From d4fd4da17300afcd50da2f46bee8a68c4e16e7ce Mon Sep 17 00:00:00 2001
From: Matthieu Schaller <schaller@strw.leidenuniv.nl>
Date: Sat, 24 Aug 2019 17:33:50 +0200
Subject: [PATCH] Added description of the PartType2 in the ICs and snapshots.

---
 doc/RTD/source/InitialConditions/index.rst | 40 ++++++++++++----------
 doc/RTD/source/Snapshots/index.rst         | 24 +++++++------
 2 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/doc/RTD/source/InitialConditions/index.rst b/doc/RTD/source/InitialConditions/index.rst
index e585c9aa55..4532fdde88 100644
--- a/doc/RTD/source/InitialConditions/index.rst
+++ b/doc/RTD/source/InitialConditions/index.rst
@@ -44,27 +44,29 @@ There are several groups that contain 'auxiliary' information, such as
 the particles. Some types are currently ignored by SWIFT but are kept in the
 file format for compatibility reasons.
 
-+---------------------+------------------------+----------------------------+
-| HDF5 Group Name     | Physical Particle Type | In code ``enum part_type`` |
-+=====================+========================+============================+
-| ``/PartType0/``     | Gas                    | ``swift_type_gas``         |
-+---------------------+------------------------+----------------------------+
-| ``/PartType1/``     | Dark Matter            | ``swift_type_dark_matter`` |
-+---------------------+------------------------+----------------------------+
-| ``/PartType2/``     | Ignored                |                            |
-+---------------------+------------------------+----------------------------+
-| ``/PartType3/``     | Ignored                |                            |
-+---------------------+------------------------+----------------------------+
-| ``/PartType4/``     | Stars                  | ``swift_type_star``        |
-+---------------------+------------------------+----------------------------+
-| ``/PartType5/``     | Black Holes            | ``swift_type_black_hole``  |
-+---------------------+------------------------+----------------------------+
++---------------------+------------------------+----------------------------------------+
+| HDF5 Group Name     | Physical Particle Type | In code ``enum part_type``             |
++=====================+========================+========================================+
+| ``/PartType0/``     | Gas                    | ``swift_type_gas``                     |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType1/``     | Dark Matter            | ``swift_type_dark_matter``             |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType2/``     | Background Dark Matter | ``swift_type_dark_matter_background``  |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType3/``     | Ignored                |                                        |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType4/``     | Stars                  | ``swift_type_star``                    |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType5/``     | Black Holes            | ``swift_type_black_hole``              |
++---------------------+------------------------+----------------------------------------+
 
 The last column in the table gives the ``enum`` value from ``part_type.h``
 corresponding to a given entry in the files.
 
-Note that the only particles that have hydrodynamical forces calculated between
-them are those in ``PartType0``.
+Note that the only particles that have hydrodynamical forces calculated
+between them are those in ``PartType0``. The background dark matter
+particles are used for zoom-in simulations and can have different masses
+(and as a consequence softening length) within the ``/PartType2`` arrays.
 
 
 Necessary Components
@@ -137,8 +139,8 @@ individual particle type (e.g. ``/PartType0/``) that have the following *dataset
   within [0, L)^3 where L is the side-length of the simulation volume. In the
   case of cosmological simulations, these are the co-moving positions.
 + ``Velocities``, an array of shape (N, 3) that is the cartesian velocities of
-  the particles. When running cosmological simulations, these are the peculiar
-  velocities. Note that this is different from GADGET which uses peculiar
+  the particles. When running cosmological simulations, these are the **peculiar
+  velocities**. Note that this is different from GADGET which uses peculiar
   velocities divided by ``sqrt(a)`` (see below for a fix).
 + ``ParticleIDs``, an array of length N that are unique identifying numbers for
   each particle. Note that these have to be unique to a particle, and cannot be
diff --git a/doc/RTD/source/Snapshots/index.rst b/doc/RTD/source/Snapshots/index.rst
index 32317aa19b..fa11058edf 100644
--- a/doc/RTD/source/Snapshots/index.rst
+++ b/doc/RTD/source/Snapshots/index.rst
@@ -107,17 +107,19 @@ There are several groups that contain 'auxiliary' information, such as
 the particles. The type use the naming convention of Gadget-2 (with
 the OWLS and EAGLE extensions).
 
-+---------------------+------------------------+----------------------------+
-| HDF5 Group Name     | Physical Particle Type | In code ``enum part_type`` |
-+=====================+========================+============================+
-| ``/PartType0/``     | Gas                    | ``swift_type_gas``         |
-+---------------------+------------------------+----------------------------+
-| ``/PartType1/``     | Dark Matter            | ``swift_type_dark_matter`` |
-+---------------------+------------------------+----------------------------+
-| ``/PartType4/``     | Stars                  | ``swift_type_star``        |
-+---------------------+------------------------+----------------------------+
-| ``/PartType5/``     | Black Holes            | ``swift_type_black_hole``  |
-+---------------------+------------------------+----------------------------+
++---------------------+------------------------+----------------------------------------+
+| HDF5 Group Name     | Physical Particle Type | In code ``enum part_type``             |
++=====================+========================+========================================+
+| ``/PartType0/``     | Gas                    | ``swift_type_gas``                     |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType1/``     | Dark Matter            | ``swift_type_dark_matter``             |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType2/``     | Background Dark Matter | ``swift_type_dark_matter_background``  |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType4/``     | Stars                  | ``swift_type_star``                    |
++---------------------+------------------------+----------------------------------------+
+| ``/PartType5/``     | Black Holes            | ``swift_type_black_hole``              |
++---------------------+------------------------+----------------------------------------+
 
 The last column in the table gives the ``enum`` value from ``part_type.h``
 corresponding to a given entry in the files.
-- 
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