Unverified Commit 25ee3486 authored by Stephan Lachnit's avatar Stephan Lachnit
Browse files

doc: fix lists with missing empty lines 



required for pandoc to properly render lists

Signed-off-by: default avatarStephan Lachnit <stephanlachnit@debian.org>
parent 5f912b90

doc/usermanual/05_geometry_detectors/03_modelgeom.md

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@@ -52,6 +52,7 @@ This geometry can be selected using `geometry = hexagon` 
## Radial Strips



Radial strip detectors feature a trapezoidal shape with curved edges and radial geometry – the strips on such a sensor are arranged in a fan-like geometry, pointing to a common focal point. Shape, size and segmentation of a radial strip detector are defined using four parameters, each passed as an array with the number of elements equal to the number of strip rows:



- `number_of_strips`

- `angular_pitch`

- `inner_pitch`

doc/usermanual/07_objects/01_object_types.md

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@@ -23,12 +23,15 @@ global coordinates of the event, the energies (total as well as kinetic only) at 
name, and the volume it took place in. Furthermore, the particle's PDG id \[[@pdg]\] is stored.



Main properties:



- Global points where track came into and went out of existence

  ([`getStartPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-getstartpoint),

   [`getEndPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-getendpoint))



- Global time when the track had its first and last appearance

  ([`getGlobalStartTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-getglobalstarttime),

   [`getGlobalEndTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-getglobalendtime))



- Initial and final kinetic and total energy

  ([`getKineticEnergyInitial()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-getkineticenergyinitial),

   [`getTotalEnergyInitial()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mctrack/#function-gettotalenergyinitial),
@@ -56,20 +59,25 @@ is counted from the beginning of the event. Local spatial coordinates are determ 
time measurement references the entry point of the *first* MCParticle of the event into the detector.



Main parameters:



- Entry and exit points of the particle in the sensor in local and global coordinates

  ([`getLocalStartPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getlocalstartpoint),

   [`getGlobalStartPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getglobalstartpoint),

   [`getLocalEndPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getlocalendpoint),

   [`getGlobalEndPoint()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getglobalendpoint))



- The arrival time of the particle in the sensor in local and global coordinates

  ([`getLocalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getlocaltime),

   [`getGlobalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getglobaltime))



- PDG id for this particle type

  ([`getParticleID()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getparticleid))



- If the particle is a primary particle or has a parent particle

  ([`isPrimary()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getprimary)),

  and the parent particle, if any

  ([`getParent()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-getparent))



- The track the particle is related to, if any

  ([`getTrack()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1mcparticle/#function-gettrack))
@@ -81,16 +89,20 @@ This is a meta class for a set of charges within a sensor. The properties of thi 
[DepositedCharge](#depositedcharge) and [PropagatedCharge](#propagatedcharge) objects.



Main parameters:



- The position of the set of charges in the sensor in local and global coordinates

  ([`getLocalPosition()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getlocalposition),

   [`getGlobalPosition()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getglobalposition))



- The associated time of the set of charges in local and global coordinates

  ([`getLocalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getlocaltime),

   [`getGlobalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getglobaltime))



- The sign of the charge carries

  ([`getSign()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getsign))

  and the amount of charges in the set

  ([`getCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-getcharge))



- The carrier type to check if the charge carriers are electrons or holes

  ([`getType()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1sensorcharge/#function-gettype))
@@ -104,7 +116,9 @@ addition, the time (in *ns* as the internal framework unit) of the deposition af 
carrier (electron or hole) is stored.



Main parameters:



- Everything from [SensorCharge](#sensorcharge)



- The [MCParticle](#mcparticle) that created the deposited charge

  ([`getMCParticle()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1depositedcharge/#function-getmcparticle))
@@ -119,25 +133,34 @@ another process. Timing information giving the total time to arrive at the final 
also be stored.



Main parameters:



- Everything from [SensorCharge](#sensorcharge)



- The associated [DepositedCharge](#depositedcharge) object

  ([`getDepositedCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1propagatedcharge/#function-getdepositedcharge))



- The associated induced [pulses](#pulse), if any

  ([`getPulses()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1propagatedcharge/#function-getpulses))



- The carrier state of the charge carriers described below

  ([`getState()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1propagatedcharge/#function-getstate))



The following values for the carrier state are possible:



- `CarrierState::UNKNOWN`:

  The final state of the charge carrier is unknown, for example because it might not have been provided by the used

  propagation algorithm



- `CarrierState::MOTION`:

  The charge carrier was still in motion when the propagation routine finished, for example when the configured integration

  time was reached



- `CarrierState::RECOMBINED`:

  The charge carrier has recombined with the silicon lattice at the given position



- `CarrierState::TRAPPED`:

  The charge carrier has been trapped by a lattice defect at the given position



- `CarrierState::HALTED`:

  The motion of the charge carrier has stopped, for example because it has reached an implant or the sensor surface
@@ -150,18 +173,23 @@ from zero for the first pixel. Only the total number of charges at the pixel is 
the individual charges can be retrieved from the related [PropagatedCharge](#propagatedcharge) objects.



Main parameters:



- The pixel corresponding to the charge

  ([`getPixel()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getpixel))

  and its index

  ([`getIndex()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getindex))



- The charge collected in the pixel

  ([`getCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getcharge),

   [`getAbsoluteCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getabsolutecharge))



- The related [propagates charges](#propagatedcharge)

  ([`getPropagatedCharges()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getpropagatedcharges))



- The associated time of the charge in local and global coordinates

  ([`getLocalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getlocaltime),

   [`getGlobalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getglobaltime))



- The recorded [charge pulse](#pulse), if any

  ([`getPulse()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelcharge/#function-getpulse))
@@ -174,8 +202,10 @@ implant, if such information is available in the simulation. A pulse object alwa 
creation of the object. It inherits from [std::vector<double>](https://en.cppreference.com/w/cpp/container/vector).



Main parameters:



- The total charge of the pulse

  ([`getCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pulse/#function-getcharge))



- The time binning of the pulse

  ([`getBinning()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pulse/#function-getbinning))
@@ -192,16 +222,20 @@ The exact type of the time and signal values depends on the digitizer module use 
[module documentation](../08_modules/_index.md) is to be consulted.



Main parameters:



- The pixel corresponding to the hit

  ([`getPixel()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getpixel))

  and its index

  ([`getIndex()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getindex))



- The related [PixelCharge](#pixelcharge)

  ([`getPixelCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getpixelcharge))

  and PixelPulse, if any

  ([`getPixelPulse()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getpixelpulse))



- The signal of the hit

  ([`getSignal()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getsignal))



- The time information of the hit in local and global coordinates

  ([`getLocalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getlocaltime),

   [`getGlobalTime()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelhit/#function-getglobaltime))
@@ -214,11 +248,14 @@ If the detector's front-end electronics provide a digitized front-end pulse, thi 
information. It inherits from the [Pulse](#pulse) object.



Main parameters:



- Everything from [Pulse](#pulse)



- The pixel corresponding to the digitized pulse

  ([`getPixel()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelpulse/#function-getpixel))

  and its index

  ([`getIndex()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelpulse/#function-getindex))



- The corresponding [pixel charge](#pixelcharge)

  ([`getPixelCharge()`](https://allpix-squared.docs.cern.ch/reference/classes/classallpix_1_1pixelpulse/#function-getpixelcharge))

src/modules/DepositionCosmics/README.md

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@@ -58,6 +58,7 @@ Note: Neutrons have a lifetime of 882 seconds and will not be propagated in the 
* `output_plots_scale` : Set the x-axis scale of the output plot, defaults to 100ke.



### CRY Framework Parameters



* `latitude`: Latitude for which the incident particles from cosmic ray showers should be simulated. Should be between `90.0` (north pole) and `-90.0` (south pole). Defaults to `53.0` (DESY).

* `date`: Date for the simulation to account for the 11-year cycle of solar activity and related change in cosmic ray flux. Should be given as string in the form `month-day-year` and defaults to the last day of 2020, i.e. `12-31-2020`.

* `return_neutrons`: Boolean to select whether neutrons should be returned to Geant4. Defaults to `true`.