Geometry definition =================== A `Geant4`_ Monte Carlo geometry consists of a hierarchy of nested `G4VPhysicalVolumes `_, starting from a single root ("World") volume. Calzone represents this structure using base Python objects (:external:py:class:`bool`, :external:py:class:`dict`, :external:py:class:`float`, :external:py:class:`int`, :external:py:class:`list` and :external:py:class:`str`) that have associated representations in common configuration languages, such as `JSON`_, `TOML`_ or `YAML`_. In the following section, we illustrate Calzone's geometry representation with some of the examples distributed with the `source `_. For a more comprehensive account of the Calzone geometry definition, please refer to the `Reference`_ section hereafter. .. note:: While Calzone supports various geometry formats, the examples provided in this section are all in `TOML`_ format. ---- Examples ******** Flat air-soil interface ----------------------- To begin with a basic example, let us consider a flat air-soil interface (as in the `gamma/benchmark `_ example). This is represented with Calzone using a :bash:`geometry.toml` file, with the following content .. literalinclude:: include/benchmark-geometry.toml :language: toml :lines: 1-8 The root volume is defined by an axis-aligned cubic box of 2 km extension (i.e. :python:`2E+05` cm), named :toml:`Environment` and filled with :toml:`"G4_AIR"` (from the Geant4 `NIST`_ database). The root volume (:toml:`Environment`) contains a daughter volume (:toml:`Ground`), which is also of box shape, with a square base of 2 km sides and a height of 1 km. The origin (i.e. the box centre) of the :python:`Ground` volume is offset by 500 m along the z-axis w.r.t. its mother volume (as specified by the :toml:`position` attribute). As a result, the :toml:`Ground` volume occupies the lower half of the root volume. .. tip:: Calzone supports various volume shapes, not only boxes. Please refer to the `Shape definition`_ section below for a description of the available volume shapes. Following the same box logic, a second :toml:`Detector` volume (:math:`20 \times 20 \times 10 \, \mathrm{m}^3`) is placed within the root volume, with its base positioned 5 cm above the top of the ground volume. This is achieved as .. literalinclude:: include/benchmark-geometry.toml :language: toml :lines: 9- The resulting geometry is represented in :numref:`fig-benchmark-geometry` below. .. warning:: It is the user's responsibility to ensure that daughter volumes do not collide with each other or with their mother volume. This can be tested by running the :py:meth:`Geometry.check ` method. .. subfigure:: AB :gap: 8px :layout-sm: A|B :name: fig-benchmark-geometry :subcaptions: above .. image:: include/benchmark-geometry.svg :alt: (A) .. image:: include/benchmark-geometry.png :alt: (B) Representations of the `gamma/benchmark `_ example. (A) Cross-section along the (xOz) plane. (B) Calzone display view (the root volume is transparent). Including a topography ---------------------- Let us now consider a more realistic example, in which the air-soil interface is described by a Digital Elevation Model (`DEM`_), as in the `geometry/topography `_ example. The corresponding `TOML`_ geometry file is .. literalinclude:: include/topography-geometry.toml :language: toml This example introduces two new shapes that are specific to Calzone. Firstly, the root volume is defined as a box-like `Envelope Shape`_. This is a dynamic shape whose extent adapts to its content. The :toml:`padding` attribute indicates that the envelope should reserve 300 m of additional space along the upward direction (i.e., along the z-axis), for the atmosphere above the ground. Secondly, the ground is represented by the :toml:`Terrain` volume using a `Mesh Shape`_. The corresponding mesh is built from the DEM specified in :toml:`"meshes/terrain.png"`, whose system of units is metres. The DEM describes a surface, :math:`z = f(x, y)`, which needs to be closed in order to be a valid Geant4 volume. This is achieved by completing the DEM surface with five axis-aligned flat faces in order to form a box-like base. In this situation, the :toml:`padding` attribute specifies that the bottom face should be located :python:`200` map units (i.e. metres) below the minimum height of the DEM surface. The resulting geometry is represented in :numref:`fig-topography-geometry` below. In addition, the :toml:`Terrain` uses a custom :toml:`"SomeRock"` material whose definition is inlined below. It is a derivative of the PDG `standard rock `_, with a lower density, e.g. representing a porous rock. .. subfigure:: AB :gap: 8px :layout-sm: A|B :name: fig-topography-geometry :subcaptions: above .. image:: include/topography-geometry.svg :alt: (A) .. image:: include/topography-geometry.png :alt: (B) Representations of the `geometry/topography `_ example. (A) Cross-section along the (xOz) plane. (B) Calzone display view (the root volume is transparent). Replicating a volume -------------------- Finally, let us consider the case of replicating a composite volume at different locations, as with the `muon/trajectograph `_ example. In this use case, we consider a toy muography detector made of four identical detection planes (i.e. replicas) and a central lead-scatterer (to reject low-energy background particles). Replication is achieved by delegating the description of a single detection plane to an auxiliary file (`layer.toml `_), which is `included `_ four times in the main geometry file, as below .. literalinclude:: include/trajectograph-geometry.toml :language: toml Note that an included geometry may itself include sub-geometries. For instance, in the current example, a detection plane is composed of six identical sub-units (named muon chambers), as below .. literalinclude:: include/trajectograph-layer.toml :language: toml where the `chamber.toml `_ file contains the geometry description of a muon chamber. The resulting geometry is represented in :numref:`fig-trajectograph-geometry` below. .. subfigure:: AB :gap: 8px :layout-sm: A|B :name: fig-trajectograph-geometry :subcaptions: above .. image:: include/trajectograph-geometry.svg :alt: (A) .. image:: include/trajectograph-geometry.png :alt: (B) Representations of the `muon/trajectograph `_ example. (A) Cross-section along the (yOz) plane. (B) Calzone display view (the root volume is transparent). ---- Reference ********* Geometry objects ---------------- All geometry objects (volumes, shapes, materials, etc.) adhere to the same data structure. A geometry object is represented by a Python :external:py:class:`dict` item (i.e. a :python:`[key: str, value: dict]` pair), where the :python:`key` is the object name, and the :python:`value` might be another :external:py:class:`dict`, e.g. containing the object's properties. To illustrate, a 1 |nbsp| cm\ :sup:`3` cubic box shape writes, .. code:: toml box = { size = [ 1.0, 1.0, 1.0 ] } .. topic:: Objects names The objects proper names (i.e. designating specific volumes, materials, etc.) must be capitalised and comprise solely alpha-numeric characters. Thus, names are typically upper `CamelCased`. Conversely, common names (designating properties, shape types, etc.) adhere to the `snake_case` syntax. Substitution rules ------------------ For the sake of convenience, the values of geometry objects are subject to certain substitution rules, which are listed in :numref:`tab-geometry-substitutions`. To illustrate, a path-:external:py:class:`str` (refering to a file) can be substituted for any :external:py:class:`dict` value. Another useful rule is that a size-one :external:py:class:`dict` whose item key can be inferred, can be substituted with the item value. This occurs, for instance, for object values that have a single mandatory property. Thus, using substitution rules, the previous cubic box shape simplifies as, .. code:: toml box = 1.0 .. _tab-geometry-substitutions: .. list-table:: Substitution rules. :width: 75% :widths: auto :header-rows: 1 * - Type - Substitute - Comment * - :python:`dict` - :python:`str` - :python:`"*.json"`, :python:`"*.toml"` or :python:`"*.yaml"`. * - :python:`{ key: value }` - :python:`value` - If the :python:`key` can be inferred. * - :python:`[T; N]` - :python:`T` - E.g., :python:`1.0 -> [ 1.0, 1.0, 1.0 ]`. * - :python:`[T]` - :python:`T` - E.g., :python:`"Detector" -> [ "Detector" ]`. * - :python:`[[float; 3]; 3]` - :python:`[float; 3]` - Rotation vector (with :underline:`angles in deg`). .. topic:: Relative path As a particular case of substitution rule, path-:python:`str`, pertaining to included files, are relative to the directory in which the including file is located, unless an absolute path is specified. Geometry structure ------------------ A geometry definition starts with a root volume, for instance as follows, .. code:: toml [RootName] box = 1.0 .. There can be only one root volume in a geometry. However, the geometry :external:py:class:`dict` might contain the additional :python:`"materials"` and :python:`"meshes"` keys, for describing the geometry materials and specific triangle meshes. The corresponding structure is summarised below, in :numref:`tab-geometry-items`. .. _tab-geometry-items: .. list-table:: Geometry items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`RootName` - :python:`dict` (:numref:`tab-volume-items`) - * - :python:`"materials"` - :python:`dict` (:numref:`tab-materials-items`) - :python:`None` * - :python:`"meshes"` - :python:`dict` (:numref:`tab-meshes-items`) - :python:`None` .. _pathname: .. topic:: Pathname Geometry volumes are identified by their absolute pathname, which is formed by the dot-jointure of their own name with all of their ancestors names. For example, the :python:`"Environment.Detector"` pathname refers to the :python:`"Detector"` volume located inside the :python:`"Environment"` volume. The :external:py:class:`dict` representation of the geometry ensures that pathnames are unique within a given geometry. Volume definition ----------------- The items of a Monte Carlo volume are presented in :numref:`tab-volume-items` below. If no *shape* is specified, then a box envelope is assumed. To illustrate, a 1 |nbsp| cm\ :sup:`3` cubic box volume filled with water would be represented as follows, .. code:: toml [VolumeName] material = "G4_WATER" box = 1.0 Note that a volume can only have a single shape item (but multiple daughter volumes). For further information on shape types and their corresponding items, see :ref:`geometry:Shape definition`. .. _tab-volume-items: .. list-table:: Volume items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"material"` - :python:`str` - :python:`"G4_AIR"` * - :python:`shape_type` - :python:`dict` (:ref:`Shape items `) - :python:`"envelope"` * - :python:`"position"` - :python:`[float; 3]` - :python:`numpy.zeros(3)` * - :python:`"rotation"` - :python:`[[float; 3]; 3]` - :python:`numpy.eye(3)` * - :python:`"role"` - :python:`[str]` - :python:`None` * - :python:`"disentangle"` - :python:`dict` (:numref:`tab-disentangle-items`) - :python:`None` * - :python:`"subtract"` - :python:`[str]` - :python:`None` * - :python:`DaughterName` - :python:`dict` (:numref:`tab-volume-items`) - :python:`None` * - :python:`"include"` - :python:`[dict]` (:numref:`tab-include-items`) - :python:`None` * - :python:`"materials"` - :python:`dict` (:numref:`tab-materials-items`) - :python:`None` * - :python:`"meshes"` - :python:`dict` (:numref:`tab-meshes-items`) - :python:`None` .. topic:: Positioning properties. The optional :python:`"position"` and :python:`"rotation"` properties are relative to the mother volume frame. By default, the volume is placed unrotated with its origin coinciding with the mother one. .. topic:: Daughter volumes. The daughter volumes are included directly with the volume properties. They are identified by their `CamelCase` syntax. .. topic:: Materials and meshes definitions. Materials and meshes can be defined together with the volume properties, should this be required. It should be noted, however, that they exist on a global level, regardless of their definition scope (see the `Materials `_ and `Meshes `_ definition sections for further information). Roles ~~~~~ By default, geometry volumes are inert, i.e. they do not record any Monte Carlo information. The :python:`"role"` property can be used to assign specific tasks. A volume *role* is formed by a two words snake-cased sentence starting with a verb (the action), and followed by a subject (the recipient). For example, the following indicates that the volume should record energy deposits, and capture outgoing particles. .. code:: toml role = [ "record_deposits", "catch_outgoing" ] Possible actions and recipients are listed in :numref:`tab-volume-roles` below. .. _tab-volume-roles: .. list-table:: Volume roles vocabulary. :width: 75% :widths: auto :header-rows: 1 * - Word - Nature - Description * - :python:`"catch"` - Verb - Extract Monte Carlo particles at the volume boundary. * - :python:`"kill"` - Verb - Silenty kill Monte Carlo particles at the volume boundary. * - :python:`"record"` - Verb - Record energy deposits and/or Monte Carlo particles. * - :python:`"all"` - Subject - Designates both energy deposits and particles. * - :python:`"deposits"` - Subject - Designates only energy deposits. * - :python:`"ingoing"` - Subject - Designates only ingoing particles. * - :python:`"outgoing"` - Subject - Designates only outgoing particles. * - :python:`"particles"` - Subject - Designates both ingoing and outgoing particles. .. note:: Unlike other geometric properties, roles are not fixed. E.g., they can be modified after the Monte Carlo geometry has been loaded (see the :py:attr:`Volume.role ` attribute). Overlaps ~~~~~~~~ The :python:`"disentangle"` and :python:`"subtract"` volume properties address the issue of overlaps between sister volumes in two distinct ways. The :python:`"subtract"` property explicitly specifies sister volumes (by their name) whose shape are to be subtracted from the current volume. This can be employed, for instance, to dig out a portion of a :python:`"Ground"` volume to accommodate a partially buried :python:`"Detector"` volume. .. note:: Only unsubtracted volumes can be subtracted from. Consequently, the *subtract* property does not permit the formation of subtraction chains. The :python:`"disentangle"` property indicates pairs of overlapping daughter volumes which should be separated, (see :numref:`tab-disentangle-items`), for instance as, .. code:: toml [VolumeName.disentangle] Bottom = [ "Left", "Right" ] Top = "Left" These volumes are separated using an iterative subtraction procedure. It should be noted that this procedure does not guarantee which volume is subtracted or not. It is therefore recommended that this method be used only for the purpose of patching small (erroneous) overlaps (e.g. due to numeric approximations). .. _tab-disentangle-items: .. list-table:: Disentangle items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`VolumeName` - :python:`[str]` - Includes ~~~~~~~~ The :python:`"include"` volume property permits the insertion of sub-geometries, defined in auxiliary files, as daughter volumes. For example, as .. code:: toml [MotherName] include = "relative/path/to/a/daughter/geometry.toml" Some of the properties of the included root volume can be overridden, as detailed in :numref:`tab-include-items` below. The following example explicitly sets the name of the included root volume. .. code:: toml [MotherName] include = { name = "DaughterName", path = "relative/path/to/a/daughter/geometry.toml" } .. _tab-include-items: .. list-table:: Include items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"path"` - :python:`str` - * - :python:`"name"` - :python:`str` - :python:`None` * - :python:`"position"` - :python:`[float; 3]` - :python:`numpy.zeros(3)` * - :python:`"rotation"` - :python:`[[float; 3]; 3]` - :python:`numpy.eye(3)` * - :python:`"subtract"` - :python:`[str]` - :python:`None` Shape definition ---------------- The available shape types are described below. Calzone only exports a limited number of the `G4VSolids `_ defined by `Geant4`_, namely the :ref:`box `, :ref:`cylinder ` and :ref:`sphere ` shapes. For more complex use cases, :ref:`meshes ` should be employed. .. note:: Shape type names follow the `snake_case` syntax (i.e. like property names). Box shape ~~~~~~~~~ An axis-aligned box (`G4Box`_), centred on the origin, and defined by its *size* (in cm) along the x, y and z-axis. .. list-table:: Box items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"size"` - :python:`[float; 3]` - Cylinder shape ~~~~~~~~~~~~~~ A cylinder of revolution around the z-axis (`G4Tubs`_), centred on the origin, and defined by its *length* (in cm) along the z-axis and its *radius* (in cm) in the xOy plane. .. list-table:: Cylinder items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"length"` - :python:`float` (cm) - * - :python:`"radius"` - :python:`float` (cm) - * - :python:`"thickness"` - :python:`float` (cm) - :python:`None` * - :python:`"section"` - :python:`[float; 2]` (deg) - :python:`None` .. topic:: Hollow cylinder. If *thickness* is not :python:`None`, then the cylinder is hollow (i.e. actually a tube, with the specified thickness). .. topic:: Cylindrical section. The optional *section* argument specifies the angular span of the cylindrical shape (in deg). By default, the cylinder is closed, i.e. it spans the whole azimuth angle ([0, 360] deg). .. figure:: include/cylinders.png Examples of cylindrical shapes visualised with Calzone display. The gold shapes are hollow cylinders, while the silver ones are plain cylinders. The shapes on the right are cylindrical sections, while those on the left are full cylinders. Envelope shape ~~~~~~~~~~~~~~ A bounding envelope with a specified *shape*, whose size is determined by the bounded daughter volumes. The *padding* parameter (in cm) allows for extra space around bounded objects. .. list-table:: Envelope items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"padding"` - :python:`[float; 6]` - :python:`0.01` (cm) * - :python:`"shape"` - :python:`str` - :python:`"box"` .. topic:: Padding The *padding* parameter specifies additional space along the :math:`-X`, :math:`X`, :math:`-Y`, :math:`Y`, :math:`-Z`, and :math:`Z` axes, in that order. As a special case, the padding can also be specified as a length-3 array with elements corresponding to the :math:`\pm X`, :math:`\pm Y`, and :math:`\pm Z` axes. A single float parameter can also be specified, following the usual `substitution rules`_, resulting in uniform padding along the 6 directions. Mesh shape ~~~~~~~~~~ A triangle mesh defined from a data file (*path* property) with the specified length *units*. .. _tab-mesh-items: .. list-table:: Mesh items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"path"` - :python:`str` - * - :python:`"algorithm"` - :python:`str` - :python:`None` * - :python:`"units"` - :python:`str` - :python:`"cm"` The actual shape depends on the data file format. If the file is a native 3D model (in `OBJ`_ or `STL`_ format), then the mesh is directly imported. Alternatively, the data can also be a surface described by a Digital Elevation Model (`DEM`_), in `GeoTIFF`_ or `Turtle`_ / `PNG`_ [NBCM20]_ format. In this case, elevation values are assumed to be along the z-axis, and the surface is closed by adding side and bottom faces. The additional properties described in :numref:`tab-topography-items` control the generated 3D shape. .. topic:: Algorithm The *algorithm* property specifies the method used to traverse the mesh. The available options are :python:`"bvh"` or :python:`"voxels"` (Geant4 method). The `BVH`_ method is an efficient solution for penetrating particles (photons, muons, etc.). However, if short-range secondaries are also simulated (e.g. electrons), the `Voxels`_ method is a more efficient CPU-wise solution, though it requires more memory (which prevents using this method with large meshes). If no *algorithm* is specified, :python:`"voxels"` is used for native 3D meshes and :python:`"bvh"` for `DEMs `_. See also the :py:attr:`algorithm ` attribute of the :py:class:`GeometryBuilder ` class, which allows for the global override of the mesh traversal algorithm across the entire geometry. .. _tab-topography-items: .. list-table:: DEM specific items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"padding"` - :python:`float` - 100.0 (in map units) * - :python:`"origin"` - :python:`[float; 3]` - :python:`numpy.zeros(3)` * - :python:`"regular"` - :python:`bool` - :python:`False` .. topic:: Geometric properties. The *origin* property defines the origin of the 3D shape in the DEM coordinates system. The *padding* property extends the shape below the DEM's minimum elevation value. .. topic:: Meshing type. The *regular* flag controls the meshing algorithm. By default, a non-regular -but optimised- mesh is used. However, this is not supported by the Geant4 traversal :py:attr:`algorithm `. Therefore, a *regular* mesh must be selected when using the latter algorithm. .. tip:: The :py:meth:`Map.dump() ` method allows one to export the generated 3D topography in `STL`_ format. Sphere shape ~~~~~~~~~~~~ A sphere (`G4Orb`_ or `G4Sphere`_), centred on the origin, and defined by its *radius* (in cm). .. list-table:: Sphere items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"radius"` - :python:`float` - * - :python:`"thickness"` - :python:`float` (cm) - :python:`None` * - :python:`"azimuth_section"` - :python:`[float; 2]` (deg) - :python:`None` * - :python:`"zenith_section"` - :python:`[float; 2]` (deg) - :python:`None` .. topic:: Hollow sphere. If *thickness* is not :python:`None`, then the sphere is hollow, with the specified thickness value. .. topic:: Spherical section. The optional *azimuth_section* and *zenith_section* arguments specify the angular span of the spherical shape (in deg). By default, the sphere is closed, i.e. it spans the whole azimuth angle ([0, 360] deg), and the whole zenith angle ([0, 180] deg). .. figure:: include/spheres.png Examples of spherical shapes visualised with Calzone display. The gold shape is a hollow sphere, while the silver ones are plain spheres. The shape on the left is a full sphere, while those on the left are spherical sections. Meshes definition ----------------- Mesh shapes can be explicitly assigned a name, enabling cross-referencing. This is achieved by first defining a mesh name along with its attributes under the :python:`meshes` field (in accordance with :numref:`tab-meshes-items` below). Subsequently, the designated mesh name can be utilized as a shape value in volume definitions, in lieu of a dictionary description. For instance, .. code:: toml [meshes] Screw = { path = "/path/to/screw.stl", units = "mm" } [LeftScrew] material = "Steel" mesh = "Screw" position = [ -3.0, 0.0, 0.0] [RightScrew] material = "Steel" mesh = "Screw" position = [ 3.0, 0.0, 0.0] .. _tab-meshes-items: .. list-table:: Meshes items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`MeshName` - :python:`dict` (:numref:`tab-mesh-items`) - :python:`None` .. topic:: Meshes scope Meshes are shared across all geometries, even when anonymous. Calzone takes care of sharing mesh data, instead of duplicating them. Materials definition -------------------- A Geant4 material (`G4Material`_) can be defined either as an assembly of atomic elements (`G4Elements `_), denoted :ref:`Molecule ` herein, or as a :ref:`Mixture ` of other materials. .. tip:: A collection of standard atomic elements and materials is readily available from the Geant4 `NIST`_ database. For example, :python:`"G4_WATER"`, :python:`"G4_AIR"`, etc. In addition, Calzone also predefines :python:`"StandardRock"` (following the `PDG `_ ). Thus, depending on your application, you may not need to define your own materials. .. tip:: In addition to the `JSON`_, `TOML`_ and `YAML`_ formats, Calzone also supports importing materials from a `Gate DB `_ file. .. topic:: Materials scope `Geant4`_ materials are defined on a global scale and are applicable to all geometries and physics. Each material is identified by a unique name. Once instanciated by `Geant4`_, a material cannot be deleted or modified. Materials table ~~~~~~~~~~~~~~~ The structure of a materials table is described by :numref:`tab-materials-items` (et al.) below. :ref:`geometry:Molecules` and :ref:`geometry:Mixtures` are explictily separated. For instance, .. code:: toml [molecules] H2O = { .. } [mixtures.Air] density = 1.205E-03 .. In addition, the materials table may also contain (custom) atomic elements. .. _tab-materials-items: .. list-table:: Materials items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"elements"` - :python:`dict` (:numref:`tab-elements-items`) - :python:`None` * - :python:`"molecules"` - :python:`dict` (:numref:`tab-molecules-items`) - :python:`None` * - :python:`"mixtures"` - :python:`dict` (:numref:`tab-mixtures-items`) - :python:`None` .. _tab-elements-items: .. list-table:: Atomic elements items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`ElementName` - :python:`dict` (:numref:`tab-element-items`) - .. _tab-molecules-items: .. list-table:: Molecules items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`MoleculeName` - :python:`dict` (:numref:`tab-molecule-items`) - .. _tab-mixtures-items: .. list-table:: Mixtures items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`MixtureName` - :python:`dict` (:numref:`tab-mixture-items`) - Atomic elements ~~~~~~~~~~~~~~~ Atomic elements are specified by their atomic number (*Z*) and by their mass number (*A*, in g/mol). Optionally, a *symbol* can be specified. .. _tab-element-items: .. list-table:: Atomic element items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"Z"` - :python:`float` - * - :python:`"A"` - :python:`float` - * - :python:`"symbol"` - :python:`str` - :python:`None` Molecules ~~~~~~~~~ Molecules are defined by their density (expressed in in g/cm\ :sup:`3`) and their atomic elements *composition*. Additionally, a *state* may be specified (:python:`"gas"`, :python:`"liquid"` or :python:`"solid"`). In the absence of an explicit composition specification, it is inferred from the molecule name, which is interpreted as a chemical formula. For example, .. code:: toml [molecules] H2O = { density = 1.0, state = "liquid" } .. _tab-molecule-items: .. list-table:: Molecule items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"density"` - :python:`float` - * - :python:`"composition"` - :python:`dict` (:numref:`tab-molecule-component`) - :python:`None` * - :python:`"state"` - :python:`str` - :python:`None` .. _tab-molecule-component: .. list-table:: Molecule component. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`ElementName` - :python:`int` - Mixtures ~~~~~~~~ Mixtures are specified by their *density* (in g/cm\ :sup:`3`) and their **mass** *composition*. Optionaly, a *state* can be specified ( :python:`"gas"`, :python:`"liquid"` or :python:`"solid"`). For instance, .. code:: toml [mixtures.Air] density = 1.205E-03 state = "gas" composition = { N = 0.76, O = 0.23, Ar = 0.01 } .. _tab-mixture-items: .. list-table:: Mixture items. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`"density"` - :python:`float` - * - :python:`"composition"` - :python:`dict` (:numref:`tab-mixture-component`) - * - :python:`"state"` - :python:`str` - :python:`None` .. _tab-mixture-component: .. list-table:: Mixture component. :width: 75% :widths: auto :header-rows: 1 * - Key - Value type - Default value * - :python:`ElementName` - :python:`float` - * - :python:`MaterialName` - :python:`float` - .. ============================================================================ .. .. URL links. .. .. ============================================================================ .. _BVH: https://en.wikipedia.org/wiki/Bounding_volume_hierarchy .. _ChamberDescription: https://github.com/niess/calzone/tree/master/examples/muon/trajectograph/chamber.toml .. _DEM: https://en.wikipedia.org/wiki/Digital_elevation_model .. _Examples: https://github.com/niess/calzone/tree/master/examples/ .. _ExampleBenchmark: https://github.com/niess/calzone/tree/master/examples/gamma/benchmark .. _ExampleTrajectograph: https://github.com/niess/calzone/tree/master/examples/muon/trajectograph .. _ExampleTopography: https://github.com/niess/calzone/tree/master/examples/geometry/topography .. _G4Box: https://geant4.kek.jp/Reference/11.2.0/classG4Box.html .. _G4Element: https://geant4.kek.jp/Reference/11.2.0/classG4Element.html .. _G4Material: https://geant4.kek.jp/Reference/11.2.0/classG4Material.html .. _G4Orb: https://geant4.kek.jp/Reference/11.2.0/classG4Orb.html .. _G4Sphere: https://geant4.kek.jp/Reference/11.2.0/classG4Sphere.html .. _G4Tubs: https://geant4.kek.jp/Reference/11.2.0/classG4Tubs.html .. _G4VPhysicalVolume: https://geant4.kek.jp/Reference/11.2.0/classG4VPhysicalVolume.html .. _G4VSolid: https://geant4.kek.jp/Reference/11.2.0/classG4VSolid.html .. _Geant4: https://geant4.web.cern.ch/docs/ .. _GeoTIFF: https://fr.wikipedia.org/wiki/GeoTIFF .. _JSON: https://www.json.org/json-en.html .. _LayerDescription: https://github.com/niess/calzone/tree/master/examples/muon/trajectograph/layer.toml .. _NIST: https://geant4-userdoc.web.cern.ch/UsersGuides/ForApplicationDeveloper/html/Appendix/materialNames.html?highlight=nist# .. _OBJ: https://en.wikipedia.org/wiki/Wavefront_.obj_file .. _OpenGate: http://www.opengatecollaboration.org/ .. _PNG: https://en.wikipedia.org/wiki/PNG .. _StandardRock: https://pdg.lbl.gov/2024/AtomicNuclearProperties/HTML/standard_rock.html .. _STL: https://en.wikipedia.org/wiki/STL_(file_format) .. _TOML: https://toml.io/en/ .. _Turtle: https://github.com/niess/turtle .. _Voxels: https://en.wikipedia.org/wiki/Voxel .. _YAML: https://yaml.org/