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Page](assets/geometry/geometry.png) - * list of abstract figures (boxes, cylinders, spheres, etc.). The figures are defined by their position and size and has no material assigned to them. - * list of zones. The zones are defined by the boolean operations on the abstract figures and have assigned material. +Geometry definition varies between different types of simulation software. For simulators using Constructive Solid Geometry (CSG) - FLUKA and SHIELDHIT-12A, +shapes are defined by set of primitive Figures (boxes, cylinders, spheres) joined together by boolean operators. The order of operators to apply is defined +within a Zone. -An example geometry is shown below: +For simulators using nested geometry, like Geant4, primitive shapes are defined in a tree-like structure, and all properties are set directly on the Figures. -![Alt text](assets/geometry/geometry_example1.png) +## Starting a new project -In following sections we will go through generation of simple geometry. It will consist of: +### Blank Project - * water phantom box - * lead collimator with 2cm radius hole and 1cm thickness - * world filled with air +To start assembling the simulation geometry, you can either create a blank project or use an existing one as a base. +To create a new blank project, click Project > New. -## Creating new project +![Blank project](assets/geometry/blank_project.png) -Let us go through the process of defining simple simulation geometry. -The starting point would be a modification of existing project or creation of a new one. -Let us start with a new project as this will be good opportunity to introduce most of the Yaptide features. -It can be done using "New" button in the upper left part of the Editor window (select Editor in left menu). +You will be prompted that this operation will overwrite the current project. Save your previous work if you want to keep it. -![Alt text](assets/geometry/image.png){: style="height:150px"} +![New project alert](assets/geometry/new_project_alert.png) -You will be prompted that this operation will overwrite the current project. Save your previous work if you want to keep it. +Next, you will be asked to provide a project title, and, optionally, project description. Click `SAVE` to close the modal and enter the editor. + +![Title and description](assets/geometry/project_info.png) + +For blank project, you can select which simulator you want to use by clicking the dropdown in the header bar. -![Alt text](assets/geometry/image-1.png) +![Simulator Dropdown](assets/geometry/select_simulator.gif) -New project can get a name and description. The name can be adjusted by double click the title panel in the Editor window. +> [!NOTE] +> The COMMON option represents the set of features supported by both FLUKA and SHIELDHIT-12A. You can switch from COMMON +> to either of these simulators. -![Alt text](assets/geometry/image-title1.png) +> [!NOTE] +> You can modify the title and description by clicking the title in the header bar. +> +> ![Edit project info](assets/geometry/edit_project_info.gif) -another way is the right click on the project name in the title menu and choosing "Rename" option. +### Example project -![Alt text](assets/geometry/image-desc1.png) +Navigate to Examples page. The available examples are grouped by the simulation software they were created with. +With the exception of COMMON, they will only work with that simulator. -This way the description can be adjusted as well: +![Select example](assets/geometry/examples.png) -![Alt text](assets/geometry/image-desc2.png) +Next, you will get similar Alert as when creating blank project. After confirmation, you are presented with editor page. + +![Load project alert](assets/geometry/load_project_alert.png) + +The title and description come from the example, you can modify them by clicking the title in header bar. ## Adding figures -### Main box +In the following sections we will go through generation of simple geometry. It will consist of: + +- water phantom box +- lead collimator with 2cm radius hole and 1cm thickness +- world filled with air + +### World filled with air Lets start with adding a box filled with air with dimensions large enough to fit the other object we would like to simulate. -There are two ways to add a box, either from upper left menu in the Editor tab or by going to Geometry tab in right menu and expanding "Figures" block. Both entries are in the "Editor" window. +There are two ways to add a box, either selecting `Object > Box` in Menu Bar, or clicking `+ BOX` in FIGURES section in GEOMETRY tab. + +![Add Figure from Object Menu](assets/geometry/menu_object_add.png) -![Alt text](assets/geometry/image-2.png) -![Alt text](assets/geometry/image-3.png) +![Add Figure from FIGURES section](assets/geometry/figures_add.png) Lets create a box spanning from -2 to 10 in z direction and from -5 to 5 in x and y direction. -In the yaptide we need to provide box center (named "Position") and its dimensions (named "X/Y/Z side"). +We do this by providing box center (named "Position") and its dimensions (named "X/Y/Z side"). In our case the position will be (4,0,0) and dimensions 12cm x 10cm x 10cm. -Note that basic dimensions units in yaptide are centimeters. -Leta also assign a meaningful name to the created figure. +Note that basic dimensions units in YAPTIDE are centimeters. +Let's also assign a meaningful name to the created figure. -![Alt text](assets/geometry/image-4.png) +![Object details](assets/geometry/object_details.png) The figure is created and its cross-sections in YX, XZ and ZY planes visible in the 3 windows in the center of the screen. The 3-D projection is visible as well. ### Large phantom -Then lets proceed with adding a box which will represend a water phantom in which the simulated beam will stop. +Let's now add a box which will represent a water phantom in which the simulated beam will stop. This box will be placed inside the world box and will be 8cm x 8cm x 8cm in size. We are going to place it at (4,0,0) position as well. The dimensions are given in such way that the water phantom is fully contained in the world box. -This time we will use a different technique of adding a figure: we will duplicate the WorldBox and modify the dimensions. -Such action can be achieved by right click on the WorldBox entry visible in the "Figures" section of the Geometry tab in right menu. +This time we're going to demonstrate how to duplicate existing figure, and then modify its dimensions. +Right-click on the WorldBox entry visible in the FIGURES section and click Duplicate. -![Alt text](assets/geometry/image-5.png) +![Duplicate WorldBox](assets/geometry/duplicate.png) The newly created figure will inherit the name from the duplicated object. An `_1` suffix will be added to the name to keep all the names unique. All other properties (like position and dimensions) will be copied as well. -![Alt text](assets/geometry/image-6.png) +![Duplicated WorldBox](assets/geometry/duplicated.png) Now lets adjust the dimensions of the newly created figure to 8cm x 8cm x 8cm, as the position can stay the same. Also the name needs an update to `PhantomBox`. Note that the two figures are visible in the 3-D projection window, while only current one is visible in the cross-sections. -![Alt text](assets/geometry/image-7.png) +![PhantomBox](assets/geometry/phantom_box.png) ### Collimator -Finally lets add two cylinders represending outer envelope and inner hole inside the collimator. -The cylinders have thickness of 1cm and are radius of 4 and 2 cm appropriately. +Finally lets add two cylinders representing outer envelope and inner hole inside the collimator. +The cylinders have thickness of 1cm and are radius of 4 and 2 cm respectively. Both are centered around (0,0,0) point. You can use drag operation by clicking and dragging on the 3-D projection view. This would help to adjust the view, so the collimator is visible. -![Alt text](assets/geometry/image-8.png) +![Cylinders](assets/geometry/cylinders.png) ## Adding new zone -With all the basic figures defined we can use then to construct the zones which will be used in the simulation. +With the figures defined above, we can construct the zones which will be used in the simulation. Here we follow the naming of SHIELD-HIT12A, as Fluka calls the zones "regions". -Lets start with adding the zone which will represent the large box willed with air. -This can be done in a similar way as adding the figures, either from upper left menu in the Editor tab or by going to Geometry tab in right menu and expanding "Zones" block. Both entries are in the "Editor" window. -Note that by defaul an automatically created "World Zone" is visible. - -![Alt text](assets/geometry/image-9.png) -![Alt text](assets/geometry/image-10.png) +Lets start with adding a zone which will represent the large box filled with air. +This can be done in a similar way as adding the figures, either from upper left menu in the Editor tab +or by going to Geometry tab in right menu and expanding ZONES section in GEOMETRY tab. -### Main zone -We start by defining first zone from the main box, assigning it the material: Air. +![Add Boolean Zone from Object Menu](assets/geometry/menu_boolean_zone_add.png) +![Add Boolean Zone from ZONES section](assets/geometry/boolean_zone_add.png) -After creating new Zone we should see a following entry in the right-menu. -New entry appears as well in the list of Zones. -The newly created zone named "Boolean Zone" has liquid water attached as a meterial by default. -Note that in "Zone Operations" we see "Not selected" message. This means that the zone has no figures attached. +> [!NOTE] +> A special "World Zone" which represents the whole simulation environment is defined by default, and can't be removed. -![Alt text](assets/geometry/image-11.png) +### Air zones -Lets attach the correct figure to the zone by clicking on the "Not selected" message and choosing the "WorldBox" figure. +Zones describe a volume of space by combining multiple figures using boolean operations to define shape, +and define physical material that the volume is made of. -![Alt text](assets/geometry/image-12.png) +> [!IMPORTANT] +> Defining zone operations requires special considerations. Each point in space should belong to exactly +> one Zone so that it is clear for the simulator which material the particle is going through. +> This means that the volume enclosing another volume with different material needs to have a cutout that will fit the inner volume. -Then lets rename the zone to "MainZone" and assign the material to it. -The material can be selected from the list of materials in the "Simulation" menu ("Material" area). -After selecting the list of materials you can type few letters ("ai" in our case) and list of materials containing the typed letters will be shown. +Let's expand ZONE OPERATIONS and define the MainAirZone and CollimatorAirZone. +Together they represent the air that fills the empty space around the phantom and the collimator. +To get precisely the air volume, we need to subtract both the phantom and the collimator. +- For the phantom, it only requires subtracting the phantom figure. +- For the collimator, we need to subtract the whole outer cylinder, and add back the inner cylinder. The "adding back" +is performed with second zone. -![Alt text](assets/geometry/image-13.png) - -To improve visual properties we adjust the color and set opacity to 0.05: -![Alt text](assets/geometry/image-14.png) - -### Water phantom zone +Defining the MainAirZone is shown below: -Then we proceed with adding the water phantom zone. Lets add new zone and assign the "PhantomBox" as the figure. -We rename the zone to "PhantomZone". There is no need to assign the material as we stay with defaul "Liquid Water" material. +![Defining zone operations for MainZone](assets/geometry/zone_operations.gif) -![Alt text](assets/geometry/image-15.png) +CollimatorAirZone is then simply: -We change the color and inspect the zone in the 3-D projection window. +![Collimator air zone](assets/geometry/collimator_air_zone.png) -![Alt text](assets/geometry/image-16.png) +Zones are visualized in the 3D view by solid colors. We can see the cutouts for the phantom and the collimator. -There is a caveat with defining the zones by boolean operations. Each point in the space needs to belong to exactly one zone. -This ensures that each point has exactly one material assigned to it. -Currently the interior of the phantom box belongs to both zones: "MainZone" and "PhantomZone". Its unclear which material should be assigned to it: air or water. -Therefore we modify the "MainZone" by subtracting the "PhantomBox" from it. -This is done by selecting "MainZone" on list of zones and choosing "Subtract" operations: +![Zone in 3D view](assets/geometry/zone_vis.png) -![Alt text](assets/geometry/image-17.png) +> [!NOTE] +> To better see what's inside the zone, you can set the Opacity under MATERIAL section. +> ![Custom opacity](assets/geometry/custom_opacity.png) -Then the "Not selected field" appears - -![Alt text](assets/geometry/image-18.png) - -We choose "PhantomBox" figure there: +### Water phantom zone -![Alt text](assets/geometry/image-19.png) +We repeat the same thing for water phantom zone. Let's add new zone and assign the "PhantomBox" as the figure. +There is no need to assign the material as we stay with default "Liquid Water" material. -Finally the zone operations for "MainZone" are updated: +Under the MATERIAL section, instead of Opacity, we change the color and inspect the zone in the 3D view. -![Alt text](assets/geometry/image-20.png) +![Phantom Zone](assets/geometry/phantom_zone.png) ### Collimator zone -We are going to define the collimator zone now. -The collimator is a large cylinder (represented by `OuterCylinder` figure with radius 4cm) with a hole inside (represented by `InnerCylinder` figure, radius 2cm) - -The zone is created by attaching `OuterCylinder` figure and subtracting `InnerCylinder` from it. -We select `Lead` material for the zone. - -![Alt text](assets/geometry/image-21.png) - -This time again the `MainZone` needs to be updated as the collimator zone is inside it. -First we subtract the `OuterCylinder` from the `MainZone`: - -![Alt text](assets/geometry/image-22.png) - -Lets note that after this operation the `InnerCylinder` doesn't have a material assigned, it shoult be filled with air. -This can be done by adding a separate zone and assigning the `InnerCylinder` to it. - -### Air inside collimator - -We add a new zone and assign the `InnerCylinder` to it. - -![Alt text](assets/geometry/image-23.png) - -No other zones needs to be modified. +The collimator is a lead ring that is created by subtracting inner cylinder from outer cylinder. +We name the zone appropriately and set the material. -Finally our geometry is complete: +![Collimator Zone](assets/geometry/collimator_zone.png) -![Alt text](assets/geometry/image-24.png) \ No newline at end of file +These are the basic steps for defining geometry for CSG-based simulators. \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 002e433..8bc9ae4 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,38 +1,41 @@ -# User documentation +
+ +

YAPTIDE User Documentation

+
-The yaptide platform provides an easy way to work with particle transport simulations. +The YAPTIDE platform provides an easy way to work with particle transport simulations. Most popular particle transport codes, like Geant4, TOPAS, MCNP require preparation of the input text files and running the simulation in a terminal. The FLUKA code has an graphical user interface, called Flair, but it requires Linux (or Windows with WSL) to run. -The yaptide platform provides a way to define a simulation in a web browser without the need to install any software. This is possible without the need to register or login in the platform. -Having access to the computing resources (i.e. by registering in the PLGRID platform or deploying the platform locally) allows to run the simulation in a parallel way using our web platform. The results of simulation can be visualized in the web browser or downloaded to the local computer. +The YAPTIDE platform provides a way to define a simulation in a web browser without the need to install any software. This is possible without any login or registration. +Having access to the computing resources (i.e. by registering in the [PlGrid](https://portal.plgrid.pl/) platform or deploying the project locally) allows to run the simulation in a parallel way using our web platform. The results of simulation can be visualized in the web browser or downloaded to the local computer. ## How to use the platform ### Demo version -Demo version of the platform is hosted on the GitHub pages as [yaptide.github.io](https://yaptide.github.io). +![Demo landing page](assets/demo.png) + +Demo version of the platform is hosted on the GitHub pages as [yaptide.github.io](https://yaptide.github.io/web_dev). This version is free for use and doesn't require to register or login. -In demo version the platform works as online editor for simulation input and results browser. Following functionalities are available: +In demo version the platform works as an online editor for simulation input and results browser. The following functionalities are available: - - defining and visualisation of simulation geometry and materials + - defining and visualizing simulation geometry and materials - defining scoring geometry, scored quantities and advanced scoring options (like filtering) - defining particle source - specifying simulation settings (like physics parameters) - - generating files with simulation input (to be executed on a user resources) - - browsing results of simulation (previously calculated using yapide platform or other software) - -![Alt text](assets/image.png) + - generating files with simulation input (to be executed on user resources) + - browsing results of simulation (previously calculated using YAPTIDE platform or other software) ### Full version -Full version is hosted in the PLGRID infrastructure and requires registration and login. To access the platform visit [yaptide.c3.plgrid.pl](https://yaptide.c3.plgrid.pl). - -Full version allows execution of simulation on a cloud (few machines in C3 PLGRID Cloud) or HPC resources (Ares supercomputer in ACK Cyfronet). +![Simulations page - available for logged in users](assets/simulations.png) -![Alt text](assets/index/image.png) +Full version is hosted in the PlGrid infrastructure and requires registration and login. To access the platform visit [yaptide.c3.plgrid.pl](https://yaptide.c3.plgrid.pl). -The platform requires registration and allows the access for selected group of users with accound in the PLGRID infrastructure. To register in the platform, please contact the administrator. +You'll be able to execute your simulations in the cloud (few machines in C3 PlGrid Cloud) or HPC resources (Ares supercomputer in ACK Cyfronet). -![Alt text](assets/index/image-1.png) \ No newline at end of file +> [!NOTE] +> The platform requires registration and allows the access for selected group of users +> with account in the PLGrid infrastructure. To register in the platform, please contact the administrator. \ No newline at end of file diff --git a/docs/running.md b/docs/running.md index ff56dab..fc56723 100644 --- a/docs/running.md +++ b/docs/running.md @@ -5,41 +5,54 @@ We assume that you have already registered and logged in to the platform. To run the simulation you need to have proper project loaded in the editor window. -![Alt text](assets/running/image.png) +![Simulation set up](assets/running/simulation_set_up.png) -To run the simulation please select `Simulation` item in the left menu. You will be presented with list of already completed simulations: +To run the simulation, click `RUN` in the title bar, or select Simulation page from the Navigation Bar on the left. -![Alt text](assets/running/image-1.png) +## Simulations Page -The simulation can be started by clicking on `RUN NEW SIMULATION` button which will present couple of options. +The Simulations Page consists of 3 main sections: + +1. Simulations Archive, where all previously run simulations are presented in paginated view +2. Run new simulation form which presents different ways to run the simulation currently loaded to Editor +3. Last 5 simulations, which always displays the 5 most recent simulations + +> [!NOTE] +> For convenience, the sidebar with sections 2. and 3. is pinned to Simulations, Input files, and Results pages. +> You can run and see recent simulations from each of these pages. + +![Simulations Page](assets/running/simulations_page.png) + +## Running the simulation You could choose where to run simulation: - - as *DIRECT RUN* in the dedicated cloud resources (currently limited to 15 cores machine in the C3 PLGRID Cloud) + - as *DIRECT RUN* in the dedicated cloud resources (currently limited to 15-core machine in the C3 PLGrid Cloud) - as *BATCH RUN* in the HPC resources (by submitting the job to the SLURM batch management system in Ares supercomputer) - The direct run may have much shorter time to start the simulation, but the parallelism is limited to 15 cores. The batch run may take longer to start the simulation, but the parallelism is limited only by the resources available in the HPC cluster. - -![Alt text](assets/running/image-2.png) + The direct run may have much shorter time to start the simulation, but the parallelism is limited to 15 cores. + The batch run may take longer to start the simulation, but the parallelism is limited only by the resources available in the HPC cluster. ## Direct run -### Submission -Lets start by submitting the simulation with 15 cores, selecting proper number of tasks and `DIRECT RUN` option. Press start to submit the simulation. +Direct run is the default option. In the form, you can change the name (doesn't need to be the same as the project title), +number of tasks, and overwrite the number of primary particles (the default is specified under SETTINGS in Editor page). -![Alt text](assets/running/image-7.png) +![Direct Run](assets/running/direct_run.png) -You will see a new entry in the list of simulations with status `PENDING`. The simulation will start automatically when the resources will be available. +When the parameters are set, click `START SIMULATION` to send it to the YAPTIDE server. +After successful submission, the simulation is in PENDING state. +The simulation will start automatically when the resources will be available, then it will change to RUNNING state, +and you will be able to see the progress of the simulation by observing the progress bar. -![Alt text](assets/running/image-3.png) +![Pending state](assets/running/direct_run_pending.png) +![Running state](assets/running/direct_run_running.png) -Once the simulation is running, the status will change to `RUNNING` and you will be able to see the progress of the simulation by observing the progress bar of each task. +The simulation is also present in the pinned "Last 5 simulations" section. -![Alt text](assets/running/image-4.png) +![Pinned to Last 5 simulations section](assets/running/direct_run_queue.png) -You can see that some of the tasks may be already completed (green), while others are running (dark). - -![Alt text](assets/running/image-5.png) +When the simulation finishes, it will automatically navigate to Results page and display the results. ### Viewing results @@ -47,50 +60,41 @@ Once all tasks are completed, the status of the simulation will change to `COMPL You will be automatically redirected to the `Results` tab in the left menu. First you will see a depth dose profile for the `AlongBeamAxis` scoring geometry. -![Alt text](assets/running/image-6.png) - -The plots are interactive, using mouse coursor you can zoom selected fragments of the plot: +![Results of a finished simulation](assets/running/finished_results.png) -![Alt text](assets/running/image-8.png) +The plots are interactive, using mouse cursor you can zoom selected fragments of the plot: -![Alt text](assets/running/image-9.png) +![Selecting fragments to zoom](assets/running/zoom_selected.png) -Both axis scale can be changed to logarithmic by right click in the axis area: +![Alt text](assets/running/zoomed.png) -![Alt text](assets/running/image-10.png) -![Alt text](assets/running/image-11.png) +To revert the view you can click in the plot area and disable the logarithmic scale and zooming. +Both axes scale can be changed to logarithmic by right click in the axis area. -To revert the view you can click in the plot area and disable the logarithmic scale and zooming: -![Alt text](assets/running/image-12.png) +![Changing plot settings](assets/running/plot_settings.gif) Plots data can be saved to CSV file by clicking on the `Export graph to CSV` button: -![Alt text](assets/running/image-13.png) -![Alt text](assets/running/image-14.png) +![Alt text](assets/running/export_csv.png) The YZ profile can be seen by selecting proper Output item. As we see collimator is stopping most of the protons on radius larger than 2 cm. -![Alt text](assets/running/image-15.png) +![Alt text](assets/running/collimator_results.png) -Two dimensional plots can be also inspected by plotting the profiles. On right click in the blue colored are we see proper menu: +Two-dimensional plots can be also inspected by plotting the profiles. On right click in the blue colored area we see proper menu: -![Alt text](assets/running/image-16.png) -![Alt text](assets/running/image-17.png) -![Alt text](assets/running/image-18.png) - -X projection reveals that with 10^4 primaries statitics is not enough: -![Alt text](assets/running/image-19.png) +![Alt text](assets/running/profiles.gif) ## Batch run -When executing simulation with 10^4 primaries and 15 cores, the process completed in 37 seconds. To obtain better statistics we will try to run 10^6 primaries on 100 parallel tasks. This is not possible with direct run, so we will use batch run. - -![Alt text](assets/running/image-20.png) +If the plots need more precision, then we need to rerun the simulation with more primaries. We can quickly reach the Run new simulation form +and increase the number. This will make the simulation run take much more time. For the case of computationally expensive simulations, +we can utilize the Batch Run. -The jobs may stay longer in `PENDING` state, waiting for the resources to be available. +![Batch Run](assets/running/batch_run.png) -![Alt text](assets/running/image-22.png) +The job pops up in the queue, and we can use the application in the meantime. -once the simulation is running, the status will change to `RUNNING` and you will be able to see the progress of the simulation by observing the progress bar of each task. -The estimated time of each tasks may be seen by moving mouse cursor over the progress bar. +![Queued Batch Run](assets/running/batch_run_queue.png) -![Alt text](assets/running/image-23.png) \ No newline at end of file +> [!NOTE] +> Large Batch Jobs may stay longer in `PENDING` state, waiting for the resources to be available. \ No newline at end of file diff --git a/docs/scoring.md b/docs/scoring.md index 4a5da72..3686764 100644 --- a/docs/scoring.md +++ b/docs/scoring.md @@ -2,46 +2,39 @@ Scoring requires user to define several items: - * Scoring geometry, here named as detector + * Scoring geometry, here named "detector" * Scoring quantity * Scoring output, which is a group of quantities scored in the same detectors In addition, there are several optional items: - * Scoring filter, which can be attached to some quantities, like score the quantities for protons only + * Scoring filter, which can be attached to selected quantities, i.e. "score the quantities for protons only" * Differential modifiers, i.e. allowing to score quantities in different energy bins - * Other settings, rescaling factors or custom material definitions + * Other settings, rescaling factors or custom material definitions -In the section below we will add couple of items to demontrate the scoring capabilities of Yaptide. +In the section below we will add a couple of items to demonstrate the scoring capabilities of YAPTIDE. ## Detectors -Detectors can be added from `Detector` area in the right menu of Editor view. +Detectors can be added either by selecting `Object > Detector` in Menu Bar or clicking `+ DETECTOR` in DETECTORS section in GEOMETRY tab. -![Alt text](assets/scoring/image.png) +![Adding a detector from menu bar](assets/scoring/menu_detector_add.png) -another option is the menu in upper left corner of the Editor view: - -![Alt text](assets/scoring/image-1.png) +![Adding a detector from DETECTORS section](assets/scoring/detector_add.png) ### Narrow cylinder along the beam axis -Lets start with adding a cylinder with radius of 1cm and length of 12cm along the beam axis, spanning from -2cm to 12cm along Z axis. -By pressing "Add detector" button a new item will be added to the list of detectors. - -![Alt text](assets/scoring/image-2.png) - -We follow by assigning a name to the detector: `AlongBeamAxis`. -Then we change the detector type to `Cyl`: +Let's start with adding a cylinder with radius of 1cm and length of 12cm along the beam axis, spanning from -2cm to 12cm along Z axis. +By pressing `+ DETECTOR` button a new item will be added to the list of detectors. Change the settings as follows: -![Alt text](assets/scoring/image-3.png) +- Rename the detector to `AlongBeamAxis`. +- Set the position in PLACEMENT section. To get correct span we set center to (0,0,4) cm. +- Select the geometry type. For this example, use Cyl for cylinder geometry. Change the depth and radius as below. +- Under GRID, change the number of bins. We divide the detector into 120 bins along the Z axis, so that each bin is 1mm long. -Finally we can adjust the size and position of the detector. To get correct span we set center to (0,0,4) cm. -We also divide the detector into 120 bins along the Z axis, so that each bin is 1mm long. +![Setting up new detector](assets/scoring/detector_details.png) -![Alt text](assets/scoring/image-4.png) - -When selected the detector should be visible in the 3D and cross-section views. +When selected, the detector should be visible in the 3D and cross-section views. ### Slab in YZ plane @@ -50,83 +43,82 @@ Lets add a 1mm thick slab detector in YZ plane, spanning from -2cm to 12cm in Z We select the detector type to be `Mesh` and set the center to (0,0,4) cm and dimensions to 0.1 x 10 x 12 cm. This time the bins are defined in Y and Z directions, so we set 100 bins in Y and 120 bins in Z directions to get 1x1mm bins. -![Alt text](assets/scoring/image-6.png) - +![Setting up second detector](assets/scoring/detector_details_slabyz.png) ## Scoring output -To define scoring output we switch to `Scoring` tab i the right menu of Editor view. +To define scoring output we switch to SCORING tab in the right menu of Editor view. -![Alt text](assets/scoring/image-7.png) +![Scoring tab](assets/scoring/scoring_tab.png) ### Along the beam axis To define new scoring output we press "Add output" button in the Outputs area. A new item will be added to the list of outputs. This item will have no detector assigned. -![Alt text](assets/scoring/image-8.png) - -First we select proper detetor from a drop-down list: +![Scoring Output added](assets/scoring/output_added.png) -![Alt text](assets/scoring/image-9.png) +Let's assign the output an appropriate name `AlongBeamAxis` and select the detector from the dropdown list. +The chosen detector will be visible in the 3D and cross-section views. -Then we assign a proper name to the output: `AlongBeamAxis`. We may use the same name as the name of the detector, but it is not required. -The choosen detector will be visible in the 3D and cross-section views: - -![Alt text](assets/scoring/image-10.png) +![Setting up the Scoring Output](assets/scoring/output_details.png) ### YZ plane slab -We repeat similar exercise to define the output for the slab detector. - -![Alt text](assets/scoring/image-11.png) +We repeat the steps for the slab detector. +![Setting up the YZSlab Scoring Output](assets/scoring/output_details_yzslab.png) ## Scoring quantity ### Depth dose profile Lets start by defining a scoring for depth dose profile in cylinder detector along the beam axis. -This can be done by expanding the `AlongBeamAxis` item in the Outputs list by clicking on `>` icon. +This can be done by expanding the `AlongBeamAxis` item in the Outputs list by clicking on `+` icon. We can see that the output has already a first scoring quantity added, named `Quantity`. -![Alt text](assets/scoring/image-12.png) +![Default quantity](assets/scoring/default_quantity.png) -By default scoring of dose was selected, so we stay with this, just adding a meaningful name. +By default scoring of dose was selected, so we stay with this, just adding a meaningful name: `Dose`. -We are planning to simulate the interaction of beam of protons with the phantom, therefore with such scoring we could see the characteristic Bragg peak. +We are planning to simulate the interaction of beam of protons with the phantom, and with such scoring we could see the +characteristic Bragg peak. ### Fluence profile in YZ plane -As in our geometry we applied a 1 cm thick collimator made of lead, we would like to see the effect of the collimator on the fluence of protons. -Such thickness should be enough to stop most completely 70 MeV protons (the CSDA range in lead at that kinetic energy is about 8mm). +Since in our geometry we applied a 1 cm thick collimator made of lead, we would like to see the effect of the collimator +on the fluence of protons. Such thickness should be enough to stop most completely 70 MeV protons +(the CSDA range in lead at that kinetic energy is about 8mm). -To score the fluence we need to change the scoring quantity to `Fluence` and add a meaningful name. +To score the fluence, we need to change the scoring quantity to `Fluence` and add a meaningful name. We select default quantity in `YZSlab` item, define proper name and quantity type: -Note that we can type some letters to get list of available quantities filtered by the typed letters. +![Defining Fluence quantity](assets/scoring/quantity_fluence.png) -![Alt text](assets/scoring/image-13.png) +> [!NOTE] +> Quantity type supports typing letters to filter the list of available quantities. Such quantity won't be very useful, as it will show the fluence of all particles, including neutrons and other charged particles. -To limit the scoring to protons only we need to add a filter. +To limit the scoring to protons only, we need to add a filter. #### Scoring filter -We define a filter in the "Filters" area of the Scoring tab. -By pressing `Add Filter` new item will be added to the list of filters. - -![Alt text](assets/scoring/image-14.png) - +We define a filter in the FILTERS section of the SCORING tab. +By pressing `+ FILTER` (or `+ CUSTOM FILTER` in SHIELD-HIT), new filter will be added to the list of filters. We adjust the name of the filter to `Protons` and add two rules to define proton (A=1 and Z=1): -First rule is added by clicking on `Add Rule` button and then selecting `Z` and `=` from the drop-down lists. +First rule is added by clicking `ADD RULE` button and then selecting `Z` and `=` from the drop-down lists. Then we type `1` in the text field. -![Alt text](assets/scoring/image-15.png) +![Rule for protons](assets/scoring/protons_rule_z_eq_1.png) Second rule defines the `A=1` condition. -Finally we apply the filter by selecting the Filter checkbox in the `Fluence` item in the list of `YZSlab` quantities. +![Rule for protons](assets/scoring/protons_rule_a_eq_1.png) + +Finally, we apply the filter by selecting the Filter checkbox in the `Fluence` item in the list of `YZSlab` quantities. Then we choose `Protons` from the drop-down list of filters. -![Alt text](assets/scoring/image-16.png) \ No newline at end of file +![Alt text](assets/scoring/apply_filter.png) + +> [!NOTE] +> For SHIELD-HIT12A specifically, you can use `+ PARTICLE FILTER` and select Protons to get the same filter effect. \ No newline at end of file diff --git a/docs/settings.md b/docs/settings.md index e650106..fb76739 100644 --- a/docs/settings.md +++ b/docs/settings.md @@ -2,18 +2,18 @@ Particle source is defined in the `Settings` tab in the right menu of Editor view: -![Alt text](assets/settings/image.png) +![Beam settings](assets/settings/beam_settings.png) User can define the place of the source, its direction and energy. Also the beam divergence and shape can be defined. Finally particle type and number of primaries can be set. In our case we will move the beam to be located in front of the collimator by setting the beam position to (0,0,-1.5) cm. The energy is adjusted to 70 MeV with 1% of energy spread, this way we can stop the beam using 1cm of lead. -Beam shape we adjust to a circular shape with 3cm radius (to be larger than the collimator hole). +Beam shape is set to a circular shape with 3cm radius (to be larger than the collimator hole). -![Alt text](assets/settings/image-1.png) +![Setting up beam](assets/settings/beam_adjustments.png) -Rest of parameters stays withing default values. +Rest of parameters are left with default values. # Physics settings @@ -21,4 +21,4 @@ Physics settings are defined in the `Physics` area just below the `Beam` definit User is allowed to tune the step length via relative energy loss parameter (decreasing it will reduce the step size). Also nuclear reactions can be turned on or off and scattering models can be selected. -![Alt text](assets/settings/image-2.png) \ No newline at end of file +![Alt text](assets/settings/physics_settings.png) \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 77e5b2e..736cb90 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -2,7 +2,7 @@ site_name: User Documentation site_url: https://yaptide.github.io/docs/ repo_url: https://github.com/yaptide/docs repo_name: yaptide/docs -copyright: Copyright © 2023-2024 the Yaptide team +copyright: Copyright © 2023-2025 the YAPTIDE team theme: