diff --git a/doc/RTD/source/VELOCIraptorInterface/index.rst b/doc/RTD/source/VELOCIraptorInterface/index.rst
index e2582107eefed09b6bfd94d6cf208197d2e82e0f..3ae17f04b9950d30d1484ac5117b65063b7739c6 100644
--- a/doc/RTD/source/VELOCIraptorInterface/index.rst
+++ b/doc/RTD/source/VELOCIraptorInterface/index.rst
@@ -4,173 +4,21 @@
 VELOCIraptor Interface
 ======================
 
-In SWIFT it is possible to run a cosmological simulation and at the same time
-do on the fly halo finding at specific predefined intervals.  Because of this
-we will explain on this page how we can set up an simulation using VELOCIraptor
-(formerly STructure Finder).  After this we will explain what the outputs of
-VELOCIraptor will be.
+This section includes information on the VELOCIraptor interface implemented in
+SWIFT. There are mainly four subsection; the first section explains shortly 
+how VELOCIraptor works, the second subsection explains how to configure SWIFT
+with VELOCIraptor, the third subsection explains how to configure a standalone
+version of VELOCIraptor and the last subsection explains how the output format
+of VELOCIraptor works.
 
-Configuring SWIFT
------------------
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
 
-In the following three paragraphs we will explain how to setup VELOCIraptor,
-how to compile it and how to compile SWIFT with VELOCIraptor. 
+   whatis
+   stfwithswift
+   stfalone
+   output
 
 
-Setting up VELOCIraptor
-~~~~~~~~~~~~~~~~~~~~~~~
 
-Before we can run SWIFT with VELOCIraptor we first need to download
-VELOCIraptor. This can be done by cloning the repository on GitHub_::
-
-  git clone https://github.com/pelahi/VELOCIraptor-STF
-
-Currently the best version that works with SWIFT is the swift-interface branch
-of VELOCIraptor, to get this branch use::
-
-  cd VELOCIraptor-STF git fetch git checkout swift-interface
-
-To get the default that works with SWIFT simply copy the SWIFT template file in
-the ``Makefile.config``::
-
-  cd stf cp Makefile.config.SWIFT-template Makefile.config
-
-Depending on your compiler you want to change the first 20 lines of your
-``Makefile.config`` to work with your compiler and whether you want to use MPI
-or not. 
-
-
-Compiling VELOCIraptor
-~~~~~~~~~~~~~~~~~~~~~~
-
-After we downloaded the files and made a configuration file we can compile
-VELOCIraptor as follows::
-
-  make lib make libstf
-
-After the compilation of your code, there is an additional folder created in
-the ``VELOCIraptor-stf/stf`` directory called ``lib`` this directory has the
-libary of VELOCIraptor and is required to run SWIFT with
-VELOCIraptor. Note that VELOCIraptor needs a serial version of the
-HDF5 library, not a parallel build.
-
-Compiling SWIFT
-~~~~~~~~~~~~~~~
-The next part is compiling SWIFT with VELOCIraptor and assumes you already
-downloaded SWIFT from the GitLab_, this can be done by running::
-
-  ./autogen.sh ./configure
-  --with-velociraptor=/path/to/VELOCIraptor-STF/stf/lib make 
-
-In which ``./autogen.sh`` only needs to be run once after the code is cloned
-from the GitLab_, and ``/path/to/`` is the path to the ``VELOCIraptor-STF``
-directory on your machine. In general ``./configure`` can be run with other
-options as desired. After this we can run SWIFT with VELOCIraptor, but for this
-we first need to add several lines to the yaml file of our simulation::
-
-  
-  #structure finding options
-  StructureFinding:
-    config_file_name:     stf_input_6dfof_dmonly_sub.cfg
-    basename:             ./stf
-    output_time_format:   1
-    scale_factor_first:   0.02
-    delta_time:           1.02
-
-In which we specify the ``.cfg`` file that is used by VELOCIraptor. In the case
-of the Small Cosmological Volume DMO example we can run a simulation with halo
-finder as::
-
-  cd examples/SmallCosmoVolume_DM 
-  ../swift -c -s -G -x -t 8 small_cosmo_volume_dm.yml
-
-In which there is an additional ``-x`` option which activates the VELOCIraptor
-interface. 
-
-
-VELOCIraptor Output
--------------------
-
-In general VELOCIraptor outputs six files per snapshot, of which 2 files are
-for unbound particles specifically.  In this part we will explain what is
-inside the different files.
-
-Catalog_groups file
-~~~~~~~~~~~~~~~~~~~
-
-The first file that is output by VELOCIraptor is the ``.catalog_group`` file,
-this file contains all the information that is group specific, the interesting
-data in the ``.catalog_group`` files are: 
-
-+ The ``group_size``: gives a list of all the halos and the number of particles
-  in the halo, this list is numbered from 0 until the number of groups minus
-  one. 
-+ The ``Num_of_groups`` or ``Total_num_of_groups``: gives the total number of
-  groups in the snapshot.
-+ The ``Offset`` list: This list gives the offset off the particles. In the
-  output of VELOCIraptor there is no file which has an ID for every particle
-  and a corresponding group, rather the particles are ordered according to in
-  which group they are. So if we want to access the particles in group 0, we
-  need to look at the particles from ``Offset[0]`` until ``Offset[1]`` in the
-  ``.catalog_particles`` hdf5 file. In general this means that for group N we
-  need to look at particles ``Offset[N]`` until ``Offset[N+1]``. 
-+ The ``Offset_unbound`` list: This list works exactly the same as the
-  ``Offset`` list only this list is for the gravitational unbound particles.
-
-Catalog_particles file
-~~~~~~~~~~~~~~~~~~~~~~
-
-The second file that is produced by VELOCIraptor is the ``.catalog_particles``
-file, this file contains mainly all the IDs of the particles and mainly has two
-interesting things:
-
-+ The ``Num_of_particles_in_groups`` and ``Num_of_particles_in_groups``
-  parameter: Gives the total number of particles in the file or which are found
-  in the halo. 
-+ The ``Particle_IDs``: The list of particles as sorted by halo, in which halo
-  the individual particles are present can be found by using the
-  ``.catalog_group`` file and the corresponding ``Offset`` list. 
-
-Besides the ``.catalog_particles`` file, there is also a
-``.catalog_particles.unbound`` file, this file contains the same information
-but only for the unbound particles, a particle can only be present in one of
-these two lists. 
-
-Catalog_parttypes file
-~~~~~~~~~~~~~~~~~~~~~~
-
-The third file that is produced by VELOCIraptor is the ``.catalog_parttypes``
-file, this file contains the information what type of particle every particle
-is, ordered the same as in ``Particle_IDs`` in ``.catalog_particles``. There
-are only two interesting parameters of the file which are:
-
-+ The ``Num_of_particles_in_groups`` parameter: Gives the total number of
-  particles in the file which are in a halo.
-+ The ``Particle_types`` list: Gives a list of particles types similar to the
-  snap shots (0 - gas, 1 - dm, 4 - stars).
-
-Besides the ``.catalog_parttypes`` file, there is also a
-``.catalog_parttypes.unbound`` file, this file contains this information for
-the unbound particles.
-
-Properties file
-~~~~~~~~~~~~~~~
-
-The Fourth file is the ``.properties`` file, this file contains mainly physical
-useful information of the corresponding halos. Some usefull physical parameters
-are:
-
-+ ``Mass_200crit``: The mass of a halo with an overdensity on average of
-  :math:`\Delta=200` based on the critical density of the Universe.
-+ ``Mass_200mean``: The mass of a halo with an overdensity on average of
-  :math:`\Delta=200` based on the mean density of the Universe.
-+ ``Mass_FOF``: The friends-of-friends mass of the halos.
-+ ``Mvir``: The viral mass of the halos.
-+ ``Other parameters``: Soon
-
-
-
-
-.. _GitHub: https://github.com/pelahi/VELOCIraptor-STF
-.. _GitLab: https://gitlab.cosma.dur.ac.uk/swift/swiftsim
-   
diff --git a/doc/RTD/source/VELOCIraptorInterface/output.rst b/doc/RTD/source/VELOCIraptorInterface/output.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d3c5ea087b8251347d3e90e20076084a5a7bef6f
--- /dev/null
+++ b/doc/RTD/source/VELOCIraptorInterface/output.rst
@@ -0,0 +1,284 @@
+.. VELOCIraptor output
+   Folkert Nobels 12th of October
+
+VELOCIraptor Output
+===================
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Contents: 
+
+In general VELOCIraptor outputs six files per snapshot, of which 2 files are
+for unbound particles specifically.  In this part we will explain what is
+inside the different files.
+
+Catalog_groups file
+-------------------
+
+The first output file of VELOCIraptor is the ``.catalog_group`` file,
+this file contains all the information that is group specific, and does not go
+into depth of physical properties but only on numbers of particles and 
+group sizes, the interesting data in the ``.catalog_group`` files are: 
+
++ The ``group_size``: gives a list of all the halos and the number of particles
+  in the halo, this list is numbered from 0 until the number of groups minus
+  one. It is important that the groups are not ordered in any way [#order]_ 
++ The ``Num_of_groups`` or ``Total_num_of_groups``: gives the total number of
+  groups in the snapshot.
++ The ``Offset`` list: This list gives the offset off the particles. In the
+  output of VELOCIraptor there is no file which has an ID for every particle
+  and a corresponding group, rather the particles are ordered according to in
+  which group they are. So if we want to access the particles in group 0, we
+  need to look at the particles from ``Offset[0]`` until ``Offset[1]`` in the
+  ``.catalog_particles`` hdf5 file. In general this means that for group N we
+  need to look at particles ``Offset[N]`` until ``Offset[N+1]``. 
++ The ``Offset_unbound`` list: This list works exactly the same as the
+  ``Offset`` list only this list is for the gravitational unbound particles.
+
+Catalog_particles file
+----------------------
+
+The second file that is produced by VELOCIraptor is the ``.catalog_particles``
+file, this file contains mainly all the IDs of the particles and has two
+interesting parameters:
+
++ The ``Num_of_particles_in_groups`` and ``Num_of_particles_in_groups``
+  parameter: Gives the total number of particles in the file or the total 
+  number of particles that are in halos.
++ The ``Particle_IDs``: The list of particles as sorted by halo, in which halo
+  the individual particles are present can be found by using the
+  ``.catalog_group`` file and the corresponding ``Offset`` list. 
+
+Besides the ``.catalog_particles`` file, there is also a
+``.catalog_particles.unbound`` file, this file contains the same information
+but only for the unbound particles, a particle can only be present in one of
+these two lists. 
+
+Catalog_parttypes file
+----------------------
+
+The third file that is produced by VELOCIraptor is the ``.catalog_parttypes``
+file, this file contains the information what type of particle every particle
+is, it is ordered the same as the ``Particle_IDs`` in ``.catalog_particles``. 
+There are only two interesting parameters of the file which are:
+
++ The ``Num_of_particles_in_groups`` parameter: Gives the total number of
+  particles in the file which are in a halo.
++ The ``Particle_types`` list: Gives a list of particles types similar to the
+  snap shots (0 - gas, 1 - dm, 4 - stars).
+
+Besides the ``.catalog_parttypes`` file, there is also a
+``.catalog_parttypes.unbound`` file, this file contains this information for
+the unbound particles.
+
+Properties file
+---------------
+
+The Fourth file is the ``.properties`` file, this file contains many physical
+useful information of the corresponding halos. This can be divided in several
+useful groups of physical parameters, on this page we have divided the several
+variables which are present in the ``.properties`` file. This file has most 
+physical interesting parameters of the halos.
+
+Mass-Radius determination:
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``.properties`` file contains many ways to determine the size and mass 
+of the halos, in this subsection we will list several available variables in
+the output of VELOCIraptor and we list several mass and radius parameters in
+the output which are not classified as a mass-radius pair.
+
+Critical Density related:
+"""""""""""""""""""""""""
+
++ ``Mass_200crit``: The mass of a halo with an over density on average of
+  :math:`\Delta=200` based on the critical density of the Universe 
+  (:math:`M_{200}`).
++ ``R_200crit``: The :math:`R_{200}` radius of the halo based on the 
+  critical density of the Universe
+
+Mean Density related:
+"""""""""""""""""""""
+
++ ``Mass_200mean``: The mass of a halo with an over density on average of
+  :math:`\Delta=200` based on the mean density of the Universe 
+  (:math:`M_{200}`).
++ ``R_200mean``: The :math:`R_{200}` radius of the halo based on the 
+  mean density ofthe Universe.
+
+Virial properties:
+""""""""""""""""""
+
++ ``Mvir``: The virial mass of the halos.
++ ``Rvir``: The virial radius of the halo (:math:`R_{vir}`).
+
+Bryan and Norman 1998 properties:
+"""""""""""""""""""""""""""""""""
+
++ ``Mass_BN98``, The Bryan and Norman (1998) determination of the mass of the
+  halo [#BN98]_. 
++ ``R_BN98``, the Bryan and Norman (1998) corresponding radius[#BN98]_.
+
+Several Mass types:
+"""""""""""""""""""
+This is a list of masses which cannot be categorized as easy as the other 
+properties.
+
++ ``Mass_FOF``: The friends-of-friends mass of the halos.
++ ``M_gas``: The gas mass in the halo.
++ ``Mass_tot``: The total mass of the halo
++ ``M_gas_30kpc``: The gas mass within 30 kpc of the halo centre.
++ ``M_gas_500c``: The gas mass of the overdensity of 500 times the critical
+  density
++ ``M_gas_Rvmax``: The gas mass within the maximum rotation velocity.
+
+Several Radius types:
+"""""""""""""""""""""
+
++ ``R_HalfMass``: Radius of half the mass of the halo.
++ ``R_HalfMass_gas``: Radius of half the gas mass of the halo.
++ ``R_size``:
++ ``Rmax``: 
+
+Mass Structure of the Halos:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this subsection we listed the properties of the halos that are determining 
+the mass structure of the halo, so the exact profile and the inertia tensor.
+
+NFW profile properties:
+"""""""""""""""""""""""
+
++ ``cNFW``: The concentration of the halo.
++ ``Xc``, ``Yc`` and ``Zc``: The x,y and z centre positions of the halos 
+  [#center]_.
++ ``Xc_gas``, ``Yc_gas``, ``Zc_gas``: The offset of the centre positions of
+  the halo based on the gas, to find the position of the gas the offsets 
+  need to be added to ``Xc``, ``Yc`` and ``Zc``. 
++ ``VXc``, ``VYc`` and ``VZc`` are the velocities in the centre of the halo
+  [#check]_.
++ ``VXc_gas``, ``VYc_gas`` and ``VZc_gas`` are the velocities of the gas  in
+  the centre of the halo [#check]_.
+
+Intertia Tensor properties:
+"""""""""""""""""""""""""""
+
++ ``eig_ij``: Are the normalized eigenvectors of the inertia tensor.
++ The eigenvalue ratios: 
+
+  1. ``q`` is the semi-major over major; 
+  2. ``s`` is the minor over major.
+
++ ``eig_ij_gas``: Are the normalized eigenvectors of the inertia tensor for
+  only the gas particles.
++ The eigenvalue ratios for only the gas, similar to all particles:
+
+  1. ``q_gas`` is the semi-major over major for only gas; 
+  2. ``s_gas`` is the minor over major for only gas.
+
+Dynamical Structure of the Halos:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this subsection we list several properties that determine the dynamical
+structure of the halo, like the angular momentum and the velocity dispersion
+tensor.
+
+Angular momentum and spin parameters:
+"""""""""""""""""""""""""""""""""""""
+
++ ``lambda_b`` is the bullock spin parameter, see the paper by Bullock et al.
+  (2001) [#Bullock]_. 
++ ``Lx``, ``Ly`` and ``Lz`` are the angular momentum of the halos, the 
+  calculation includes all the particle types.
++ ``Lx_gas``, ``Ly_gas`` and ``Lz_gas`` are the angular momentum for only 
+  the gas particles in the snapshot.
+
+Velocity Dispersion related:
+""""""""""""""""""""""""""""
+
++ The complete velocity dispersion tensor (:math:`\sigma_{ij}`) which has 
+  an array per component which gives the value for all the halos. In 
+  general these components are called ``veldisp_ij`` in which i and j are 
+  given by ``x``, ``y`` or ``z``. This means that there are nine 
+  components stored in the ``.properties`` file. This omits the fact 
+  that the dispersion tensor by nature is a symmetric tensor. All the 
+  components are given by: 
+  ``veldisp_xx``, ``veldisp_xy``, ``veldisp_xz``, ``veldisp_yx``, 
+  ``veldisp_yy``, ``veldisp_yz``, ``veldisp_zx``, ``veldisp_zy``, 
+  and ``veldisp_zz`` [#velodisp]_.
++ ``sigV``, the scalar velocity dispersion which corresponds with the 
+  trace of the velocity dispersion tensor 
+  (:math:`\sigma = \text{Tr}(\sigma_{ij})`).
+
+
+Energy properties of the halos:
+"""""""""""""""""""""""""""""""
+
++ ``Ekin``, the kinetic energy of the halo.
++ ``Epot``, the potential energy of the halo.
++ ``Krot``, the rotational energy of the halo.
++ ``Krot_gas``, the rotational energy of the gas in the halo.
+
+
+Halo and subhalo abstract variables:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this subsection we list the ID convention for subhalos and halos and 
+some other abstract quantities of the halo which are not physical but 
+rather properties of the simulations.
+
+Structure types:
+""""""""""""""""
+
++ ``ID`` is the halo ID.
++ ``Structuretype`` is the parameter that indicates what kind of structure 
+  the current halo is. Halos have a structure type of ``10`` and subhalos
+  have a structure type of ``15``.
++ ``hostHaloID``, indicates the halo ID number of the host halo, in the case
+  that the halo has no parent (e.g. is the largest halo), the hostHaloID will
+  be ``-1``.
++ ``numSubStruct``, the number of substructures or subhalos in the halo.
+
+Particle types:
+"""""""""""""""
+
++ ``npart`` is the number of particles in the halo (all types of particles).
++ ``n_gas`` is the number of gas particles in the halo.
+
+Not specified parameters:
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this section we list parameters which cannot specifically be classified 
+in a group.
+
+
+Most Bound Particle (MBP):
+""""""""""""""""""""""""""
+
++ ``ID_mbp``, the ID of the most bound particle in the halo.
++ ``Xcmbp``, ``Ycmbp`` and ``Zcmbp`` are the positions of the most bound 
+  halo particle [#check]_.
++ ``VXcmbp``, ``VYcmbp`` and ``VZcmbp`` are the velocities of the most bound
+  halo particle [#check]_.
+
+.. [#order] In most cases more massive groups appear earlier in the list, but 
+   this is not guaranteed for larger simulations. The order of the groups is 
+   more a matter of the way that VELOCIraptor searches instead of a physical 
+   reason.
+.. [#center] This is not the average positions of the halos particles, but
+   the halo position found by the VELOCIraptor algorithm. This includes a 
+   fit for all the parameters including the gas particles or other types of
+   particles.
+.. [#velodisp] In the velocity dispersion tensor ( :math:`\sigma_{ij}` )  
+   the following relations are satisfied between components:
+
+   + :math:`\sigma_{xy}=\sigma_{yx}`
+   + :math:`\sigma_{xz}=\sigma_{zx}`
+   + :math:`\sigma_{yz}=\sigma_{yz}`
+.. [#Bullock] The Bullock spin parameter is given by 
+   :math:`\lambda = \frac{J}{\sqrt{2}MVR}`, for more information see 
+   https://arxiv.org/abs/astro-ph/0011001. 
+.. [#BN98] The Bryan and Norman (1998) paper can be found here: 
+   https://arxiv.org/abs/astro-ph/9710107
+.. [#check] Needs to be checked.
diff --git a/doc/RTD/source/VELOCIraptorInterface/stfalone.rst b/doc/RTD/source/VELOCIraptorInterface/stfalone.rst
new file mode 100644
index 0000000000000000000000000000000000000000..113cff53a51e446d321f6a912222c565f2bdb38e
--- /dev/null
+++ b/doc/RTD/source/VELOCIraptorInterface/stfalone.rst
@@ -0,0 +1,92 @@
+.. VELOCIraptor stand alone 
+   Folkert Nobels 12th October 2018
+
+Stand alone VELOCIraptor configuration
+======================================
+
+
+.. toctree::    
+   :maxdepth: 2    
+   :hidden:    
+   :caption: Contents: 
+   
+Besides running VELOCIraptor on the fly when using SWIFT, it is also possible
+to run VELOCIraptor alone without using SWIFT. In this section we explain how 
+VELOCIraptor can be run stand alone without using SWIFT.
+
+Setting up VELOCIraptor
+-----------------------
+
+The first step is setting up VELOCIraptor, this requires us to download the 
+git repository as::
+  
+  git clone https://github.com/pelahi/VELOCIraptor-STF
+
+Similar to the SWIFT with VELOCIraptor configuration, we can use the 
+swift-interface branch to analyse individual snapshots. We can use this branch
+by doing::
+
+  cd VELOCIraptor-STF
+  git fetch
+  git checkout swift-interface
+
+Again we need to copy the default SWIFT config file to a other config file by
+doing::
+
+  cd stf
+  cp Makefile.config.SWIFT-template Makefile.config
+
+Similar to configuring VELOCIraptor with swift we need to change the first 20
+lines of ``Makefile.config`` to work with our compiler, but we also need to 
+change the fact that we do not use the swift-interface but the standalone 
+version of the code, so change ``SWIFTINTERFACE="on"`` to 
+``SWIFTINTERFACE="off"``.
+
+Compiling VELOCIraptor
+----------------------
+
+Compoling goes completely different as compared to the on the fly halo finder
+configuration with SWIFT. In this case we can compile the code as::
+
+  make 
+
+After this an additional folder is created in ``VELOCIraptor-stf/stf`` called
+``bin``, in which the binary files of ``stf-gas`` is present (assuming you 
+run a simulation with SPH [#nosph]_)
+
+Running VELOCIraptor on a Snapshot
+----------------------------------
+
+After the code is compile the next step is using VELOCIraptor on a single 
+snapshot of a simulation. The code has several options which can be used, which
+can be displayed by running a terminal command of an invalid letter like::
+
+  ./stf-gas -h
+
+which gives the information about the usage of the command::
+
+  USAGE:
+
+  -C <configuration file (overrides other options)> 
+  -I <input format [Gadget (Default) 1, HDF (if implemented)2, TIPSY 3, RAMSES 4, HDF 2, NCHILADA 5>
+  -i <input file> 
+  -s <number of files per output for gadget input 1 [default]>
+  -Z <number of threads used in parallel read (1)>
+  -o <output filename>
+   ===== EXTRA OPTIONS FOR GADGET INPUT ====== 
+  -g <number of extra sph/gas blocks for gadget>
+  -s <number of extra star blocks for gadget>
+  -b <number of extra bh blocks for gadget>
+   ===== EXTRA OPTIONS REQUIRED FOR RAMSES INPUT ====== 
+  -t <ramses snapnumber>
+
+After this we can run a VELOCIraptor on a snapshot as::
+  
+  ./stf-gas -i input -o output -C configfile.txt
+
+
+.. [#nosph] In the case that in the ``Makefile.config`` it is indicate that the 
+   simulation does only contain dark matter this will reflect back on the 
+   generated binary file. So ``stf-gas`` will change to ``stf`` in the case of 
+   a dark matter only simulation.
+
diff --git a/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst b/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ac8dcc5b0b3c4b6b77dbd5dc79be2613eae0edc6
--- /dev/null
+++ b/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst
@@ -0,0 +1,95 @@
+.. SWIFT with VELOCIraptor
+   Folkert Nobels 12th October 2018
+
+
+Configuring SWIFT with VELOCIraptor
+===================================
+
+.. toctree::    
+   :maxdepth: 2    
+   :hidden:    
+   :caption: Contents:
+
+In the following three paragraphs we will explain how to setup VELOCIraptor,
+how to compile it and how to compile SWIFT with VELOCIraptor. 
+
+
+Setting up VELOCIraptor
+-----------------------
+
+Before we can run SWIFT with VELOCIraptor we first need to download
+VELOCIraptor. This can be done by cloning the repository on GitHub_::
+
+  git clone https://github.com/pelahi/VELOCIraptor-STF
+
+Currently the best version that works with SWIFT is the swift-interface branch
+of VELOCIraptor, to get this branch use::
+
+  cd VELOCIraptor-STF 
+  git fetch 
+  git checkout swift-interface
+
+To get the default that works with SWIFT simply copy the SWIFT template file in
+the ``Makefile.config``::
+
+  cd stf 
+  cp Makefile.config.SWIFT-template Makefile.config
+
+Depending on your compiler you want to change the first 20 lines of your
+``Makefile.config`` to work with your compiler and whether you want to use MPI
+or not. 
+
+
+Compiling VELOCIraptor
+----------------------
+
+After we downloaded the files and made a configuration file we can compile
+VELOCIraptor as follows::
+
+  make lib 
+  make libstf
+
+After the compilation of your code, there is an additional folder created in
+the ``VELOCIraptor-stf/stf`` directory called ``lib`` this directory has the
+library of VELOCIraptor and is required to run SWIFT with
+VELOCIraptor. Note that VELOCIraptor needs a serial version of the
+HDF5 library, not a parallel build.
+
+Compiling SWIFT
+---------------
+The next part is compiling SWIFT with VELOCIraptor and assumes you already
+downloaded SWIFT from the GitLab_, this can be done by running::
+
+  ./autogen.sh 
+  ./configure --with-velociraptor=/path/to/VELOCIraptor-STF/stf/lib 
+  make 
+
+In which ``./autogen.sh`` only needs to be run once after the code is cloned
+from the GitLab_, and ``/path/to/`` is the path to the ``VELOCIraptor-STF``
+directory on your machine. In general ``./configure`` can be run with other
+options as desired. After this we can run SWIFT with VELOCIraptor, but for this
+we first need to add several lines to the yaml file of our simulation::
+
+    
+  #structure finding options
+  StructureFinding:
+  config_file_name:     stf_input_6dfof_dmonly_sub.cfg
+  basename:             ./stf
+  output_time_format:   1
+  scale_factor_first:   0.02
+  delta_time:           1.02
+
+In which we specify the ``.cfg`` file that is used by VELOCIraptor and the 
+other parameters which SWIFT needs to use. In the case of 
+the Small Cosmological Volume DMO example we can run a simulation with halo
+finder as::
+
+  cd examples/SmallCosmoVolume_DM 
+  ../swift -c -s -G -x -t 8 small_cosmo_volume_dm.yml
+
+In which there is an additional ``-x`` option which activates the VELOCIraptor
+interface.
+
+
+.. _GitHub: https://github.com/pelahi/VELOCIraptor-STF
+.. _GitLab: https://gitlab.cosma.dur.ac.uk/swift/swiftsim
diff --git a/doc/RTD/source/VELOCIraptorInterface/whatis.rst b/doc/RTD/source/VELOCIraptorInterface/whatis.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e7f067ec4723e41da0f3a95dddad8f55d9897e85
--- /dev/null
+++ b/doc/RTD/source/VELOCIraptorInterface/whatis.rst
@@ -0,0 +1,65 @@
+.. What is VELOCIraptor
+   Folkert Nobels 12th October 2018
+
+
+What is VELOCIraptor?
+=====================
+
+.. toctree::    
+   :maxdepth: 2    
+   :hidden:    
+   :caption: Contents: 
+
+In SWIFT it is possible to run a cosmological simulation and at the same time
+do on the fly halo finding at specific predefined intervals. For finding the 
+Halos SWIFT uses VELOCIraptor (Elahi, Thacker and Widrow; 2011) [#velo]_, this 
+is a C++ halo finder that can use MPI. It differs from other halo finder 
+algorithms in the sense that it uses the velocity distributions of the 
+particles in the simulations and the the positions of the particles to get
+a better estimate of which particles are part of a specific halo and 
+whether there are substructures in halos. 
+
+The Algorithm
+-------------
+
+The VELOCIraptor algorithm consist basically off the following steps [#ref]_:
+
+1. A kd-tree is constructed based on the maximization of the Shannon-entropy,
+   this means that every level in the kd-tree an equal number of particles 
+   are distributed between the 8 lower nodes. This is based on their position
+   and their corresponding density, this results in more equal density 
+   distributed nodes. This is also the implicit step in the algorithm that 
+   takes into account the absolute positions of the particles.
+2. The next part is calculating the the centre of mass velocity and the 
+   velocity distribution for every individual node in the kd-tree. 
+3. Than the algorithm estimates the background velocity density function for
+   every particle based on the cell of the particle and the six nearest
+   neighbour cells. This prevents the background velocity density function 
+   to be over sensitive for variations between different cells due to dominant
+   halo features in the velocity density function. 
+4. After this the algorithm searches for the nearest velocity neighbours 
+   (:math:`N_v`) from a set of nearest position neighbours (:math:`N_x>N_v`).
+   The position neighbours do not need to be in the cell of the particles, in
+   general the set of nearest position neighbours is substantially larger than
+   the nearest velocity neighbours, the default is set as :math:`N_x=32 N_v`.
+5. The individual local velocity density function is calculated for every 
+   particle.
+6. The fractional difference is calculated between the local velocity density 
+   function and the background velocity density function.
+7. Based on the calculated ratio outliers are picked and the outliers are  
+   grouped together in halos and subhalos.
+  
+
+
+.. Every halo finder has limitations, the limitations of VELOCIraptor are:
+
+.. 1. The algorithm is mostly sensitive to substructures that are on the tail
+   of the Gaussian velocity density function, this means that VELOCIraptor
+   is most sensitive for subhalos which are cold (slow ratating) but have 
+   a large bulk velocity
+
+
+.. _Velociraptor: http://adsabs.harvard.edu/abs/2011MNRAS.418..320E
+.. [#velo] For technical information regarding VELOCIraptor see: Velociraptor_
+.. [#ref] This part is based on the explanation given in the Elahi, Thacker and
+   Widrow (2011) paper (Velociraptor_)