.. _[t-sed]:

[ T-SED ] section
==================================================

Calculation of the probability density of deposition energies in microscopic sites, called the lineal energy :math:`y` or specific energy :math:`z`, is of great importance in the estimation of the relative biological effectiveness (RBE) of charged particles.
However, such microscopic probability densities cannot be directly calculated by PHITS simulation using the **[t-deposit]** tally, as PHITS is designed to simulate particle motion on a macroscopic scale and employs a continuous-slowing-down approximation (CSDA) for calculating the energy loss of charged particles.
We therefore introduced a special tally named **[t-sed]** for calculating the microscopic probability densities using a mathematical function that can instantaneously calculate quantities around trajectories of charged particles.
The function was developed on the basis of track structure simulations considering productions of :math:`\delta`-rays and Auger electrons.
Note that the name 'SED' derives from 'Specific Energy Distribution.'
Details of the calculation procedure are given elsewhere. [#tsed1]_ [#tsed2]_
The function of the **[delta ray]** section should not be used together with this tally.
When you use **[t-sed]**, you have to activate the EGS mode, **negs=1** or **2**, and set the cut-off energy of electrons and positrons to 10 keV or 100 keV, **emin(12-13)=0.01** or **0.1**.

Using this tally, information on the probability densities of :math:`y` and :math:`z` in water can be obtained.
It is also possible to calculate probability densities in different materials, although the accuracy of doing so has not yet been checked.
Similar to **[t-let]**, the dose is only counted from the energy loss of charged particles and nuclei, and therefore the Event Generator mode, **e-mode>=1**, must be used to transport low-energy neutrons.
The deposition energy in microscopic sites can be expressed as the deposit energy :math:`\varepsilon` in MeV, the lineal energy :math:`y` in keV/um, or the specific energy :math:`z` in Gy.
The definitions of these quantities are given in ICRU Report 36.
Usage of **[t-sed]** is similar to that of **[t-let]**.

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.. list-table:: **mesh**
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   * - value
     - explanation
   * - **reg, r-z, xyz**
     - Mesh type.
       A mesh type subsection is required below this option.

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.. list-table:: **volume**
   :header-rows: 0

   * - value
     - explanation
   * - (optional)
     - This option defines the volume for each region for **reg** mesh.
       Volume definitions are required below this option.
       Default values are given in input echo in the case of no definition.
   * - **reg vol**
     - Volume definition.
       For details see the **[volume]** section.

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.. list-table:: **model**
   :header-rows: 0

   * - value
     - explanation
   * - **0, 1** (D=0)
     - **0**: old model.
       **1**: new model (paper under preparation).

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.. list-table:: **se-unit**
   :header-rows: 0

   * - value
     - explanation
   * - **0, 1, 2, 3**
     - Unit of deposition energy in microscopic sites.
       **0**: Number of ionizations and electronic excitations.
       Selectable only when **model=1**.
       **1**: deposit energy :math:`\varepsilon` in MeV.
       **2**: lineal energy :math:`y` in keV/um.
       **3**: specific energy :math:`z` in Gy.

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.. list-table:: **cdiam**
   :header-rows: 0

   * - value
     - explanation
   * - (optional, D=1.0)
     - Diameter of the target site in um.
       A value from 0.001 to 2.0 can be specified.
       If **cdiam** is set to a negative value, the peak due to the production of Auger electron is ignored.

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.. list-table:: **se-type**
   :header-rows: 0

   * - value
     - explanation
   * - **1, 2, 3, 4, 5**
     - :math:`\varepsilon`, :math:`y`, or :math:`z` mesh, where the unit is defined by **se-unit**.
       See :numref:`sec-mesh-type` for mesh subsection format.
       If a 'Warning: Z bin is not enough!' message occurs, the **emin**, **emax**, and **ne** parameters must be changed.
       This warning indicates that the microdosimetric function cannot calculate the :math:`y` or :math:`z` distribution because the range is too small or the mesh resolution is too poor.
       For example, set **se-type=3**, **emin=0.01**, **emax=10000.0**, **ne=60** or higher for calculating the :math:`y` distribution for site diameter = 1 um, **cdiam=1.0** and **se-unit=2**.

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.. list-table:: **axis**
   :header-rows: 0

   * - value
     - explanation
   * - **sed, reg, x, y, z, r**
     - x axis value of output data.
   * - **xy, yz, xz, rz**
     - 2-dimensional.

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.. list-table:: **unit**
   :header-rows: 0

   * - value
     - explanation
   * - **1, 2, 3, 4, 5, 6**
     - **1**: Track [cm/(keV/um)/source]
       **2**: Dose [MeV/(keV/um)/source], proportional to :math:`y*f(y)`.
       **3**: Track [cm/ln(keV/um)/source]
       **4**: Dose [MeV/ln(keV/um)/source], proportional to :math:`y*d(y)`.
       **5**: Track [cm/source]
       **6**: Dose [MeV/source]
   * - **7, 8**
     - **7**: :math:`y*f(y)` [dimensionless], where :math:`\int f(y)dy=1`.
       **8**: :math:`y*d(y)` [keV/um], where :math:`\int d(y)dy=1`.
       These units are for the case of **se-unit=2**.
       For **se-unit=1** and **3**, [keV/um] is replaced by [MeV] and [Gy], respectively.

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From version 3.02, new options, **unit=7** and **8**, were implemented.
Using them, the frequency and dose probability densities of :math:`y`, :math:`f(y)`, and :math:`d(y)`, respectively, can be easily calculated.
The results obtained from **unit=7** and **8** are proportional to those obtained from **unit=2** and **4**, respectively, but their absolute values are different because the integral of the probability densities are normalized to 1 in the cases of the new options.
In place of **sum over**, the frequency mean is output when **unit=7**, and the dose mean is output when **unit=8**, though their statistical errors are not calculated and are always shown as 0.000.
Note that **unit=7** and **8** can be set only when **axis=sed**.

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.. list-table:: **rshow**
   :header-rows: 0

   * - value
     - explanation
   * - **0** (default), **1, 2, 3**
     - When **mesh=xyz** and **axis=xy,yz,xz**, region border (1), material name (2), and region name (3) are plotted using this option.
       A **xyz** mesh section must be added below this option.

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.. list-table:: **letmat**
   :header-rows: 0

   * - value
     - explanation
   * - (optional)
     - Material id for LET, :math:`dE/dx`.
       If not defined, a real material is assumed.
       If a material not used in the geometry is selected, its material density must be defined in **[material]**.
       To calculate LET in water, define water with 1 g/cm^3 in **[material]**.
       When **letmat<0** is set, PHITS automatically calculates :math:`dE/dx` for water with 1 g/cm^3 for electrons and positrons.
       Please see ``ParticleTherapy`` in the recommendation setting for more details.

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.. list-table:: **rhomat**
   :header-rows: 0

   * - value
     - explanation
   * - (optional, D=1.0)
     - Density of the material, g/cm^3, specified by **letmat**.
       The definition of **rhomat** is required when the material specified by **letmat** is other than water, although **[t-sed]** was originally developed for water.

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.. [#tsed1] T. Sato, R. Watanabe and K. Niita, "Development of a calculation method for estimating the specific energy distribution in complex radiation fields," Radiat. Prot. Dosim. 122, 41-45 (2006).
.. [#tsed2] T. Sato, Y. Kase, R. Watanabe, K. Niita and L. Sihver, "Biological dose estimation for charged-particle therapy using an improved PHITS code coupled with a microdosimetric kinetic model," Radiat. Res. 171, 107-117 (2009).