### Various spelling corrections

 ... ... @@ -66,7 +66,7 @@ TODO How to Implement a New Cooling ------------------------------ The developper should provide at least one function for: The developer should provide at least one function for: * writing the cooling name in HDF5 * cooling a particle * the maximal time step possible ... ...
 ... ... @@ -17,7 +17,7 @@ give a short overview of the potentials that are implemented in the code: 1. No potential (none) 2. Point mass potential (point-mass): classical point mass, can be placed at a position with a mass. 3. Plummer potential (point-mass-softened): in the code a softended point mass 3. Plummer potential (point-mass-softened): in the code a softened point mass corresponds to a Plummer potential, can be placed at a position with a mass. 4. Isothermal potential (isothermal): An isothermal potential which corresponds to a density profile which is :math:\propto r^{-2} and a potential which is ... ... @@ -28,7 +28,7 @@ give a short overview of the potentials that are implemented in the code: :math:\Phi(r) = - \frac{GM}{r+a}. The free paramters of Hernquist potential are mass, scale length, The free parameters of Hernquist potential are mass, scale length, and softening. The potential can be set at any position in the box. 6. NFW potential (nfw): The most used potential to describe dark matter halos, the potential is given by: ... ... @@ -36,7 +36,7 @@ give a short overview of the potentials that are implemented in the code: :math:\Phi(r) = - \frac{4\pi G \rho_0 R_s^3}{r} \ln \left( 1+ \frac{r}{R_s} \right). This potential has as free paramters the concentration of the DM halo, the This potential has as free parameters the concentration of the DM halo, the virial mass (:math:M_{200}) and the critical density. 7. Sine wave (sine-wave) 8. Point mass ring (point-mass-ring) ... ...
 ... ... @@ -45,6 +45,6 @@ Several cooling implementations (including GRACKLE) are available. Many external potentials are available for use with SWIFT. You can choose between them at compile time. Some examples include a central potential, a softened central potential, and a sinusoidal potential. You will need to configure, for example, the mass in your parameterfile at runtime. configure, for example, the mass in your parameter file at runtime.
 ... ... @@ -9,4 +9,4 @@ and the other swift_mpi. Current wisdom is to run swift if you are only using one node (i.e. without any interconnect), and one MPI rank per NUMA region using swift_mpi for anything larger. You will need some GADGET-2 HDF5 initial conditions to run SWIFT, as well as a compatible yaml parameterfile. parameter file.
 ... ... @@ -13,7 +13,7 @@ Adding Hydro Schemes SWIFT is engineered to enable you to add your own hydrodynamics schemes easily. We enable this through the use of header files to encapsulate each scheme. Note that it's unlikely you will ever have to consider paralellism or 'loops over Note that it's unlikely you will ever have to consider parallelism or 'loops over neighbours' for SWIFT; all of this is handled by the tasking system. All we ask for is the interaction functions that tell us how to a) compute the density and b) compute forces. ... ... @@ -69,7 +69,7 @@ will need to 'fill out' the following: + hydro_compute_timestep(p, xp, hydro_props, cosmo) returns the timestep for the hydrodynamics particles. + hydro_timestep_extra(p, dt) does some extra hydro operations once the physical timestel for the particle is known. physical timestep for the particle is known. + hydro_init_part(p, hydro_space) initialises the particle in preparation for the density calculation. This essentially sets properties, such as the density, to zero. ... ...
 ... ... @@ -10,7 +10,7 @@ GIZMO-Like Scheme :caption: Contents: There is a meshless finite volume (MFV) GIZMO-like scheme implemented in SWIFT There is a mesh-less finite volume (MFV) GIZMO-like scheme implemented in SWIFT (see Hopkins 2015 for more information). You will need a Riemann solver to run this, and configure as follows: ... ... @@ -19,7 +19,7 @@ this, and configure as follows: ./configure --with-hydro="gizmo-mfv" --with-riemann-solver="hllc" We also have the meshless finite mass (MFM) GIZMO-like scheme. You can select We also have the mesh-less finite mass (MFM) GIZMO-like scheme. You can select this at compile-time with the following configuration flags: .. code-block:: bash ... ...
 ... ... @@ -22,7 +22,7 @@ place in SWIFT. A single file can contain any number of particles (well... up to compute node. The original GADGET-2 file format only contains 2 types of particles: gas particles and 5 sorts of collisionless particles that allow users to run with 5 particles and 5 sorts of collision-less particles that allow users to run with 5 separate particle masses and softenings. In SWIFT, we expand on this by using two of these types for stars and black holes. ... ... @@ -39,7 +39,7 @@ You can find out more about the HDF5 format on their webpages Structure of the File --------------------- There are several groups that contain 'auxilliary' information, such as There are several groups that contain 'auxiliary' information, such as Header. Particle data is placed in separate groups depending of the type of the particles. Some types are currently ignored by SWIFT but are kept in the file format for compatibility reasons. ... ... @@ -102,7 +102,7 @@ In the /Header/ group, the following attributes are required: NumPart_Total to be >2^31, the use of NumPart_Total_HighWord is only here for compatibility reasons. + Flag_Entropy_ICs, a historical value that tells the code if you have included entropy or internal energy values in your intial conditions files. included entropy or internal energy values in your initial conditions files. Acceptable values are 0 or 1. We recommend using internal energies over entropy in the ICs and hence have this flag set to 0. ... ... @@ -147,7 +147,7 @@ individual particle type (e.g. /PartType0/) that have the following *dataset + Masses, an array of length N that gives the masses of the particles. For PartType0 (i.e. particles that interact through hydro-dynamics), you will need the following auxilliary items: need the following auxiliary items: + SmoothingLength, the smoothing lengths of the particles. These will be tidied up a bit, but it is best if you provide accurate numbers. In ... ... @@ -169,7 +169,7 @@ h-free quantities. Switching this parameter on will also affect the box size read from the /Header/ group (see above). Similarly, GADGET cosmological ICs have traditionally used velocities expressed as peculiar velocities divided by sqrt(a). This can be undone by swicthing as peculiar velocities divided by sqrt(a). This can be undone by switching on the parameter InitialConditions:cleanup_velocity_factors in the :ref:Parameter_File_label. ... ...
 ... ... @@ -24,7 +24,7 @@ Comments can be inserted anywhere and start with a hash: .. code:: YAML # Descrption of the physics # Description of the physics viscosity_alpha: 2.0 dt_max: 1.5 # seconds ... ... @@ -113,7 +113,7 @@ schemes that make use of the unit of electric current. There is also no incentive to use anything else than Kelvin but that makes the whole system consistent with any possible unit system. If one is interested in using the more humourous FFF unit If one is interested in using the more humorous FFF unit system _ one would use .. code:: YAML ... ... @@ -133,8 +133,8 @@ Cosmology --------- When running a cosmological simulation, the section Cosmology sets the values of the cosmological model. The epanded :math:\Lambda\rm{CDM} parameters governing the background evolution of the Univese need to be specified here. These are: cosmological model. The expanded :math:\Lambda\rm{CDM} parameters governing the background evolution of the Universe need to be specified here. These are: * The reduced Hubble constant: :math:h: h, * The matter density parameter :math:\Omega_m: Omega_m, ... ... @@ -146,7 +146,7 @@ The last parameter can be omitted and will default to :math:\Omega_r = 0. Note that SWIFT will verify on start-up that the matter content of the initial conditions matches the cosmology specified in this section. This section als specifies the start and end of the simulation expressed in This section also specifies the start and end of the simulation expressed in terms of scale-factors. The two parameters are: * Initial scale-factor: a_begin, ... ... @@ -157,7 +157,7 @@ state of dark energy :math:w(a). We use the evolution law :math:w(a) = w_0 + w_a (1 - a). The two parameters in the YAML file are: * The :math:z=0 dark energy equation of state parameter :math:w_0: w_0 * The dark energy equation of state evolutio parameter :math:w_a: w_a * The dark energy equation of state evolution parameter :math:w_a: w_a If unspecified these parameters default to the default :math:\Lambda\rm{CDM} values of :math:w_0 = -1 and :math:w_a = 0. ... ... @@ -179,13 +179,13 @@ use the following parameters: w_0: -1.0 # (Optional) w_a: 0. # (Optional) When running a non-cosmological simulation (i.e. without the -c runtime When running a non-cosmological simulation (i.e. without the -c run-time flag) this section of the YAML file is entirely ignored. Gravity ------- The behaviour of the self-gravity solver can be modifed by the parameters The behaviour of the self-gravity solver can be modified by the parameters provided in the Gravity section. The theory document puts these parameters into the context of the equations being solved. We give a brief overview here. ... ... @@ -206,7 +206,7 @@ The last tree-related parameter is * The tree rebuild frequency: rebuild_frequency. Thqe tree rebuild frequency is an optional parameter defaulting to The tree rebuild frequency is an optional parameter defaulting to :math:0.01. It is used to trigger the re-construction of the tree every time a fraction of the particles have been integrated (kicked) forward in time. ... ... @@ -219,12 +219,12 @@ Particle-Mesh part of the calculation. The last three are optional: * The scale above which the short-range forces are assumed to be 0 (in units of the mesh cell-size multiplied by :math:a_{\rm smooth}) :math:r_{\rm cut,max}: r_cut_max (default: 4.5), * The scale bewlo which the short-range forces are assumed to be exactly Newtonian (in units of * The scale below which the short-range forces are assumed to be exactly Newtonian (in units of the mesh cell-size multiplied by :math:a_{\rm smooth}) :math:r_{\rm cut,min}: r_cut_min (default: 0.1), For most runs, the default values can be used. Only the number of cells along each axis needs to be sepcified. The remaining three values are best described each axis needs to be specified. The remaining three values are best described in the context of the full set of equations in the theory documents. As a summary, here are the values used for the EAGLE :math:100^3~{\rm Mpc}^3 ... ... @@ -308,7 +308,7 @@ Whilst for a cosmological run, one would need: Initial Conditions ------------------ This IntialConditions section of the parameter file contains all the options related to This InitialConditions section of the parameter file contains all the options related to the initial conditions. The main two parameters are * The name of the initial conditions file: file_name, ... ... @@ -410,15 +410,15 @@ this mechanism is driven by the options in the Restarts section of the YAML parameter file. All the parameters are optional but default to values that ensure a reasonable behaviour. * Wether or not to enable the dump of restart files: enable (default: * Whether or not to enable the dump of restart files: enable (default: 1). This parameter acts a master-switch for the check-pointing capabilities. All the other options require the enable parameter to be set to 1. * Wether or not to save a copy of the previous set of check-pointing files: * Whether or not to save a copy of the previous set of check-pointing files: save (default: 1), * Wether or not to dump a set of restart file on regular exit: onexit * Whether or not to dump a set of restart file on regular exit: onexit (default: 0), * The wall-clock time in hours between two sets of restart files: delta_hours (default: 6.0). ... ... @@ -433,7 +433,7 @@ smaller value to allow for enough time to safely dump the check-point files. If the directory does not exist, SWIFT will create it. When resuming a run, SWIFT, will look for files with the name provided in the sub-directory specified here. The files themselves are named basename_000001.rst where the basenme here. The files themselves are named basename_000001.rst where the basename is replaced by the user-specified name and the 6-digits number corresponds to the MPI-rank. SWIFT writes one file per MPI rank. If the save option has been activated, the previous set of restart files will be named ... ... @@ -490,7 +490,7 @@ Scheduler Domain Decomposition -------------------- .. [#f1] The thorough reader (or overly keen SWIFT tester) would find that the speed of light is :math:c=1.8026\times10^{12}\,\rm{fur}\,\rm{ftn}^{-1}, Newton's contant becomes :math:G_N=4.896735\times10^{-4}~\rm{fur}^3\,\rm{fir}^{-1}\,\rm{ftn}^{-2} and Planck's constant turns into :math:h=4.851453\times 10^{-34}~\rm{fur}^2\,\rm{fir}\,\rm{ftn}^{-1}. .. [#f1] The thorough reader (or overly keen SWIFT tester) would find that the speed of light is :math:c=1.8026\times10^{12}\,\rm{fur}\,\rm{ftn}^{-1}, Newton's constant becomes :math:G_N=4.896735\times10^{-4}~\rm{fur}^3\,\rm{fir}^{-1}\,\rm{ftn}^{-2} and Planck's constant turns into :math:h=4.851453\times 10^{-34}~\rm{fur}^2\,\rm{fir}\,\rm{ftn}^{-1}. .. [#f2] which would translate into a constant :math:G_N=1.5517771\times10^{-9}~cm^{3}\,g^{-1}\,s^{-2} if expressed in the CGS system.
 .. Parameter File Loic Hausammann, 1 june 2018 Loic Hausammann, 1 June 2018 .. _Output_list_label: ... ... @@ -53,7 +53,7 @@ default all fields are written. This field is mostly used to remove unnecessary output by listing them with 0's. A classic use-case for this feature is a DM-only simulation (pure n-body) where all particles have the same mass. Outputing the (pure n-body) where all particles have the same mass. Outputting the mass field in the snapshots results in extra i/o time and unnecessary waste of disk space. The corresponding section of the yaml parameter file would look like this:: ... ...
 ... ... @@ -67,7 +67,7 @@ wish to extract. The python snippet below should give you an idea of how to go about doing this for the bound particles. First, we need to extract the offset from the .catalog_group file, and work out how many _bound_ partices are in our halo. We can do this by work out how many _bound_ particles are in our halo. We can do this by looking at the next offset. Then, we can ID match those with the snapshot file, and get the mask for the _positions_ in the file that correspond to our bound particles. (Note this requires numpy > 1.15.0). ... ... @@ -97,7 +97,7 @@ to our bound particles. (Note this requires numpy > 1.15.0). # Again, we're done with that file. particles_file.close() # Now, the tricky bit. We need to create the correspondance between the # Now, the tricky bit. We need to create the correspondence between the # positions in the snapshot file, and the ids. # Let's look for the dark matter particles in that halo. ... ... @@ -166,7 +166,7 @@ Mean Density related: :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. mean density of the Universe. Virial properties: """""""""""""""""" ... ... @@ -190,7 +190,7 @@ properties. + 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 + M_gas_500c: The gas mass of the over-density of 500 times the critical density + M_gas_Rvmax: The gas mass within the maximum rotation velocity. ... ... @@ -232,7 +232,7 @@ NFW profile properties: + VXc_gas, VYc_gas and VZc_gas are the velocities of the gas in the centre of the halo [#check]_. Intertia Tensor properties: Inertia Tensor properties: """"""""""""""""""""""""""" + eig_ij: Are the normalized eigenvectors of the inertia tensor. ... ...
 ... ... @@ -45,7 +45,7 @@ version of the code, so change SWIFTINTERFACE="on" to Compiling VELOCIraptor ---------------------- Compoling goes completely different as compared to the on the fly halo finder Compiling 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 ... ...
 ... ... @@ -55,7 +55,7 @@ The VELOCIraptor algorithm consists basically of the following steps [#ref]_: .. 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 is most sensitive for subhalos which are cold (slow rotating) but have a large bulk velocity ... ...
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