**************************************************
General Format Of Input And Output Files
**************************************************

The PHITS input file is made in a text format that can be edited with a text editor.
The input file consists of several sections beginning with **[*]**, and the required information is read in sections according to the purpose and option.
The sections can be in any order.
Note that up to four spaces at the beginning of **[*]** are ignored, but any more than that will not be recognized as the beginning of a section.
The input format depends on each section, but it basically takes the two formats shown below.
One is a method where keywords unique to each section are set as numeric values or strings:

.. code-block:: text

   keyword(parameter) = value or character

In this case, spaces are ignored.
The other is to set multiple numbers with a space as a delimiter:

.. code-block:: text

   parameter1    parameter2    parameter3  ...

The output file is basically in text format, usually ``.out``.
By setting an option, an image file in ``.eps`` format can also be output.

The units of each physical quantity in PHITS are basically as follows: length in cm, time in ns, and energy in MeV, or MeV/n for quantities per nucleon.
The coordinate system is right-handed.


Sections
==================================================

:numref:`tbl-secname1` and :numref:`tbl-secname2` show the sections used in PHITS.

.. _tbl-secname1:

.. list-table:: Sections (1)
   :widths: 34 66
   :header-rows: 1

   * - **name**
     - description
   * - **[title]**
     - Title
   * - **[parameters]**
     - Various types of parameters
   * - **[source]**
     - Source definition
   * - **[material]**
     - Material definition
   * - **[surface]**
     - Surface definition
   * - **[cell]**
     - Cell definition
   * - **[transform]**
     - Definition of the coordinate transform
   * - **[temperature]**
     - Cell temperature definition
   * - **[mat time change]**
     - Definition of time-dependent materials
   * - **[magnetic field]**
     - Magnetic field definition
   * - **[electro magnetic field]**
     - Electro-magnetic field definition
   * - **[delta ray]**
     - Definition of :math:`\delta`-ray production
   * - **[track structure]**
     - Definition for using the track-structure simulation mode
   * - **[super mirror]**
     - Definition of super mirror for low-energy neutrons
   * - **[elastic option]**
     - Definition of elastic scattering options for low-energy neutrons
   * - **[data max]**
     - Definition of maximum energies, **dmax**, of each nucleus for using data libraries
   * - **[frag data]**
     - Definition of user-defined cross sections
   * - **[importance]**
     - Definition of region importances
   * - **[weight window]**
     - Definition of region weight windows
   * - **[ww bias]**
     - Definition of values to bias in **[weight window]**
   * - **[forced collisions]**
     - Forced collision definition
   * - **[repeated collisions]**
     - Repeated collision definition
   * - **[volume]**
     - Region volume definition
   * - **[multiplier]**
     - Multiplier definition
   * - **[mat name color]**
     - Material name and color definition for graphical plot
   * - **[reg name]**
     - Region name definition for graphical plot
   * - **[counter]**
     - Counter definition
   * - **[timer]**
     - Timer and clock definition
   * - **[user defined interaction]**
     - Control of user-defined interactions
   * - **[user defined particle]**
     - Control of user-defined particles
   * - **[libout]**
     - Control for **icntl=1** and **inucr=100** mode

.. _tbl-secname2:

.. list-table:: Sections (2)
   :widths: 40 60
   :header-rows: 1

   * - **name**
     - description
   * - **[t-track]**
     - Particle fluence in a given region
   * - **[t-cross]**
     - Particle fluence or current across a given surface
   * - **[t-point]**
     - Particle fluence at a given point
   * - **[t-deposit]**
     - Deposit energy in a given region
   * - **[t-deposit2]**
     - Deposit energies in two given regions
   * - **[t-heat]**
     - Heat generation in a given region. Not recommended. [#theat]_
   * - **[t-yield]**
     - Residual nuclei yields in a given region
   * - **[t-product]**
     - Reaction products in a given region
   * - **[t-dpa]**
     - Displacement Per Atom, DPA, in a given region
   * - **[t-let]**
     - LET distribution in a given region
   * - **[t-sed]**
     - Microdosimetric quantity distribution in a given region
   * - **[t-time]**
     - Time information of particles in a given region
   * - **[t-interact]** (former name **[t-star]**)
     - Number of interactions that occurred in a given region
   * - **[t-dchain]**
     - Residual nuclide yields for the use of DCHAIN
   * - **[t-wwg]**
     - Output parameters for **[weight window]**
   * - **[t-wwbg]**
     - Output parameters for **[ww bias]**
   * - **[t-volume]**
     - Automatic calculation of the volume for a given region
   * - **[t-userdefined]**
     - Any quantities defined by users
   * - **[t-gshow]**
     - 2D geometry visualization
   * - **[t-rshow]**
     - 2D geometry visualization with physical quantities
   * - **[t-3dshow]**
     - 3D geometry visualization
   * - **[T-4Dtrack]**
     - Particle track files for displaying particle tracks in PHIG-3D
   * - **[end]**
     - End of input file

Note that PHITS does not read any input information written below the **[end]** section.

.. [#theat] Until version 3.04, the **[t-heat]** tally had been used to calculate deposit energy using the kerma approximation, because the **[t-deposit]** tally did not have that option.


Reading Control
==================================================

Uppercase, lowercase, blank
  Discrimination between lowercase and uppercase characters is not performed in PHITS input except in file names.
  Blanks at the beginning and the end of a line are ignored except for the declaration of **[Section Name]** as described above.

Tab
  A tab is replaced by eight blanks.

Line connecting
  The maximum number of characters that can be written in a line is 200.
  If ``\`` is added at the end of a line, the next line is considered to be a continued line.
  Multiple lines can be used to write input data using this method, but ``\`` is not necessary in the **[surface]** and **[cell]** sections, in which lines are automatically connected without the use of an additional symbol.
  Note that more than four blanks are required at the beginning of a continued line.

Line dividing
  Several short lines can be displayed in one line and divided by ``;`` as follows:

  .. code-block:: text

     idbg = 0;  ibod = 1;  naz = 0

  However, this function is not available when the format is defined in the mesh description.

Comment marks
  In a PHITS input file, the following characters can be used as comment marks, and characters written after them are ignored.

  - ``$`` is regarded as a comment mark anywhere in a PHITS input file.
  - ``#`` and ``!`` are regarded as comment marks except when they are used in **[surface]** and **[cell]**.
  - The character ``c`` followed by a half-width space is regarded as a comment mark only when it is used within the first five columns of each line.

  Note that ``c`` followed by a half-width space cannot be used as a comment mark in the **[material]** section by the default setting.
  To use it as a comment mark in the **[material]** section, set **icommat=1** in the **[parameters]** section.
  Note also that ``%`` could be used as a comment mark before version 3.30, but because ``%`` is now used for defining character variables, it can no longer be used as a comment mark.
  If you need to use ``%`` as a comment mark, write ``$RWT=0`` before the first section begins.

Blank lines
  Blank lines and lines beginning with a comment mark are skipped.

Section reading skip
  Adding ``off`` after a section name, for example ``[Section Name] off``, disables all definitions in that section.
  Note that ``infl:`` or ``set:`` written in the skipped section is also skipped.

Skipping lines within a section
  To skip from any place in a section, put ``qp:`` at the line head.
  Lines from ``qp:`` to the end of the section are skipped.

Skip all
  ``q:`` can be used as a terminator of an input file; this works in the same way as **[end]**.


.. _sec-include:
.. _sec-include_file:
.. _include_file:

Inserting Files
==================================================

Files can be inserted using the following format:

.. code-block:: text

   infl: {file.name}[n1-n2]

The name of the file to be inserted should be enclosed in curly brackets, ``{}``, and the number of lines from n1 to n2 of the file should be enclosed in square brackets, ``[]``.
If ``[]`` is omitted, PHITS includes all lines of the specified file.

The following styles can also be used to specify line numbers: ``[n1-]`` or ``[-n2]``.
These expressions specify the range from the n1-th line to the end, and from the initial line to the n2-th line, respectively.
Inserted files can be nested more than once, up to eight times.
After reading the end of the included file, the reading process returns to its parent file.

Care should be taken when using the command-line interpreter, Command Prompt, to execute PHITS.
If **infl:** is used, the following text should be written in the first line of the input file:

.. code-block:: text

   file = phits.inp

Here, ``phits.inp`` is the input file name.


.. _sec-user_const:

User-Defined Variables
==================================================

In the input file, where numbers should be entered, user-defined variables from **c1** to **c999** can be written instead of numbers.
User-defined variables can be set as follows:

.. code-block:: text

   set: c1[52.3] c2[2*pi] c3[c1*1.e-8]

The **set:** definition can be written anywhere.
Note that there should be no space between **ci** and **[** in the format **ci[]**.
User-defined variables can be used as numerical values in the input file, and the variables can be re-defined at any time, with the values retained until they are re-defined.
In the third case of the above example, **c3**, another variable, **c1**, is called in the definition.
In this case, the value held by **c1** at that time is used.
Therefore, even if **c1** is re-defined after the definition of **c3**, the value of **c3** is not changed.
By default, **pi** is set to the value of :math:`\pi`.

The numbers of **ci** can be output in **file(6)**, with **D** set to ``phits.out``, by setting **ncvalout** in **[parameters]**.
The number is output as many times as specified by **ncvalout**.
If you want to check the actual numbers used as user-defined constants, set this parameter.

The **set:** definition is ignored in the sumtally subsection.

User-defined variables can also be used in user-defined programs such as ``usrsors.f``, ``usrtally.f``, and ``usrdfn1.f`` by setting the following:

.. code-block:: text

   parameter ( mfc = 100 )
   common /rval1/ cval(mfc), aval(mfc)

For example, cval(1) corresponds to **c1** defined in the PHITS input file.
If a certain user-defined variable is specified multiple times in the input file, the lastly defined value is effective in the user-defined programs.


.. _sec-cha_var:
.. _cha-var:

User-Defined Characters
==================================================

From version 3.31 onward, it is possible to use character variables.
You can define a character variable as follows:

.. code-block:: text

   set: %part_name%[neutron proton alpha]

Parameter names must be defined with % around them.
Only character-variable names are case-sensitive in the PHITS input file.
As with user-defined variables, they are effective from the next line after they are defined, and the same character variable can be re-set as many times as necessary.
However, only one character variable can be defined in one line, unlike user-defined variables.
Variables and their values, strings, that can be defined are limited to 100 characters.

To use this feature, PHITS from version 3.31 onward outputs the input information after replacing character variables to a separate file, hereafter called the rewrite file, and then reads that file.
The rewrite file is named by adding _rwt before the extension of the original input file name.
For example, if the original input file name is ``phits.inp``, the rewrite file name is ``phits_rwt.inp``. [#rwt]_
The rewrite file also contains the input information read from files included using the **infl** command.

Whether the rewrite file is created and deleted can be controlled by the special parameter **$RWT**.
**$RWT** must be defined before the first section begins, and its meaning is as follows:

- **$RWT=0**: No rewrite file is created. In this case, character variables cannot be used.
- **$RWT=1**: Rewrite file is temporarily created and deleted at the end of the calculation. This is the default.
- **$RWT=2**: Rewrite file is created and kept after the PHITS simulation finishes.
- **$RWT=3**: Rewrite file is created and PHITS execution stops immediately afterward. This option is available only for **icntl=0**.

.. [#rwt] If you use the PHITS executable file directly via a terminal or command prompt, without using a batch file or script file, the rewrite file name will be ``phits_rwt.inp`` without reference to the original input file name.


.. _tbl-intfunc:

Using Mathematical Expressions
==================================================

Mathematical expressions can be used in an input file following Fortran style guidelines.
Available intrinsic functions are shown in :numref:`tbl-intfunc`.

.. list-table:: Intrinsic functions
   :widths: 25 75
   :header-rows: 0

   * - FLOAT, INT, ABS, EXP, LOG, LOG10, MAX, MIN
     - Numeric conversion, absolute value, exponent, logarithms, maximum, and minimum
   * - MOD, NINT, SIGN, SQRT, ACOS, ASIN, ATAN, ATAN2
     - Remainder, nearest integer, sign, square root, and inverse trigonometric functions
   * - COS, COSH, SIN, SINH, TAN, TANH
     - Trigonometric and hyperbolic functions

As an example:

.. code-block:: text

   parameter = c1 * 3.5 * sin(55 * pi / 180)

In the above example, because a single numerical value is expected after parameter=, blanks can be used in the expression.
However, in some sections multiple numerical values cannot be accommodated.
In such cases, an expression can be enclosed in braces, for example { c1 * 2 / pi }.


.. _partt:
.. _tbl-partt:
.. _list:
.. _sec-part-spec:

Particle specification
==================================================

The particle species that can be handled by PHITS are listed in :numref:`tbl-partt-1` and :numref:`tbl-partt-2` . 
These particle species can be specified by their respective symbols or kf-codes.
Particle species that are not assigned a symbol in :numref:`tbl-partt-2` (itype=11) are specified only by their kf-codes.
:numref:`tbl-decay` lists the particles' decay-channels and their life-times.
Note that these specifications are different from the material definition in **[material]** .

Nuclei are specified in formats such as 208Pb, Pb208, or Pb-208.
If the mass number is omitted and only the symbol is given (e.g., Pb), it represents all isotopes (however, this cannot be used in the [source] section).
To specify a nucleus using the kf code, specify the value calculated by Z * 1000000 + A (e.g., 82000208).
If you want to explicitly specify an isomer (meta- stable), append m (first isomer), n (second isomer), or g (ground state) to the mass number (e.g., Na-24m, In-116m, In-116n, In-116g).
A nucleus with ityp = 19 represents all nuclei except those with ityp = 1, 15, 16, 17, and 18, i.e., proton, deuteron, triton, 3He, and alpha.

.. _tbl-partt-1:

.. list-table:: List of transport particles (1)
   :widths: 10 24 22 44
   :header-rows: 1

   * - ityp
     - symbol
     - kf-code
     - particle name
   * - 1
     - proton
     - 2212
     - proton
   * - 2
     - neutron
     - 2112
     - neutron
   * - 3
     - pion+
     - 211
     - :math:`\pi^+`
   * - 4
     - pion0
     - 111
     - :math:`\pi^0`
   * - 5
     - pion-
     - -211
     - :math:`\pi^-`
   * - 6
     - muon+
     - -13
     - :math:`\mu^+`
   * - 7
     - muon-
     - 13
     - :math:`\mu^-`
   * - 8
     - kaon+
     - 321
     - :math:`K^+`
   * - 9
     - kaon0
     - 311
     - :math:`K^0`
   * - 10
     - kaon-
     - -321
     - :math:`K^-`
   * - 11
     - other
     - below
     - other particle
   * - 12
     - electron
     - 11
     - :math:`e^-`
   * - 13
     - positron
     - -11
     - :math:`e^+`
   * - 14
     - photon [#photon]_
     - 22
     - :math:`\gamma`
   * - 15
     - deuteron
     - 1000002
     - deuteron
   * - 16
     - triton
     - 1000003
     - triton
   * - 17
     - 3he
     - 2000003
     - :math:`{}^3\mathrm{He}`
   * - 18
     - alpha
     - 2000004
     - :math:`\alpha`
   * - 19
     - nucleus
     - :math:`Z*1000000+A`
     - nucleus

.. _tbl-partt-2:

.. list-table:: List of transport particles (2)
   :widths: 10 18 22 50
   :header-rows: 1

   * - ityp
     - symbol
     - kf-code
     - particle name
   * - 11
     - nu_e, nu_ebar
     - 12, -12
     - :math:`\nu_e`, :math:`\overline{\nu_e}`
   * - 11
     - nu_mu, nu_mubar
     - 14, -14
     - :math:`\nu_{\mu}`, :math:`\overline{\nu_{\mu}}`
   * - 11
     - pbar-
     - -2212
     - antiproton
   * - 11
     - nbar0
     - -2112
     - antineutron
   * - 11
     - Kbar0
     - -311
     - :math:`\overline{K^0}`
   * - 11
     - K_L0
     - 130
     - :math:`K_L^0`
   * - 11
     - K_S0
     - 310
     - :math:`K_S^0`
   * - 11
     - eta
     - 221
     - :math:`\eta`
   * - 11
     - eta'
     - 331
     - :math:`\eta'`
   * - 11
     - Lambda0, Lambdabar0
     - 3122, -3122
     - :math:`\Lambda^0`, :math:`\overline{\Lambda^0}`
   * - 11
     - Sigma+, Sigmabar-
     - 3222, -3222
     - :math:`\Sigma^+`, :math:`\overline{\Sigma^+}`
   * - 11
     - Sigma0, Sigmabar0
     - 3212, -3212
     - :math:`\Sigma^0`, :math:`\overline{\Sigma^0}`
   * - 11
     - Sigma-, Sigmabar+
     - 3112, -3112
     - :math:`\Sigma^-`, :math:`\overline{\Sigma^-}`
   * - 11
     - Xi0, Xibar0
     - 3322, -3322
     - :math:`\Xi^0`, :math:`\overline{\Xi^0}`
   * - 11
     - Xi-, Xibar+
     - 3312, -3312
     - :math:`\Xi^-`, :math:`\overline{\Xi^-}`
   * - 11
     - Omega-, Omegabar+
     - 3334, -3334
     - :math:`\Omega^-`, :math:`\overline{\Omega^-}`
   * - 11
     - nu_tau, nu_taubar
     - 16, -16
     - :math:`\nu_{\tau}`, :math:`\overline{\nu_{\tau}}`
   * - 11
     - tau-, tau+
     - 15, -15
     - :math:`\tau^-`, :math:`\tau^+`
   * - 11
     - rho0
     - 113
     - :math:`\rho^0`
   * - 11
     - rho+, rho-
     - 213, -213
     - :math:`\rho^+`, :math:`\rho^-`
   * - 11
     - omega
     - 223
     - :math:`\omega`
   * - 11
     - a_1(1260)+, a_1(1260)-
     - 20213, -20213
     - :math:`a_1^+`, :math:`a_1^-`
   * - 11
     - K*0, K*bar0
     - 313, -313
     - :math:`K^{*0}`, :math:`\overline{K^{*0}}`
   * - 11
     - K*+, K*-
     - 323, -323
     - :math:`K^{*+}`, :math:`K^{*-}`
   * - 11
     - phi
     - 333
     - :math:`\phi`
   * - 11
     - D+, D-
     - 411, -411
     - :math:`D^+`, :math:`D^-`
   * - 11
     - D0, Dbar0
     - 421, -421
     - :math:`D^0`, :math:`\overline{D^0}`
   * - 11
     - D_s+, D_s-
     - 431, -431
     - :math:`D_s^+`, :math:`D_s^-`
   * - 11
     - B0, Bbar0
     - 511, -511
     - :math:`B^0`, :math:`\overline{B^0}`
   * - 11
     - B+, B-
     - 521, -521
     - :math:`B^+`, :math:`B^-`
   * - 11
     - B_s0, B_sbar0
     - 531, -531
     - :math:`B_s^0`, :math:`\overline{B_s^0}`
   * - 11
     - B_c+, B_c-
     - 541, -541
     - :math:`B_c^+`, :math:`B_c^-`

.. [#photon] In previous versions of PHITS, photon was coded as gamma. In the current version, this has been changed to photon.

The particle decay channels and life times are listed in :numref:`tbl-decay`.
The branching ratio and decay mode can be changed by modifying and recompiling the source code ``src/dklos.f``.
For other particles, refer to ``data/decay/decay_data_1.dat``.

.. _decay:
.. _tbl-decay:

.. list-table:: Decay channels and life times
   :widths: 18 36 20 26
   :header-rows: 1

   * - particle
     - decay channel
     - branching ratio
     - life time [s]
   * - :math:`n`
     - :math:`p + e^- + \overline{\nu}_e`
     - 100%
     - :math:`8.867\times10^2`
   * - :math:`\pi^0`
     - :math:`\gamma + \gamma`
     - 100%
     - 0
   * - :math:`\pi^+`
     - :math:`\mu^+ + \nu_{\mu}`
     - 100%
     - :math:`2.6029\times10^{-8}`
   * - :math:`\pi^-`
     - :math:`\mu^- + \overline{\nu}_{\mu}`
     - 100%
     - :math:`2.6029\times10^{-8}`
   * - :math:`\mu^+`
     - :math:`e^+ + \nu_e + \overline{\nu}_{\mu}`
     - 100%
     - :math:`2.19703\times10^{-6}`
   * - :math:`\mu^-`
     - :math:`e^- + \overline{\nu}_e + \nu_{\mu}`
     - 100%
     - :math:`2.19703\times10^{-6}`
   * - :math:`K_L^0`
     - :math:`\pi^+ + e^- + \overline{\nu}_e`; :math:`\pi^- + e^+ + \nu_e`; :math:`\pi^+ + \mu^- + \overline{\nu}_{\mu}`; :math:`\pi^- + \mu^+ + \nu_{\mu}`; :math:`\pi^0 + \pi^0 + \pi^0`; :math:`\pi^+ + \pi^- + \pi^0`
     - 20.34%; 20.34%; 13.57%; 13.57%; 19.59%; 12.59%
     - :math:`5.116\times10^{-8}`
   * - :math:`K_S^0`
     - :math:`\pi^0 + \pi^0`; :math:`\pi^+ + \pi^-`
     - 30.72%; 69.28%
     - :math:`8.954\times10^{-11}`
   * - :math:`K^+`
     - :math:`\mu^+ + \nu_{\mu}`; :math:`\pi^0 + e^+ + \nu_e`; :math:`\pi^0 + \mu^+ + \nu_{\mu}`; :math:`\pi^+ + \pi^0`; :math:`\pi^+ + \pi^0 + \pi^0`; :math:`\pi^+ + \pi^+ + \pi^-`
     - 63.56%; 5.07%; 3.352%; 20.67%; 1.760%; 5.583%
     - :math:`1.2371\times10^{-8}`
   * - :math:`K^-`
     - :math:`\mu^- + \overline{\nu}_{\mu}`; :math:`\pi^0 + e^- + \overline{\nu}_e`; :math:`\pi^0 + \mu^- + \overline{\nu}_{\mu}`; :math:`\pi^- + \pi^0`; :math:`\pi^- + \pi^0 + \pi^0`; :math:`\pi^- + \pi^- + \pi^+`
     - 63.56%; 5.07%; 3.352%; 20.67%; 1.760%; 5.583%
     - :math:`1.2371\times10^{-8}`
   * - :math:`\eta`
     - :math:`\gamma + \gamma`; :math:`\pi^0 + \pi^0 + \pi^0`; :math:`\pi^+ + \pi^- + \pi^0`; :math:`\pi^+ + \pi^- + \gamma`
     - 38.9%; 31.9%; 23.7%; other
     - 0
   * - :math:`\eta'`
     - :math:`\pi^+ + \pi^- + \eta`; :math:`\pi^0 + \pi^0 + \eta`; :math:`\pi^+ + \pi^- + \gamma`; :math:`\gamma + \gamma`
     - 44.1%; 20.5%; 30.1%; other
     - 0
   * - :math:`\Lambda`
     - :math:`p + \pi^-`; :math:`n + \pi^0`
     - 64.1%; other
     - :math:`2.631\times10^{-10}`
   * - :math:`\Sigma^+`
     - :math:`p + \pi^0`; :math:`n + \pi^+`
     - 51.57%; other
     - :math:`7.99\times10^{-11}`
   * - :math:`\Sigma^0`
     - :math:`\Lambda + \gamma`
     - 100%
     - 0
   * - :math:`\Sigma^-`
     - :math:`n + \pi^-`
     - 100%
     - :math:`1.479\times10^{-10}`
   * - :math:`\Xi^0`
     - :math:`\Lambda + \pi^0`
     - 100%
     - :math:`2.90\times10^{-10}`
   * - :math:`\Xi^-`
     - :math:`\Lambda + \pi^-`
     - 100%
     - :math:`1.639\times10^{-10}`
   * - :math:`\Omega^-`
     - :math:`\Lambda + K^-`; :math:`\Xi^0 + \pi^-`; :math:`\Xi^- + \pi^0`
     - 67.8%; 23.6%; other
     - :math:`8.22\times10^{-11}`


.. _sec-phitsout:

Summary Output File (phits.out)
==================================================

Summary information from a PHITS calculation, such as computational time and the number of produced particles, is written to the file specified by **file(6)**, whose default is ``phits.out``.
The output information is divided into six categories, and they can be selected by the **infout** parameter in the **[parameters]** section.

The categories are as follows:

- I: Basic information, excluding the items listed separately below
- II: Input echo
- III: Information on memory usage and batches
- IV: Information on transport particles
- V: Detailed information, including variance reduction, region-wise particle scattering, and material-wise information
- VI: Information on PHITS developers

The order of the output information is roughly as follows.

Logo, version, developers (Category IV), title, and starting time (Category I except for developers)
  The version information is written near the beginning of the file.
  This version number should be quoted when sending questions to the PHITS forum or PHITS office.

Input echo (Category II)
  Input echo, which repeats all parameters defined in the input file, is written between >>> Input Echo >>> and [END] of Input Echo <<<.
  The meaning of each parameter is also output after the comment mark #.
  When parameters are specified using equations or user-defined variables, the actual values used in the PHITS simulation are output in the input echo.
  In RI source mode and cosmic-ray source mode, the actual source spectra are also provided here.

Memory usage (Category III)
  Amounts of memory used for geometry, data libraries, tally, bank memory, and others are written together with their total amount.
  These values refer only to data stored in static memory.
  Therefore, the values for data libraries and tally are often close to zero in recent PHITS versions because they are stored in dynamic memory.

Information on each source particle
  When **nwsors>0**, detailed information on each source is output up to the first **nwsors** particles.
  This includes type, region, material, energy, position, direction, and particle weight.

Information on batch (Category III)
  The total history number, **ncas**, the initial random seed, **bitseed**, and CPU time for each batch are output.

Information on calculation processes (number of analyz call vs ncol, Category I)
  PHITS has a subroutine named analyz, which is called whenever a process occurs, such as a nuclear reaction, boundary crossing, source generation, or the start or end of a batch.
  Each process is tagged with the **ncol** parameter; see :numref:`sec-dumpall` for details.
  The number of occurrences of each process is output here.

Information on variance reduction (Category V)
  Detailed information on variance reduction using **[importance]**, **[weight window]**, and **[forced collisions]** is output, including particle splitting and Russian roulette counts in each cell.

Information on region-wise particle scattering (Category V)
  Detailed region-wise particle scattering information is output, such as the numbers of high- and low-energy nuclear reactions and the gain and loss of particle fluence in each cell.

Information on medium-wise particle scattering (Category V)
  Similar information is also output on a medium-wise basis.

Information on transport particles (Category IV)
  Lists of transport particles and their produced, decayed, stopped, and leaked numbers are output.

Information on source (Category I)
  Summary information on generated sources, such as total history and batch numbers and their average and total weights, is output.

Information on stopping power database (Category I)
  When **ndedx** is set to 1 or 3, ATIMA is used for calculating the stopping power of charged particles; see :numref:`tbl-ndedx`.
  In that case, PHITS stores the stopping powers in memory with a maximum table size specified by **mdbatima**.
  If the actual size, **dedx**, reaches **mdbatima**, it is better to increase **mdbatima** in **[parameters]**.

Information on geometry error (Category I)
  Geometry errors detected during the PHITS simulation are output.
  Lost particle indicates that a particle has entered an undefined region.
  When the number of lost particles exceeds **nlost**, the calculation is terminated.
  Geometry recovering indicates that PHITS once failed to identify the current cell but recovered by slightly changing the particle coordinate.
  Unrecovered error indicates that PHITS failed to recover the problem and gave up tracing that particle any further.

Information on random seed (Category I)
  The initial random seed used in the current calculation and the next random seed to be used in a restart calculation are output.

Information on CPU time and number of events (Category I)
  CPU time and the number of each process that occurred in the PHITS simulation are output.
  When **icput=0**, which is the default, output information does not include computational time except for the total CPU time.
  When **infout=8**, the numbers of nuclear reaction models called, the numbers that succeeded, and their ratios in percent are additionally output.

  total cpu time
    Total computational time.

  transport
    Computational time for transporting particles. This item is output only when **icput>0**.

  set data
    Computational time for reading the input file. This item is output only when **icput>0**.

  analysis
    Number of all processes that occurred and their computational time.

  nevap
    Number of evaporation models used and their computational time.

  dexgam
    Number of nuclear de-excitation models used and their computational time.

  other
    Computational time for others.

  nreac
    Number of nuclear reaction models used and their computational time.

  dklos
    Number of particle decay models used and their computational time.

  hydro
    Number of nucleon-nucleon scattering models used and their computational time.

  n-data
    Number of neutron nuclear data libraries used and their computational time.

  h-data
    Number of proton, deuteron, and alpha nuclear data libraries used and their computational time.

  p-data
    Number of photon atomic data libraries used and their computational time. This item is output only for **negs=-1**.

  e-data
    Number of electron and positron atomic data libraries used and their computational time. This item is output only for **negs=-1**.

  p-egs5
    Number of EGS5 photon interaction models used and their computational time.

  e-egs5
    Number of EGS5 electron and positron interaction models used and their computational time.

  e-tsmode
    Track-structure mode usage and computational time.

  ion-tsmode
    Track-structure mode usage and computational time.

  photonucl
    Number of photonuclear reaction models used and their computational time.

  photonucl lib
    Number of photonuclear data libraries used and their computational time.

  mu-reac
    Number of muon nuclear reaction models used and their computational time.

  mu-brem
    Number of muon bremsstrahlung models used and their computational time.

  mu-pprd
    Number of muon pair-production models used and their computational time.

  mu-cap
    Number of muon capture models used and their computational time.

  elast
    Elastic scattering model usage.

  ncasc
    Number of cascade and pre-equilibrium models used and their computational time.

  bertini
    Number of the Bertini model used and their computational time.

  isobar
    Number of the isobar model used and their computational time.

  JAM
    Number of the JAM model used and their computational time.

  QMD
    Number of the JQMD and JQMD-2.0 models used and their computational time.

  JAMQMD
    Number of the JAMQMD model used and their computational time.

  INCL
    Number of the INCL model used and their computational time.

  INCELF
    Number of the INC-ELF model used and their computational time.

  frag data
    Number of frag data used and their computational time.

  SCINFUL
    Number of the SCINFUL model used and their computational time.

Citation lists (Category I)
  References that should be cited in publications using PHITS results are provided at the end of the summary output file.


.. _sec-tallyout:

Tally Output File
==================================================

Tally results are written to the file specified by the **file** parameter in each tally.
In the case of two-dimensional **axis** values, such as xy, yz, xz, rz, and chart, the statistical errors of the tally results are separately output in a file whose name has _err before the extension of the original tally output file.

When **epsout**, **vtkout**, or **bmpout** is specified in the tally, image files are also generated by changing the extension of the tally output file to .eps, .vtk, or .bmt, respectively.
For example, when **file** is set to ``track.out``, **axis** is set to xy, and **epsout=1**, four files are created:

- ``track.out``: numerical data of the tally results
- ``track_err.out``: numerical data of the statistical errors
- ``track.eps``: image data of the tally results
- ``track_err.eps``: image data of the statistical errors

The recommended extension for a tally output file is .out, but other extensions, or even no extension, can also be used.

At the beginning of a tally output file, input echo, which repeats all parameters defined in the tally section, is written.
Then, the tally results are written in a format that can be read by ANGEL.
When parameters other than those specified by **axis** are changed in a tally, multiple pages of graphs are generated and separated by the ANGEL command newpage:.

The following are representative explanations of tally output files for one-dimensional and two-dimensional axes, using ``track_eng.out`` and ``track.out`` as examples.
For two-dimensional axes, the xy plane is viewed from the positive side of the :math:`z` axis, the xz plane from the positive side of the :math:`y` axis, and the yz plane from the positive side of the :math:`x` axis.

track_eng.out
  This is an example of a one-dimensional axis plot.

  - Lines 1 to 51 contain input echo.
  - A line with #newpage: indicates the start of graph data for a page.
  - Page number and fixed parameters are output after the comment mark #.
  - Axis labels such as x: Energy [MeV/n] and y: Flux [1/cm^2/(MeV/n)/source] are written explicitly.
  - ANGEL parameters, such as xlog, ylog, and style settings, are written in the line beginning with p:.
    See the ANGEL parameter section for details of ANGEL parameters.
  - A line beginning with h: specifies how to plot each following data column.
  - A line beginning with # immediately before the data lists the meaning of each output column.
  - The numerical tally results follow.
  - A line such as #   sum over gives the total or mean values of the tally results.
  - Page titles and ANGEL title settings are written after the numerical data.
  - Information for restart calculations, such as the next random seed and total history number, is written at the end of the file.

track.out
  This is an example of a two-dimensional axis plot.

  - Lines at the beginning contain input echo.
  - #newpage: indicates the start of graph data for a page.
  - Page number and fixed parameters are output after the comment mark #.
  - The page title is written explicitly.
  - ANGEL parameters for graph settings are written next.
  - Lines beginning with # specify the order of the tally data, for example ascending order in :math:`x` and descending order in :math:`y`.
  - A line beginning with hc: provides the coordinate ranges and intervals of the plotting data.
  - The numerical tally results follow in the specified order, with line breaks inserted every 10 values.
  - If spreadsheet-friendly output is required, **2d-type=5** should be selected in the tally setting; see the explanation of **2d-type** in the tally section.
  - A line with # gshow indicates the start of geometry-drawing data.
  - After the geometry data, additional ANGEL parameter lines are written.
  - newpage: indicates the start of the next page.
    In a two-dimensional plot, one graph is created for one **part** dataset.
  - Information for restart calculations is written at the end of each tally output file.