Update README

Author: fgrosa

Detectors/Upgrades/ITS3/README.md

@@ -13,7 +13,7 @@ Events can be simulated using the `o2-sim` workflow. To include ITS3 in the simu
 
 The following command can be used to generate heavy-ion collisions:
 ```bash
-o2-sim -j 1  \
+o2-sim -j 8  \
 -n 10 -g pythia8hi --field ccdb \
 --configKeyValues "Diamond.width[2]=6.;DescriptorInnerBarrelITS3.mVersion=ThreeLayers" \
 --run 311935
@@ -22,14 +22,16 @@ In the previous command:
 - `-j` is used to set the number of threads;
 - `-n` is used to set the number of events to simulate;
 - `-g` is used to set the event generator, in this case `pythia8hi`. To simulate pp collisions one can use `pythia8pp`.
-- `--configKeyValues` is needed to set internal parameters of the workflow. Among these parameters, the geometry of the ITS3 inner barrel can be set.
+- `--configKeyValues` is needed to set internal parameters of the workflow. Among these parameters, the geometry of the ITS3 inner barrel can be set:
+  - `DescriptorInnerBarrel.mVersion` is the geometry version of the ITS3 inner barrel (`ThreeLayersNoDeadZones`, `ThreeLayers`, or `FourLayers`)
+  - `DescriptorInnerBarrel.mRadii` is a 4-element vector with the radii of the ITS3 layers
+  - `DescriptorInnerBarrel.mLength` is the length of the ITS3 in the Z direction
+  - `DescriptorInnerBarrel.mGapY` is a 4-element vector with the values of gap between the two hemicylinders, described by a translation of the hemicylinders in the vertical direction
+  - `DescriptorInnerBarrel.mGapPhi` is a 4-element vector with the values of gap of azimuthal angle between the two hemicylinders, described by the maximum distance between the two hemicylinders. Differently from `mGapY`, in this case there no shift in the vertical direction, but a smaller coverage in the azimuthal angle of the half layers.
+  - `DescriptorInnerBarrel.mGapXDirection4thLayer` is the gap in the horizontal direction for the fourth layer, analogous to the `mGapY`.
+  - `SuperAlpideParams.mDetectorThickness` is the thickness of the chip
 - `--run` is needed to set the run number.
 
-Currently, three different geometries of the ITS3 inner barrel are available:
-- `ThreeLayersNoDeadZones`
-- `ThreeLayers`
-- `FourLayers`
-
 The run number is needed to retrieve objects from the CCDB. There are specific ranges of run-numbers, according to the collision system and to the selected geometry if the ITS3 inner barrel:
 
 - **pp** collisions:
@@ -42,7 +44,6 @@ The run number is needed to retrieve objects from the CCDB. There are specific r
   - 311934—311966 (`ThreeLayers`)
   - 311967—311999 (`FourLayers`)
 
-
 ### Using external generators based on AliRoot
 It is also possible to simulate heavy-ion collision using external generators based on AliRoot. In this case, it is necessary to load both O2 and AliROOT (the order is important):
 
@@ -77,17 +78,25 @@ o2-sim-digitizer-workflow -b --run --interactionRate 50000 \
 ```
 As above, it is important to set the correct interaction rate and run number.
 
+In addition, some parameters related to the segmentation of the chips can be set with the `--configKeyValues` argument:
+- `SuperAlpideParams.mPitchCol` is the pitch of the column (Z direction)
+- `SuperAlpideParams.mPitchRow` is the pitch of the row (r$\phi$ direction)
+- `SuperAlpideParams.mDetectorThickness` is the thickness of the chip
+
+If some parameters of the geometry changed in the simulation, they should be set similarly for the digitisation. In particular, the `mVersion`, `mRadii`, and `mLength` must be set if different from the default ones.
+
 # Reconstruction
 
 In this step, clustering, vertexing and tracking are performed. This is obtained with the `o2-its3-reco-workflow`:
 
 ```bash
 o2-its3-reco-workflow --tracking-mode async -b --run \
 -—configKeyValues "
-HBFUtils.runNumber=311935;ITSCATrackerParam.trackletsPerClusterLimit=20;ITSCATrackerParam.cellsPerC
-lusterLimit=20;ITSVertexerParam.lowMultXYcut2=0."
+HBFUtils.runNumber=311935;ITSCATrackerParam.trackletsPerClusterLimit=20;ITSCATrackerParam.cellsPerClusterLimit=20;ITSVertexerParam.lowMultXYcut2=0."
 ```
 
-As above, it is important to provide the correct run number using `-—configKeyValues`, to retrieve the correct files from the CCDB. The other internal parameters provided `-—configKeyValues` via are specific to the cased here considered (Pb-Pb) and are inherited from ITS2.
+As above, it is important to provide the correct run number using `-—configKeyValues`, to retrieve the correct files from the CCDB. The other internal parameters for the vertexer and the tracker are provided `-—configKeyValues` via are specific to the cased here considered (Pb-Pb) and are inherited from ITS2.
+
+If the `FourLayers` geometry was used in the simulation, it should be set also for the reconstruction to set properly the tracker to work with the additional layer. If something else of the geometry was set differently (`mRadii`, `mLength`, `mGapY`, `mGapPhi`, `mGapXDirection4thLayer`, or `mDetectorThickness`), it is necessary to remap the file with the geometry to replace the one on the CCDB, which would be different. This can be done by copying the `o2sim_geometry-aligned.root` file created during the simulation to a directory called `GLO/Config/GeometryAligned`, with the name `snapshot.root` in a local path of choice. Then, the following argument has to be added to the reco workflow: `--condition-remap "file://local_path=GLO/Config/GeometryAligned"`.
 
-> **_NOTE:_**  reconstruction for the `FourLayers` geometry is not implemented yet.
+<!-- > **_NOTE:_**  reconstruction for the `FourLayers` geometry is not implemented yet. -->