,14 @@ report:
    - view_13
    - view_14
    - view_15
+    - view_20
    - dump_constants
    - dump_geometry
-    - convert_to_gdml
+    - dump_gdml
  script:
    - pip3 install jinja2 &&  ls -lrth
    - ./bin/make_images > doc/dawn_views.md
+    - echo "Geometry viewer at https://eic.phy.anl.gov/geoviewer/index.htm?file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/${CI_JOB_ID}/artifacts/raw/geo/detector_geo_full.root?job=finalize&item=default;1&opt=clipxyz;transp30;zoom75;ROTY290;ROTZ350;trz0;trr0;ctrl;all&"

 dump_constants:
  stage: test
@@ -141,34 +197,61 @@ overlap_check_tgeo:
  needs: 
    - ["common:detector"]
  script:
+    ## disable fibers in ECAL for normal overlap check
+    - sed -i '/<fiber/,+6d' ${DETECTOR_PATH}/compact/ecal_barrel_interlayers.xml
+    - sed -i '/<fiber/,+4d' ${DETECTOR_PATH}/ip6/far_forward/ZDC_Ecal_WSciFi.xml
    - checkOverlaps -c ${DETECTOR_PATH}/athena.xml  | tee doc/overlap_check_tgeo.out 
    - echo "$(cat doc/overlap_check_tgeo.out | grep ovlp | wc -l) overlaps..."
    - if [[ "$(cat doc/overlap_check_tgeo.out | grep ovlp | wc -l)" -gt "0" ]] ; then echo "Overlaps exist!" && false ; fi

-overlap_check_geant4:
+overlap_check_geant4:full_fast:
  stage: test
  needs: 
    - ["common:detector"]
  script:
+    ## disable fibers in ECAL for normal overlap check
+    - sed -i '/<fiber/,+6d' ${DETECTOR_PATH}/compact/ecal_barrel_interlayers.xml
+    - sed -i '/<fiber/,+4d' ${DETECTOR_PATH}/ip6/far_forward/ZDC_Ecal_WSciFi.xml
+    ## reduce the number of fibers in Hadron EMCal for overlap check
+    ## not needed, as we are running with a different setup now
+    #- sed -i 's/radius="EcalEndcapP_FiberRadius"/radius="EcalEndcapP_FiberRadius*10"/' ${DETECTOR_PATH}/compact/ci_ecal_scfi.xml
    - python scripts/checkOverlaps.py -c ${DETECTOR_PATH}/athena.xml | tee doc/overlap_check_geant4.out
    - echo "$(cat doc/overlap_check_geant4.out | grep GeomVol1002 | wc -l) overlaps..."
    - if [[ "$(cat doc/overlap_check_geant4.out | grep GeomVol1002 | wc -l)" -gt "0" ]] ; then echo "Overlaps exist!" && false ; fi

-convert_to_gdml:
+## TODO: add real full overlap check as child pipeline to run on branches only
+
+overlap_check_geant4:inner_detector:
+  stage: test
+  needs: 
+    - ["common:detector"]
+  script:
+    - cp ${DETECTOR_PATH}/compact/subsystem_views/inner_detector.xml ${DETECTOR_PATH}/inner_detector.xml
+    - python scripts/checkOverlaps.py -c ${DETECTOR_PATH}/inner_detector.xml | tee doc/overlap_check_geant4.out
+    - echo "$(cat doc/overlap_check_geant4.out | grep GeomVol1002 | wc -l) overlaps..."
+    - if [[ "$(cat doc/overlap_check_geant4.out | grep GeomVol1002 | wc -l)" -gt "0" ]] ; then echo "Overlaps exist!" && false ; fi
+
+dump_gdml:
  stage: test
  needs: 
    - ["common:detector"]
  script:
    - mkdir -p geo
-    - python scripts/convert_to_gdml.py --compact ${DETECTOR_PATH}/athena.xml --output geo/athena.gdml
+    - |
+      python scripts/convert_to_gdml.py --compact ${DETECTOR_PATH}/athena.xml --output geo/athena.gdml
+      for xml in ${DETECTOR_PATH}/compact/subsystem_views/*.xml; do
+        cp $xml ${DETECTOR_PATH}/geo.xml
+        gdml_name=`basename $xml .xml`.gdml
+        python scripts/convert_to_gdml.py --compact ${DETECTOR_PATH}/geo.xml --output geo/${gdml_name}
+      done

 tracking_geometry_debug:
  stage: test
-  allow_failure: true
  needs: 
    - ["common:detector"]
  script:
    - root -b -q "scripts/test_ACTS.cxx+(\"${DETECTOR_PATH}/athena.xml\")" | tee geo/tracking_geometry_debug.out 
+    - ./bin/acts_geo_check geo/tracking_geometry_debug.out

 detector:config_testing:
  stage: test
@@ -186,28 +269,6 @@ benchmarks:detector:
  trigger:
    project: EIC/benchmarks/detector_benchmarks
    strategy: depend
-  needs: ["overlap_check_tgeo","overlap_check_geant4","report"]
-  allow_failure: true
-
-
-    #benchmarks:reconstruction:
-    #  stage: deploy
-    #  variables:
-    #    JUGGLER_DETECTOR: "$JUGGLER_DETECTOR"
-    #    JUGGLER_DETECTOR_VERSION: "$JUGGLER_DETECTOR_VERSION"
-    #  trigger:
-    #    project: EIC/benchmarks/reconstruction_benchmarks
-    #    strategy: depend
-    #  needs: ["env","overlap_check_tgeo","overlap_check_geant4","report"]
-    #  
-    #
-    #benchmarks:physics:
-    #  stage: deploy
-    #  variables:
-    #    JUGGLER_DETECTOR: "$JUGGLER_DETECTOR"
-    #    JUGGLER_DETECTOR_VERSION: "$JUGGLER_DETECTOR_VERSION"
-    #  trigger:
-    #    project: EIC/benchmarks/physics_benchmarks
-    #    strategy: depend
-    #  needs: ["env","overlap_check_tgeo","overlap_check_geant4","report"]
-
+  needs: 
+    - overlap_check_geant4:full_fast
+    - common:detector
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
+
+# CMP0074: find_package() uses <PackageName>_ROOT variables
+cmake_policy(SET CMP0074 NEW)
+
 PROJECT(athena
  VERSION 0.0.1
  LANGUAGES CXX
@@ -6,20 +10,51 @@ PROJECT(athena
  )

 set(CMAKE_CXX_STANDARD 17)
-find_package( DD4hep REQUIRED COMPONENTS DDCore DDG4 )
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror")

-find_package(Acts REQUIRED COMPONENTS Core PluginIdentification PluginTGeo PluginDD4hep )
+find_package(DD4hep REQUIRED COMPONENTS DDCore DDG4)
+find_package(ActsDD4hep)
+if(ActsDD4hep_FOUND)
+  add_compile_definitions(USE_ACTSDD4HEP)
+  set(ActsDD4hep ActsDD4hep::ActsDD4hep)
+else()
+  find_package(Acts REQUIRED COMPONENTS Core PluginIdentification PluginTGeo PluginDD4hep)
+  set(ActsDD4hep ActsCore ActsPluginDD4hep)
+endif()
+find_package(fmt REQUIRED)

 #-----------------------------------------------------------------------------------
 set(a_lib_name athena)

 dd4hep_configure_output()

-dd4hep_add_plugin(${a_lib_name} SOURCES src/*.cpp
-          USES ActsCore ActsPluginDD4hep
+dd4hep_add_plugin(${a_lib_name} SOURCES 
+  src/BarrelBarDetectorWithSideFrame_geo.cpp
+  src/BarrelCalorimeter_geo.cpp
+  src/BarrelCalorimeterInterlayers_geo.cpp
+  src/BarrelTrackerWithFrame_geo.cpp
+  src/CompositeTracker_geo.cpp
+  src/CylinderTrackerBarrel_geo.cpp
+  src/DIRC_geo.cpp
+  src/DRICH_geo.cpp
+  src/PFRICH_geo.cpp
+  src/FileLoader.cpp
+  src/FieldMapBrBz.cpp
+  src/GaseousRICH_geo.cpp
+  src/GeometryHelpers.cpp
+  src/HomogeneousCalorimeter_geo.cpp
+  src/HybridCalorimeter_geo.cpp
+  src/MRich_geo.cpp
+  src/PolyhedraEndcapCalorimeter2_geo.cpp
+  src/ScFiCalorimeter_geo.cpp
+  src/ShashlikCalorimeter_geo.cpp
+  src/SimpleDiskDetector_geo.cpp
+  src/SolenoidCoil_geo.cpp
+  src/TrapEndcapTracker_geo.cpp
+  USES ${ActsDD4hep}
  )
 target_link_libraries(${a_lib_name}
-  PUBLIC DD4hep::DDCore  DD4hep::DDRec
+  PUBLIC DD4hep::DDCore DD4hep::DDRec fmt::fmt
  )

 #-----------------------------------------------------------------------------------
@@ -28,3 +63,15 @@ install(DIRECTORY compact/
    DESTINATION share/${PROJECT_NAME}/${a_lib_name}
    FILES_MATCHING PATTERN "*.xml"
    )
+install(DIRECTORY compact/
+    DESTINATION share/${PROJECT_NAME}/compact
+    FILES_MATCHING PATTERN "*.xml"
+    )
+install(FILES athena.xml
+    DESTINATION share/${PROJECT_NAME}/
+    )
+#-----------------------------------------------------------------------------------
+# Install the detector calibration files.
+install(DIRECTORY calibrations/
+    DESTINATION share/${PROJECT_NAME}/calibrations
+    )
--- a/README.md
+++ b/README.md
@@ -3,22 +3,34 @@ Overview
 The Athena Detector at IP6 for Electron-Ion Collider experiment.

 **Detector geometry viewer:**
- [Central detector geometry](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/geo/detector_geo.root?job=report&item=default;1&opt=clipxyz;transp30;zoom100;ROTY0;ROTZ0;trz100;trr0;ctrl;all&)
- [Full Detector geometry (including beamline)](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/geo/detector_geo_full.root?job=report&item=default;1&opt=clipxyz;transp30;zoom75;ROTY290;ROTZ350;trz0;trr0;ctrl;all&)
-
-<a href="https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/images/view01.pdf?job=report">
-<img src="https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/images/view01.png?job=report" width="400px" />
+- [Central detector](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/detector_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom120;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+- [Full Detector (including beamline)](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/detector_geo_full.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY290;ROTZ350;trz0;trr0;ctrl;all)
+- [Inner detector (without calorimetry)](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/inner_detector_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+- Subsystem views:
+  - [Calorimetry](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/calorimeters_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom120;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+  - [PID](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/pid_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+    - [dRICH](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/drich_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY290;ROTZ350;trz0;trr0;ctrl;all)
+    - [pfRICH](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/pfrich_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom55;ROTY49;ROTZ350;trz0;trr0;ctrl;all&)
+    - [DIRC](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/dirc_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom120;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+    - [ToF](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/tof_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom55;ROTY49;ROTZ350;trz0;trr0;ctrl;all&)
+  - [Tracking](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/tracking_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom75;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+    - [Vertex detector](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/vertex_only_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom120;ROTY320;ROTZ340;trz0;trr0;ctrl;all)
+  - [Far-forward](https://eic.phy.anl.gov/geoviewer/index.htm?nobrowser&file=https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/geo/ip6_geo.root?job=dump_geometry&item=default;1&opt=clipx;clipy;transp30;zoom40;ROTY290;ROTZ350;trz0;trr0;ctrl;all)
+
+<a href="https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/images/view01.pdf?job=report">
+<img src="https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/images/view01.png?job=report" width="400px" />
 </a>

 <br />
-<a href="https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/images/view01_top.pdf?job=report">
-<img src="https://eicweb.phy.anl.gov/api/v4/projects/473/jobs/artifacts/master/raw/images/view01_top.png?job=report" width="400px" />
+<a href="https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/images/view01_top.pdf?job=report">
+<img src="https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/images/view01_top.png?job=report" width="400px" />
 </a>

 [Browse latest](https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/browse/images?job=report)

-[Detector views](views/detector_views.md)
+[Detector views](https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/doc/dawn_views.md?job=report)

+[Constants listing](https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/artifacts/master/raw/doc/constants.out?job=report)

 Getting Started
 ---------------

--- a/athena.xml
+++ b/athena.xml
-<lccdd xmlns:compact="http://www.lcsim.org/schemas/compact/1.0" 
-       xmlns:xs="http://www.w3.org/2001/XMLSchema" 
+<lccdd xmlns:compact="http://www.lcsim.org/schemas/compact/1.0"
+       xmlns:xs="http://www.w3.org/2001/XMLSchema"
       xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/compact/1.0/compact.xsd">

+       <debug>
+         <type name="surface"       value="0"/>
+         <type name="material"      value="0"/>
+         <type name="readout"       value="0"/>
+         <type name="segmentation"  value="0"/>
+         <type name="limits"        value="0"/>
+         <type name="region"        value="0"/>
+         <type name="includes"      value="0"/>
+       </debug>
+
+  <documentation level="-1">
+  # Athena Detector 
+  - https://eicweb.phy.anl.gov/EIC/detectors/athena.git 
+  - https://eicweb.phy.anl.gov/EIC/detectors/ip6.git
+  </documentation>
+
  <!-- Some information about detector  -->
  <info name="Athena Detector" title="Athena Detector"
-        author="Jihee Kim, Whitney Armstrong"
+        author="Athena Collaboration"
 	url="https://eicweb.phy.anl.gov/EIC/detectors/athena.git"
 	status="development"
 	version="v1 2021-03-16">
-    <comment>Athena Detector</comment>        
+  <comment> Athena </comment>
  </info>
-
  <define>
-    <include ref="ip6/ip6_defs.xml" /> <comment> IP definitions should be first</comment>
+  <documentation level="2">
+      ## Main Constant Definitions
+
+      The ip6 (or other ip) defines should be included first.
+      These files have only a define tags.
+  </documentation>
+    <include ref="ip6/definitions.xml" /> 
+    <include ref="ip6/far_forward/fields_275.xml" />
    <include ref="compact/definitions.xml" />
  </define>

-  <properties>
-    <matrix name="RINDEX__Vacuum" coldim="2" values="
-      1.0*eV 1.0
-      5.1*eV 1.0
-      "/>
-    <matrix name="RINDEX__Air" coldim="2" values="
-      1.0*eV 1.00029
-      5.1*eV 1.00029
-      "/>
-    <matrix name="RINDEX__Quartz" coldim="2" values="
-      1.0*eV 1.46
-      5.1*eV 1.46
-      "/>
-    <matrix name="RINDEX__N2" coldim="2" values="
-      1.0*eV 1.00033
-      4.0*eV 1.00033
-      5.1*eV 1.00033
-      "/>
-    <matrix name="RINDEX__Pyrex" coldim="2" values="
-      1.0*eV 1.5
-      4.0*eV 1.5
-      5.1*eV 1.5
-      "/>
-    <matrix name= "REFLECTIVITY_mirror" coldim="2" values="
-      1.0*eV  0.9
-      4.0*eV  0.9
-      5.1*eV  0.9
-    "/>
-  </properties>
-
  <includes>
    <gdmlFile ref="compact/elements.xml"/>
    <gdmlFile ref="compact/materials.xml"/>
+    <file     ref="compact/optical_materials.xml"/>
  </includes>

-  <materials>
-    <material name="AirOptical">
-      <D type="density" unit="g/cm3" value="0.0012"/>
-      <fraction n="0.754" ref="N"/>
-      <fraction n="0.234" ref="O"/>
-      <fraction n="0.012" ref="Ar"/>
-      <property name="RINDEX" ref="RINDEX__Vacuum"/>
-    </material>
-    <material name="N2cherenkov">
-      <D type="density" value="0.00125" unit="g/cm3"/>
-      <composite n="1" ref="N"/>
-      <property name="RINDEX"  ref="RINDEX__N2"/>
-    </material>
-    <material name="PyrexGlass">
-      <D type="density" value="2.23" unit="g/cm3"/>
-      <fraction n="0.806" ref="SiliconOxide"/>
-      <fraction n="0.130" ref="BoronOxide"/>
-      <fraction n="0.040" ref="SodiumOxide"/>
-      <fraction n="0.023" ref="AluminumOxide"/>
-      <property name="RINDEX" ref="RINDEX__Pyrex"/>
-    </material>
-  </materials>
-
-  <surfaces>
-    <comment> For the values of "finish", model and type, see TGeoOpticalSurface.h !
-    </comment>
-    <opticalsurface finish="polished" model="glisur" name="MirrorOpticalSurface" type="dielectric_metal" value="0">
-      <property name="REFLECTIVITY" ref="REFLECTIVITY_mirror"/>
-      <property name="RINDEX"       coldim="2" values="1.034*eV  1.5   4.136*eV  1.5"/>
-      <!--<property name="EFFICIENCY"   ref="EFFICIENCY0x8b77240"/>-->
-    </opticalsurface>
-    <opticalsurface name="mirror2" finish="polished" model="glisur" type="dielectric_dielectric">
-      <property name="REFLECTIVITY"            coldim="2" values="1.034*eV  0.8   4.136*eV  0.9"/>
-      <property name="EFFICIENCY"              coldim="2" values="2.034*eV  0.8   4.136*eV  1.0"/>
-      <property name="RINDEX"                  coldim="2" values="1.034*eV  1.5   4.136*eV  1.5"/>
-    </opticalsurface>
-  <!-- Define the dimensions of the world volume -->
-
-  </surfaces>
  <limits>
    <limitset name="EICBeamlineLimits">
      <limit name="step_length_max" particles="*" value="1.0" unit="mm" />
@@ -104,107 +58,84 @@
  </limits>

  <display>
+  <include ref="compact/colors.xml" />
+  <!--include ref="compact/colors2.xml"/-->
  <include ref="compact/display.xml" />
+  <!--include ref="compact/display_detailed.xml"/-->
  </display>

-  <comment> Include the IP components first </comment>
-  <include ref="ip6/forward_ion_beamline.xml"/>
-  <include ref="ip6/beampipe.xml"/>
-
-  <detectors>
-    <detector id="VertexBarrelSubAssembly_ID" 
-      name="VertexBarrelSubAssembly" 
-      type="DD4hep_SubdetectorAssembly" 
-      vis="TrackerSubAssemblyVis">
-      <composite name="VertexBarrel" />
-    </detector>
-    <detector id="VertexEndcapSubAssembly_ID" 
-      name="VertexEndcapSubAssembly" 
-      type="DD4hep_SubdetectorAssembly" 
-      vis="TrackerSubAssemblyVis">
-      <composite name="VertexEndcapN" />
-      <composite name="VertexEndcapP" />
-    </detector>
-
-    <detector id="TrackerEndcapSubAssembly_Inner_ID"
-      name="TrackerSubAssembly_Inner"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerEndcapN_Inner"/>
-      <composite name="TrackerBarrel_Inner"/>
-      <composite name="TrackerEndcapP_Inner"/>
-    </detector>
-    <detector id="TrackerBarrelSubAssembly_Outer_ID"
-      name="TrackerSubAssembly_Outer"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerBarrel_Outer"/>
-      <composite name="TrackerEndcapP_Outer"/>
-      <composite name="TrackerEndcapN_Outer"/>
-    </detector>
-    <!--
-    <detector id="TrackerBarrelSubAssembly_Inner_ID"
-      name="TrackerBarrelSubAssembly_Inner"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerBarrel_Inner"/>
-    </detector>
-    <detector id="TrackerEndcapSubAssembly_Inner_ID"
-      name="TrackerEndcapSubAssembly_Inner"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerEndcapN_Inner"/>
-      <composite name="TrackerBarrel_Inner"/>
-      <composite name="TrackerEndcapP_Inner"/>
-    </detector>
-    <detector id="TrackerBarrelSubAssembly_Outer_ID"
-      name="TrackerBarrelSubAssembly_Outer"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerBarrel_Outer"/>
-    </detector>
-    <detector id="TrackerEndcapSubAssembly_Outer_ID"
-      name="TrackerEndcapSubAssembly_Outer"
-      type="DD4hep_SubdetectorAssembly"
-      vis="TrackerSubAssemblyVis">
-      <composite name="TrackerEndcapP_Outer"/>
-      <composite name="TrackerEndcapN_Outer"/>
-    </detector>
-    -->
-  </detectors>
-
-  <include ref="compact/vertex_tracker.xml"/>
-
-  <include ref="compact/central_tracker.xml"/>
-
-  <!--
-  <include ref="compact/rwell_tracker_barrel.xml"/>
-  <include ref="compact/cb_DIRC.xml"/>
-  -->
+  <documentation level="0">
+    ## Detector Subsystems
+
+    ### IP Subsystems
+
+    The interaction point subsystems are included before the central detector subsystems.
+    This is becuase the IP subsystems, for exmaple the beampipe, will define paramters
+    which are subsquently used in the central detector construction -- e.g. the vertex tracker
+    uses the beampipe OD to help define its placement. 

+    The IP subsystems include the Far forward and backward regions. The list of subsystem includes:
+     - Interaction region beampipe 
+     - B0 tracker
+     - Off-momentum tracker
+     - Far forward roman pots
+     - Zero Degree Calorimeter
+     - Beam line magnets.
+     - and more...
+  </documentation>
+
+  <documentation level="5">
+     ## Main magnet
+
+      Note: When changing magnet, also select dimensions in definitions.xml.
+  </documentation>
  <include ref="compact/solenoid.xml"/>
+
+  <documentation level="10">
+    ## Central tracking detectors
+  </documentation>
+
+  <!--include ref="compact/tracking_config_acadia.xml"/-->
+  <!--include ref="compact/tracking_config_canyonlands.xml"/-->
+  <include ref="compact/tracking_config_deathvalley.xml"/>
+
+  <documentation level="10">
+  ### PID detectors
+  </documentation>
+  <!--include ref="compact/pid_config_acadia.xml" /-->
+  <!--include ref="compact/pid_config_canyonlands.xml" /-->
+  <include ref="compact/pid_config_deathvalley.xml" />
+
+  <documentation level="10">
+  ## Central calorimetry
+  </documentation>
  <include ref="compact/ecal.xml"/>
  <include ref="compact/hcal.xml"/>
-  <!--include ref="compact/ce_GEM.xml"/-->
-  <!--include ref="compact/gem_tracker_endcap.xml"/-->
-  <include ref="compact/ce_mrich.xml"/>
-  <include ref="compact/tof_endcap.xml"/>
-  <include ref="compact/forward_trd.xml"/>
-  <include ref="compact/forward_rich.xml"/>
-
-  <include ref="compact/B0_tracker.xml"/>
-  <include ref="compact/far_forward_offM_tracker.xml"/>
-  <include ref="compact/far_forward_romanpots.xml"/>
-  <include ref="compact/far_forward_detectors.xml"/>
-
-  <!--
-  <include ref="compact/mm_tracker_barrel.xml"/>
-  <include ref="compact/cb_VTX_Barrel.xml"/>
-  -->
-   
+
+  <documentation level="11">
+  ## Far foward detectors
+  </documentation>
+  <include ref="ip6/central_beampipe.xml"/>
+
+  <documentation level="11">
+  ## Far foward detectors
+  </documentation>
+  <include ref="ip6/far_forward.xml"/>
+
+  <documentation level="11">
+  ## Far backward detectors
+  </documentation>
+  <include ref="ip6/far_backward.xml"/>
+
+  <comment>
+      FB elements
+      -----------
+      None (TODO)
+
+      What is FB?
+  </comment>

  <readouts>
  </readouts>

-
 </lccdd>
--- a/bin/acts_geo_check
+++ b/bin/acts_geo_check
+#!/bin/bash
+
+logfile=$1
+
+# parse the verobse output of scripts/test_ACTS.cxx
+res=0
+
+nlines=$(grep -in error ${logfile} | grep -in D2A_ | wc -l)
+if [[ "$nlines" > "0" ]] ; then
+  echo " ACTS geometry error: "
+  grep -in error ${logfile} | grep -in D2A_ 
+  res="1"
+fi
+
+
+nlines=$(grep -in warn ${logfile} | grep -in D2A_ | wc -l)
+if [[ "$nlines" > "0" ]] ; then
+  echo " ACTS geometry error: "
+  grep -in warn ${logfile} | grep -in D2A_ 
+  res="1"
+fi
+
+exit ${res}
+
--- a/bin/build_documentation
+++ b/bin/build_documentation
+#!/bin/bash
+
+#included files
+detector_file="./athena.xml"
+
+#filelist=$(xmllint --format --xpath '//include/@ref' ${detector_file}   | sed 's/ref=\"//g' | sed 's/\"/\n/g' )
+#echo $filelist
+
+# Searches for included files two levels down
+get_includes() {
+  local input_file="${1}"
+  #echo ${1}
+  local filelist=$(xmllint --format --xpath '//include/@ref' ${input_file}   | sed 's/ref=\"//g' | sed 's/\"//g' )
+  for afile in $filelist ; do
+    xmllint --format --xpath '//include/@ref' ${input_file}  &> /dev/null
+    local res="$?"
+    if [ "${res}" == "0" ]  ; then
+      local subincluded=$(xmllint --format --xpath '//include/@ref' ${input_file}  2> /dev/null | sed 's/ref=\"//g' | sed 's/\"//g' )
+      filelist="${filelist} ${subincluded}"
+      #echo "sub include $afile"
+    fi
+  done
+  # <includes > <gdmlFile > <file>
+  local otherfiles=$(xmllint --format --xpath '//includes/file/@ref | //includes/gdmlFile/@ref' ${input_file}   | sed 's/ref=\"//g' | sed 's/\"/\n/g' )
+  #echo $otherfiles
+  filelist=$(echo "${filelist} ${otherfiles}" | sed 's/ /\n/g' | sort | uniq )
+  echo "$input_file $filelist"
+}
+
+
+xml_files=$(get_includes ${detector_file})
+#echo $xml_files
+
+get_doc_levels() {
+  # levels
+  local levels=0
+  for afile in $xml_files ; do
+    xmllint --format --xpath '//documentation/@level' $afile  &> /dev/null
+    local res="$?"
+    if [ "${res}" == "0" ]  ; then
+      local new_levels=$(xmllint --format --xpath '//documentation/@level' $afile  2> /dev/null  | sed 's/level=\"/ /g' | sed 's/\"//g' )
+      levels="${levels} ${new_levels}"
+    fi
+    # see if there are tags without level attribute
+    xmllint --format --xpath '//documentation[not(@level)]' $afile  &> /dev/null 
+    if [ "${?}" == "0" ] ; then 
+      #echo "DERP"
+      levels="${levels} 100"
+    fi
+  done
+  echo "$levels" | sed 's/ /\n/g' | sort  | uniq
+}
+
+all_levels=$(get_doc_levels ${xml_file_array})
+#echo " levels: "
+#echo $all_levels
+
+for alevel in $(echo ${all_levels} | sed 's/ /\n/g' | sort -n  | uniq ) ; do
+  #echo " doing level $alevel ..."
+  for afile in $(echo $xml_files | sed 's/ / \n/g') ; do
+    #echo $afile
+    #xmllint --format --xpath '//documentation[@level="'"$alevel"'"]/text()' $afile
+    level_doc=$(xmllint --format --xpath '//documentation[@level="'$alevel'"]' ${afile} 2> /dev/null )
+    if [ "$?" -eq "0" ] ;  then
+      xmllint --format --xpath '//documentation[@level="'$alevel'"]/text()' ${afile} | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/g' 
+    fi
+    # sets the tags without attribute level to 100
+    xmllint --format --xpath '//documentation[not(@level)]/text()' ${afile} &> /dev/null 
+    if [ "$?" -eq "0" ] ;  then
+      if [ "$alevel" -eq "100" ] ; then
+        xmllint --format --xpath '//documentation[not(@level)]/text()' ${afile} | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/g' 
+      fi
+    fi
+  done
+done
+
+
+
+#${DETECTOR_PATH}=.
+#
+#
+#xmllint --format --xpath '//
+#
+#xmllint --format --xpath '//documentation/text()' ${DETECTOR_PATH}/athena.xml | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee  doc/detector.md
+#xmllint --format --xpath '//documentation/text()' ${DETECTOR_PATH}/ip6/ip6_defs.xml | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee -a doc/detector.md || true
+#for afile in ${DETECTOR_PATH}/compact/*.xml ; do
+#  xmllint --format --xpath '//documentation/text()' ${afile} | sed -re 's/<\/?\w+>//g' | sed 's/^[[:space:]]*#/#/' | tee -a doc/detector.md || true
+#done
+#
+
--- a/bin/dawn_tweak
+++ b/bin/dawn_tweak
@@ -99,6 +99,20 @@ do
      shift # past argument
      shift # past value
      ;;
+    --light-theta)
+      echo "updating drawing to ${2}"
+      sed -i '19d' ${DAWN_RUN_DIR}/${OUT_FILE}
+      sed -i '19i'${2} ${DAWN_RUN_DIR}/${OUT_FILE}
+      shift # past argument
+      shift # past value
+      ;;
+    --light-phi)
+      echo "updating drawing to ${2}"
+      sed -i '18d' ${DAWN_RUN_DIR}/${OUT_FILE}
+      sed -i '18i'${2} ${DAWN_RUN_DIR}/${OUT_FILE}
+      shift # past argument
+      shift # past value
+      ;;
    -i|--input)
      OUT_FILE="$2"
      shift # past argument

--- a/bin/debug_mrich
+++ b/bin/debug_mrich
+#!/bin/bash
+
+npsim --enableG4GPS \
+  --compact athena.xml \
+  --runType vis \
+  --macro macro/mrich_vis.mac \
+  -O derp.root
+
--- a/bin/generate_prim_file
+++ b/bin/generate_prim_file
+#!/usr/local/bin/python
+
+# same as make_dawn_views but stops at generating the prim file.
+# W. Armstrong (ANL), original bash script
+# C. Peng (ANL), translate to python and add flexible run time for simulation
+
+import os
+import signal
+import subprocess
+import argparse
+import atexit
+import time
+from datetime import datetime
+import fcntl
+import psutil
+
+
+def readline_nonblocking(output):
+    fd = output.fileno()
+    fl = fcntl.fcntl(fd, fcntl.F_GETFL)
+    fcntl.fcntl(fd, fcntl.F_SETFL, fl | os.O_NONBLOCK)
+    try:
+        return output.readline()
+    except:
+        return ''
+
+
+# arguments
+parser = argparse.ArgumentParser()
+
+parser.add_argument('-c', '--compact-file', type=str, dest='compact',
+        default=os.path.join(os.environ.get('DETECTOR_PATH', '.'), 'athena.xml'),
+        help='Top level compact file for detectors')
+
+parser.add_argument('-s', '--skip', type=int,
+        default=0,
+        help='Number of events number to skip in the input')
+
+parser.add_argument('-i', '--input', type=str,
+        default='scripts/input_data/few_events.hepmc',
+        help='Input hepmc file')
+
+parser.add_argument('-o', '--output-dir', type=str, dest='out_dir',
+        default='sim_output',
+        help='output directory')
+
+parser.add_argument('-D', '--detector-only', action='store_true', dest='detector_only',
+        help='only generate the prim files for the detector geometry')
+
+parser.add_argument('-t', '--tag', type=str,dest='file_tag',
+        default='view',
+        help='Output file tag')
+
+parser.add_argument('--timeout', type=int,
+        default=3600,
+        help='Timeout in seconds')
+
+parser.add_argument('passthrough', nargs='*')
+
+args = parser.parse_args()
+
+macro = 'macro/dawn_picture.mac' if args.detector_only else 'macro/dawn_picture2.mac'
+
+# raise error if cannot create a temporary working dir
+# os.makedirs('dawn_view_tmp', exist_ok=False)
+os.makedirs(args.out_dir, exist_ok=True)
+
+# use absolute path so the chdir does not affect them
+args.input = os.path.abspath(args.input)
+args.out_dir = os.path.abspath(args.out_dir)
+args.compact = os.path.abspath(args.compact)
+macro = os.path.abspath(macro)
+
+# adjust fiber radius to reduce the number of fibers
+compact_dir = os.path.dirname(os.path.realpath(args.compact))
+ci_ecal = os.path.join(compact_dir, 'compact', 'ci_ecal_scfi.xml')
+os.system('sed -i \'s/radius=\"EcalEndcapP_FiberRadius\"/radius=\"EcalEndcapP_FiberRadius*10\"/\' {}'.format(ci_ecal))
+
+prim_file = 'g4_0000.prim'
+dawn_env = os.environ.copy()
+dawn_env['DAWN_BATCH'] = 'a'
+# sdir = os.path.dirname(os.path.realpath(__file__))
+
+# Using a python warpper such as npsim introduces some problem in managing the subprocess.
+# The process1 managed by subprocess will generate another process with proc2_pid = proc1_pid + 1, which will not
+# be terminated by terminating or killing the process1.
+# In addition, running Geant4 with vis mode will never exit automatically (it waits for input).
+# Thus the created process 2 will occupy the system resources.
+sim_cmd = ['npsim', '--runType', 'vis',
+        '--compact', args.compact,
+        '--inputFiles', args.input,
+        '--outputFile', 'derp.root',
+        '--numberOfEvents', '1',
+        '--skipNEvents', str(args.skip),
+        '--macroFile', macro]
+
+start = datetime.now()
+elapse = datetime.now() - start
+last_update = datetime.now()
+finished = False
+
+# run simulation
+print(' '.join(sim_cmd))
+p = subprocess.Popen(args=sim_cmd, env=dawn_env,
+                     stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)
+__child_pid = p.pid
+while elapse.seconds < args.timeout:
+    line = readline_nonblocking(p.stdout)
+    elapse = datetime.now() - start
+    time_left = args.timeout - elapse.seconds
+    time_str = '[{:02d}:{:02d}]'.format(elapse.seconds // 60, elapse.seconds % 60)
+
+    if time_left < 10:
+        print('{} === TIMEOUT ===: Terminating in {:d} seconds'.format(time_str, time_left))
+
+    if line:
+        decoded_line = line.decode('utf-8').strip()
+        print('{} {}'.format(time_str, decoded_line))
+        # what we are looking for
+        if decoded_line == 'File  {}  is generated.'.format(prim_file):
+            print('{} === FINISHED ===: Got the prim file, terminating.'.format(time_str))
+            finished = True
+            break
+        if decoded_line == 'Idle>':
+            p.stdin.write(b'exit')
+            break
+        # do not sleep
+        continue
+
+    # ended early before file
+    if p.poll() is not None:
+        print(p.poll())
+        break
+
+    time.sleep(1)
+
+p.kill()
+# use to kill the subprocess generated from the python wrapper
+# this is unsafe so maybe more checks required
+for proc in psutil.process_iter():
+    pinfo = proc.as_dict(attrs=['pid', 'name', 'create_time'])
+    if pinfo['pid'] == p.pid + 1 and pinfo['name'] == 'python':
+        print('kill {}, generated from {}'.format(pinfo, p.pid))
+        os.kill(pinfo['pid'], signal.SIGTERM)
+
+# revert the change
+os.system('sed -i \'s/radius=\"EcalEndcapP_FiberRadius*10\"/radius=\"EcalEndcapP_FiberRadius\"/\' {}'.format(ci_ecal))
+
+line = b'stderr outputs:\n'
+while line:
+    print(line.decode('utf-8'), end='')
+    line = readline_nonblocking(p.stderr)
+
+if finished:
+    print('Simulation finished')
+else:
+    print('Simulation failed')
+    exit(1)
+
+# move the prim files (which can be quite large)
+# to the local pipeline storage path
+os.system('mv g4_0000.prim {}/{}.prim'.format(args.out_dir,args.file_tag))
+
+
--- a/bin/make_dawn_views
+++ b/bin/make_dawn_views
-#!/bin/bash
-
-#git clone --depth 1 https://eicweb.phy.anl.gov/EIC/datasets.git
-export DAWN_PS_PREVIEWER="ls "
-export G4DAWNFILE_VIEWER="ls -lrth "
-export G4DAWNFILE_PS_VIEWER="ls "
-
-function print_the_help {
-  echo "USAGE: ${0} [-s <skip_events>] -d <dawn_run_dir> "
-  echo "  OPTIONS: "
-  echo "            -D,--detector-only            Only generate the prim files for the detector geometry."
-  echo "            -s,--skip <skip_events>       Required run number"
-  echo "            -i,--input <input_file>       Input hepmc file"
-  echo "            -d,--dawn-dir <dawn_run_dir>  Directory with the .DAWN files and a generate script "
-  echo "            -t,--tag <file_tag>           Output file tag"
-  exit 
-}
-
-function yes_or_no {
-  while true; do
-    read -p "$* [y/n]: " yn
-    case $yn in
-      [Yy]*) return 0 ;;
-      [Nn]*) echo "No entered" ; return 1 ;;
-    esac
-  done
-}
-
-if [[ $# -eq 0 ]] ; then
-  print_the_help
-  exit 
-fi
-
-SKIP_EVENTS=0
-DETECTOR_ONLY=0
-FILE_TAG="view"
-DAWN_RUN_DIR="scripts/view1"
-DETECTOR_FILE="${DETECTOR_PATH}/athena.xml"
-
-POSITIONAL=()
-while [[ $# -gt 0 ]]
-do
-  key="$1"
-
-  case $key in
-    -h|--help)
-      shift # past argument
-      print_the_help
-      ;;
-    -c|--compact-file)
-      DETECTOR_FILE="$2"
-      shift # past argument
-      shift # past value
-      ;;
-    -s|--skip)
-      SKIP_EVENTS="$2"
-      shift # past argument
-      shift # past value
-      ;;
-    -i|--input)
-      INPUT_FILE="$2"
-      shift # past argument
-      shift # past value
-      ;;
-    -o|--ouput-dir)
-      OUTPUT_DIR="$2"
-      shift # past argument
-      shift # past value
-      ;;
-    -D|--detector-only)
-      DETECTOR_ONLY=1
-      shift # past argument
-      #shift # past value
-      ;;
-    -d|--dawn-dir)
-      DAWN_RUN_DIR=$2
-      shift # past argument
-      shift # past value
-      ;;
-    -t|--tag)
-      FILE_TAG=$2
-      shift # past argument
-      shift # past value
-      ;;
-    *)    # unknown option
-      #POSITIONAL+=("$1") # save it in an array for later
-      echo "unknown option $1"
-      print_the_help
-      shift # past argument
-      ;;
-  esac
-done
-set -- "${POSITIONAL[@]}" # restore positional parameters
-
-
-rm -f *.prim
-
-if [  "${DETECTOR_ONLY}" -eq "1" ] ; then
-
-  ./scripts/run_detector_simulation.py  \
-    --compact ${DETECTOR_PATH}/athena.xml \
-  -i scripts/input_data/few_events.hepmc \
-  -o derp.root -n 1 \
-  --ui csh --vis -b -m macro/dawn_picture.mac & 
-
-sleep 10
-echo "sleeping 20 secs ..  " 
-sleep 10
-echo "sleeping 10 secs " 
-sleep 5 
-echo "sleeping 5 secs " 
-sleep 5 
-kill %1
-
-else 
-
-  echo " Running simulation for tracks"
-./scripts/run_detector_simulation.py \
-    --compact ${DETECTOR_PATH}/athena.xml \
-  -i scripts/input_data/few_events.hepmc \
-  -o derp.root -s ${SKIP_EVENTS} -n 1 \
-  --ui csh --vis -b -m macro/dawn_picture2.mac & 
-
-sleep 40 
-kill %1
-
-fi
-
-#./scripts/run_detector_simulation.py -i scripts/input_data/few_events.hepmc \
-#  -o derp.root -s 2 -n 1 \
-#  --ui csh --vis -b -m macro/dawn_picture2.mac & 
-#
-#sleep 20 
-#kill %1
-
-#./scripts/run_detector_simulation.py -i scripts/input_data/few_events.hepmc \
-#  -o derp.root -s 5 -n 1 \
-#  --ui csh --vis -b -m macro/dawn_picture2.mac & 
-#
-#sleep 20 
-#kill %1
-#
-#./scripts/run_detector_simulation.py -i scripts/input_data/few_events.hepmc \
-#  -o derp.root -s 6 -n 1 \
-#  --ui csh --vis -b -m macro/dawn_picture2.mac & 
-#
-#sleep 20 
-#kill %1
-
-[[ -f "g4_0000.prim" ]]  || exit -1
-
-echo "simulating done" 
-#npsim --runType vis \
-#      -v WARNING \
-#      --macroFile macro/dawn_picture.mac \
-#      --numberOfEvents 1 \
-#      --compactFile topside.xml \
-#      --inputFiles scripts/input_data/few_events.hepmc \
-#      --outputFile  derp.root \
-#      --dumpSteeringFile >> derp.out
-
-
-ls -lrth
-mkdir -p images
-#mkdir -p images/prim
-
-pushd ${DAWN_RUN_DIR}
-
-if [  "${DETECTOR_ONLY}" -eq "1" ] ; then
-  ./generate_eps -t ${FILE_TAG} -i ../../g4_0000.prim
-else 
-  ./generate_eps -t ${FILE_TAG} -i ../../g4_0000.prim
-fi
-ls -lrth
-
-cp *.pdf ../../images/.
-cp *.png ../../images/.
-#cp *.prim ../../images/prim/.
-popd
-
+#!/usr/local/bin/python
+
+# get dawn view of detectors
+# W. Armstrong (ANL), original bash script
+# C. Peng (ANL), translate to python and add flexible run time for simulation
+
+import os
+import signal
+import subprocess
+import argparse
+import atexit
+import time
+from datetime import datetime
+import fcntl
+import psutil
+
+
+def readline_nonblocking(output):
+    fd = output.fileno()
+    fl = fcntl.fcntl(fd, fcntl.F_GETFL)
+    fcntl.fcntl(fd, fcntl.F_SETFL, fl | os.O_NONBLOCK)
+    try:
+        return output.readline()
+    except:
+        return ''
+
+
+# arguments
+parser = argparse.ArgumentParser()
+
+parser.add_argument('-c', '--compact-file', type=str, dest='compact',
+        default=os.path.join(os.environ.get('DETECTOR_PATH', '.'), 'athena.xml'),
+        help='Top level compact file for detectors')
+
+parser.add_argument('-s', '--skip', type=int,
+        default=0,
+        help='Number of events number to skip in the input')
+
+parser.add_argument('-i', '--input', type=str, dest='input',
+        default='sim_output',
+        help='Input hepmc file')
+
+parser.add_argument('-o', '--output-dir', type=str, dest='out_dir',
+        default='images',
+        help='output directory')
+
+parser.add_argument('-D', '--detector-only', action='store_true', dest='detector_only',
+        help='only generate the prim files for the detector geometry')
+
+parser.add_argument('-d', '--dawn-dir', type=str, dest='dawn_dir',
+        default='scripts/view1',
+        help='Directory to dawn script dir (with .DAWN files and a generate_eps script)')
+
+parser.add_argument('-t', '--tag', type=str,dest='file_tag',
+        default='view',
+        help='Output file tag')
+
+parser.add_argument('--timeout', type=int,
+        default=60,
+        help='Timeout in seconds')
+        
+parser.add_argument('passthrough', nargs='*')
+
+args = parser.parse_args()
+
+macro = 'macro/dawn_picture.mac' if args.detector_only else 'macro/dawn_picture2.mac'
+
+# raise error if cannot create a temporary working dir
+# os.makedirs('dawn_view_tmp', exist_ok=False)
+os.makedirs(args.out_dir, exist_ok=True)
+
+# use absolute path so the chdir does not affect them
+args.input = os.path.abspath(args.input)
+args.out_dir = os.path.abspath(args.out_dir)
+args.compact = os.path.abspath(args.compact)
+macro = os.path.abspath(macro)
+
+prim_file = 'g4_0000.prim'
+dawn_env = os.environ.copy()
+dawn_env['DAWN_BATCH'] = 'a'
+# sdir = os.path.dirname(os.path.realpath(__file__))
+
+
+# generate DAWN images
+out_dir = os.path.abspath(args.out_dir)
+input_file = os.path.abspath(args.input)
+#prim_file = '{}/{}.prim'.format(input_dir,args.file_tag)
+#prim_file = os.path.abspath(prim_file)
+owd = os.getcwd()
+os.chdir(args.dawn_dir)
+subprocess.run(['pwd'])
+subprocess.run(['./generate_eps', '-t', args.file_tag, '-i', input_file] + args.passthrough)
+subprocess.run(['ls', '-lrth'])
+
+# upload the results
+os.system('cp *.pdf {}'.format(out_dir))
+os.system('cp *.png {}'.format(out_dir))
+os.chdir(owd)

--- a/bin/make_images
+++ b/bin/make_images
@@ -7,9 +7,15 @@ env = Environment(
    autoescape=select_autoescape(['html', 'xml'])
 )

+import os
 import glob

-base_url = "https://eicweb.phy.anl.gov/api/v4/projects/390/jobs/artifacts/master/raw"
+if "CI_PROJECT_ID" in os.environ:
+    CI_PROJECT_ID = str(os.environ["CI_PROJECT_ID"])
+else:
+    CI_PROJECT_ID = "473"
+
+base_url = f"https://eicweb.phy.anl.gov/api/v4/projects/{CI_PROJECT_ID}/jobs/artifacts/master/raw"

 #images = ["images/view2a.png","images/view2b.png", "images/view1.png"]
 images = glob.glob("images/*.png")

--- a/bin/set_beam_energy
+++ b/bin/set_beam_energy
+#!/bin/bash
+
+function print_the_help {
+  echo "USAGE:    --ebeam E --pbeam E -c compact.xml"
+  echo "REQUIRED ARGUMENTS:"
+  echo "          -h|--help     Print this message"
+  echo "          --ebeam       Electron beam energy (5, 10 or 18)"
+  echo "          --pbeam       Ion beam energy (41, 100 or 275)"
+  echo "          -c|--compact  Compact file to set beam energy for"
+  exit
+}
+
+EBEAM=
+PBEAM=
+COMPACT=
+
+while [ $# -gt 0 ]
+do
+  key="$1"
+  case $key in
+    -h|--help)
+      print_the_help
+      ;;
+    --ebeam)
+      EBEAM=$2
+      shift
+      shift
+      ;;
+    --pbeam)
+      PBEAM=$2
+      shift
+      shift
+      ;;
+    -c|--compact)
+      COMPACT=$2
+      shift
+      shift
+      ;;
+    *)    # unknown option
+      echo "unknown option"
+      exit 1
+      ;;
+  esac
+done
+
+echo "Setting beam energies to $EBEAM on $PBEAM for $COMPACT"
+
+if [ -z $COMPACT ]; then
+  echo "Error: no compact file given, use -h for help"
+  exit 1
+fi
+if [ -z $EBEAM ]; then
+  echo "Error: --ebeam argument missing, use -h for help"
+  exit 1
+fi
+if [ -z $PBEAM ]; then
+  echo "Error: --pbeam argument missing, use -h for help"
+  exit 1
+fi
+
+if [[ $PBEAM != "41" &&  $PBEAM != "100" && $PBEAM != "275" ]]; then
+  echo "Error: Ion beam energy should be 41, 100, or 275 GeV"
+  exit 1
+fi
+if [[ $EBEAM != 5 && $EBEAM != 10 && $EBEAM != 18 ]]; then
+  echo "Error: Electron beam energy should be 5, 10, or 18 GeV"
+  exit 1
+fi
+if [ ! -f ${COMPACT} ]; then
+  echo "Error: Compact file ${COMPACT} does not exist"
+  exit 1
+fi
+
+sed -i "s?far_forward_fields_.\{2,3\}.xml?far_forward_fields_${PBEAM}.xml?" athena.xml
+sed -i "s?far_backward_fields_.\{1,2\}.xml?far_backward_fields_${EBEAM}.xml?" athena.xml
--- a/calibrations/README.md
+++ b/calibrations/README.md
+## Calibrations for the ATHENA detector
+
+Calibrations and constants for this ATHENA detector setup. These values are used in the
+reconstruction. Each relevant subsystem that requires calibration data should have
+its own subdirectory with relevant calibration files, preferably in JSON format.
+
+Note that these calibrations are strongly versioned and tied directy to this specific
+detector configuration. Therefore, please do not add an extra layer of versioning in the
+file names, but rather only add those calibrations relevant for this particular setup.
--- a/calibrations/calo_digi_acadia.json
+++ b/calibrations/calo_digi_acadia.json
+{
+    "ecal_neg_endcap": {
+        "readout": "module",
+        "dynamicRange": "20*GeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 100,
+        "pedestalSigma": 1,
+        "thresholdValue": 3
+    },
+    "hcal_neg_endcap": {
+        "readout": "tile",
+        "dynamicRange": "20*MeV",
+        "capacityBitsADC": 8,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    },
+    "ecal_pos_endcap": {
+        "readout": "module",
+        "dynamicRange": "3*GeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 100,
+        "pedestalSigma": 0.7,
+        "thresholdValue": 2
+    },
+    "hcal_pos_endcap": {
+        "readout": "tile",
+        "dynamicRange": "3.6*GeV",
+        "capacityBitsADC": 10,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.8,
+        "thresholdValue": 3
+    },
+    "ecal_barrel_imaging": {
+        "readout": "pixel",
+        "dynamicRange": "3*MeV",
+        "capacityBitsADC": 13,
+        "pedestalMean": 100,
+        "pedestalSigma": 14,
+        "thresholdValue": 50
+    },
+    "ecal_barrel_scfi": {
+        "readout": "light_guide",
+        "dynamicRange": "750*MeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    },
+    "hcal_barrel": {
+        "readout": "tile",
+        "dynamicRange": "20*MeV",
+        "capacityBitsADC": 8,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    }
+}
--- a/calibrations/calo_digi_canyonlands.json
+++ b/calibrations/calo_digi_canyonlands.json
+{
+    "ecal_neg_endcap": {
+        "readout": "module",
+        "dynamicRange": "20*GeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 100,
+        "pedestalSigma": 1,
+        "thresholdValue": 3
+    },
+    "hcal_neg_endcap": {
+        "readout": "tile",
+        "dynamicRange": "20*MeV",
+        "capacityBitsADC": 8,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    },
+    "ecal_pos_endcap": {
+        "readout": "module",
+        "dynamicRange": "3*GeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 100,
+        "pedestalSigma": 0.7,
+        "thresholdValue": 2
+    },
+    "hcal_pos_endcap": {
+        "readout": "tile",
+        "dynamicRange": "3.6*GeV",
+        "capacityBitsADC": 10,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.8,
+        "thresholdValue": 3
+    },
+    "ecal_barrel_imaging": {
+        "readout": "pixel",
+        "dynamicRange": "3*MeV",
+        "capacityBitsADC": 13,
+        "pedestalMean": 100,
+        "pedestalSigma": 14,
+        "thresholdValue": 50
+    },
+    "ecal_barrel_scfi": {
+        "readout": "light_guide",
+        "dynamicRange": "750*MeV",
+        "capacityBitsADC": 14,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    },
+    "hcal_barrel": {
+        "readout": "tile",
+        "dynamicRange": "20*MeV",
+        "capacityBitsADC": 8,
+        "pedestalMean": 20,
+        "pedestalSigma": 0.3,
+        "thresholdValue": 1
+    }
+}
--- a/calibrations/calo_digi_default.json
+++ b/calibrations/calo_digi_default.json
+calo_digi_canyonlands.json
\ No newline at end of file
--- a/calibrations/calo_digi_table_v3.xlsx
+++ b/calibrations/calo_digi_table_v3.xlsx
--- a/calibrations/emcal_barrel_calibration.json
+++ b/calibrations/emcal_barrel_calibration.json
+{
+    "electron": {
+        "particle_name": "electron",
+        "sampling_fraction": 0.1053739677993623,
+        "sampling_fraction_error": 0.00014385360879111712,
+        "sampling_fraction_error_img": 7.262477989358573e-05,
+        "sampling_fraction_error_scfi": 0.0001238835428684493,
+        "sampling_fraction_img": 0.006008855583640059,
+        "sampling_fraction_scfi": 0.09940809338992981,
+        "thrown_energy": 5.000000028019361
+    }
+}
--- a/calibrations/ffi_zdc.json
+++ b/calibrations/ffi_zdc.json
+{
+    "ffi_zdc_ecal": {
+        "sampling_fraction": 1.0,
+        "minClusterCenterEdep": "3.*MeV",
+        "minClusterHitEdep": "0.1*MeV",
+        "localDistXY": ["50*mm", "50*mm"],
+        "splitCluster": true
+    },
+    "ffi_zdc_hcal": {
+        "sampling_fraction": 1.0,
+        "minClusterCenterEdep": "1.*MeV",
+        "minClusterHitEdep": "0.1*MeV",
+        "localDistXY": ["200*mm", "200*mm"],
+        "splitCluster": false
+    }
+}
No results found