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help.html
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help.html
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{% extends "text_base.html" %}
{% block title %}HMFcalc | Help {% endblock %}
{% block subheading %}
<div class="col-9 page-header mx-auto">
<h1>Help</h1>
</div>
{% endblock %}
{% block content %}
<div class="col-9 mx-auto">
<p class="lead muted">
This page outlines the common usage of HMF<em>calc</em>, along with
information concerning the various parameters and options included.
Much of this information is a modified rendition of
<a href=http://arxiv.org/abs/1306.6721>this article</a>, which
accompanied the publishing of HMF<em>calc</em>, though the backend
has changed significantly since this publication.
Read on for information about common usage, the transfer function
used, the cosmological parameters and the fitting functions.
</p>
<h3>Using HMF<em>calc</em></h3>
<p>
HMF<em>calc</em> is built to be easy to use. In the simplest example,
the only action required on your part is to navigate to the
<a href="/hmfcalc/">calculator</a> and click "Calculate".
All required options and parameters are filled with
sensible defaults and ready to go. Nevertheless, most users will
want to fiddle with the parameters to tune them to their
particular needs -- be it a survey, simulation or investigation.
</p>
<p>
The options and parameters in HMF<em>calc</em> were chosen to give
as much flexibility as possible without making things overly
complicated. They are split over tabs in the calculator, each
governing a different sub-model.
</p>
<p>
The organisation of these tabs is no accident -- it mirrors the
internal organisation of the <code>hmf</code> code.
<code>hmf</code> is composed of a series of <code>components</code>,
integrated into <code>frameworks</code>. Each <code>component</code>
and <code>framework</code> receives its own Tab in HMF<em>calc</em>.
</p>
<p>
In particular, <code>components</code> often have many different
<span class="font-italic">models</span> which can be chosen for them.
One obvious example is the hmf model itself (i.e. the fitting function
chosen to model f(σ)). Each of these models (for the same
<code>component</code>) may have different parameters. These parameters
will be shown dynamically as you chose the relevant models.
</p>
<h4>Model Creation and Editing</h4>
<p>
New to HMF<em>calc</em> is the ability to view and edit the models
that have been thus-far created. Each created model receives its
own entry in a table below the main plotting interface. From there,
you can choose to edit or delete the model. Also, you can create a
new model based on the existing model (all parameter defaults for
the new model will match the parameters of the model that was
chosen as a starting point).
</p>
<p>
HMF<em>calc</em> starts with a default model (matching the default
model of <code>hmf</code>) and allows you to edit or create more
models based on this default. You can delete all but one model,
as HMF<em>calc</em> always expects to have at least one model
defined.
</p>
<p>
Models are persistent -- you can navigate to this help page and
back to the <a href="/hmfcalc/">calculator</a> and your models
will remain. To restart calculations from the original default
model and delete all the models you've created in the session,
use the big red restart button in the calculator.
</p>
<!--
<h3>Transfer Function</h3>
The transfer function is handled in one of three ways. It is either
<ol>
<li> Previously computed at high resolution by <a href="http://camb.info">CAMB</a> and included as a default
option.
</li>
<li> Previously computed <em>by the user</em> either with CAMB or saved in the same format as CAMB, and uploaded
to HMF<em>calc</em></li>
<li> Computed on-the-fly with arbitrary cosmological parameters.
</ol>
We describe some of the details of each method in this section.
<h5>Pre-Computed High-Res Transfer</h5>
<p>This is the default option. It is selected by choosing a popular cosmology from the "Transfer Function" drop-down
list.
Parameters of that cosmology that affect that transfer function in any way
are internally set and made non-modifiable so that no confusion arises. Parameters that are relevant to the
cosmology and prescribed in
the relevant paper, but which do not affect the transfer function, are set by default to their proper values but
are still modifiable.
</p>
<p>
This option does not allow the automatic generation of HMF's for several cosmologies, except for in the
transfer-independent parameters,
as only one default may be chosen at a time. However, you may use the "Add Extra Plots" feature after generating
a HMF to add different
default cosmologies.
</p>
<p>
As mentioned, each of the default cosmologies is a high-resolution transfer function from CAMB. In each case,
all parameters of the run
(and there are many) were the same, except for the cosmological parameters. The following table shows the values
for each of the cosmologies, where
each set of parameters was taken from a corresponding paper, linked from the heading. Note that the
n<sub>s</sub> and σ<sub>8</sub> are not used
to calculate the transfer function within CAMB, but we list their values here for completeness.
<div class='row'>
<div class='span7'>
<table id="cosmo_quantities" class='table table-bordered table-condensed table-hover table-striped'>
<thead>
<th scope='col'> Parameter</th>
<th scope='col'><a href='http://arxiv.org/abs/1303.5076'>Planck</a></th>
<th scope='col'><a href='http://arxiv.org/abs/1212.5226'>WMAP9</a></th>
<th scope='col'><a href='http://adsabs.harvard.edu/abs/2011ApJS..192...18K'>WMAP7</a></th>
<th scope='col'><a
href='http://stacks.iop.org/0067-0049/180/i=2/a=330?key=crossref.355ec98555761e3f8a6a38d88962d16f'>WMAP5</a>
</th>
<th scope='col'><a
href="http://stacks.iop.org/0067-0049/180/i=2/a=330?key=crossref.355ec98555761e3f8a6a38d88962d16f">GiggleZ</a>
</th>
<th scope='col'><a href="http://adsabs.harvard.edu/abs/2007ApJS..170..377S">WMAP3</a></th>
<th scope='col'><a href="http://adsabs.harvard.edu/abs/2003ApJS..148..175S">WMAP1</a></th>
<th scope='col'><a
href="http://tao.it.swin.edu.au/partner-resources/simulations/millennium/">Millennium</a></th>
</thead>
<tbody>
<tr>
<td> Ω<sub>Λ</sub></td>
<td> 0.6817</td>
<td> 0.7181</td>
<td> 0.728</td>
<td> 0.723</td>
<td> 0.726</td>
<td> 0.732</td>
<td> 0.710</td>
<td> 0.750</td>
</tr>
<tr>
<td> Ω<sub>c</sub></td>
<td> 0.2678</td>
<td> 0.236</td>
<td> 0.226</td>
<td> 0.231</td>
<td> 0.228</td>
<td> 0.224</td>
<td> 0.243</td>
<td> 0.205</td>
</tr>
<tr>
<td> Ω<sub>b</sub></td>
<td> 0.049</td>
<td> 0.0461</td>
<td> 0.0455</td>
<td> 0.0459</td>
<td> 0.0456</td>
<td> 0.044</td>
<td> 0.047</td>
<td> 0.045</td>
</tr>
<tr>
<td> n<sub>s</sub></td>
<td> 0.9619</td>
<td> 0.9646</td>
<td> 0.967</td>
<td> 0.962</td>
<td> 0.960</td>
<td> 0.99</td>
<td> 0.947</td>
<td> 1</td>
</tr>
<tr>
<td> H<sub>0</sub></td>
<td> 67.04</td>
<td> 69.7</td>
<td> 0.704</td>
<td> 0.702</td>
<td> 0.705</td>
<td> 0.704</td>
<td> 0.72</td>
<td> 0.73</td>
</tr>
<tr>
<td> σ<sub>8</sub></td>
<td> 0.8347</td>
<td> 0.817</td>
<td> 0.81</td>
<td> 0.817</td>
<td> 0.812</td>
<td> 0.776</td>
<td> 0.9</td>
<td> 0.9</td>
</tr>
</tbody>
</table>
</div>
</div>
</p>
-->
<!--
For completeness, we also list here the values of the other parameters used for the CAMB runs. Note that these are
values used for
the high-resolution default transfer functions. Where the on-the-fly runs differ from these, we note their value in
parentheses.
Parameters that do not affect the transfer function whatsoever are intentionally omitted here for brevity.
<div class='row'>
<div class='span5'>
<table id="cosmo_quantities" class='table table-bordered table-condensed table-hover table-striped'>
<thead>
<th scope='col'> Parameter</th>
<th scope='col'> Value</th>
<th scope='col'> Parameter</th>
<th scope='col'> Value</th>
<th scope='col'> Parameter</th>
<th scope='col'> Value</th>
</thead>
<tbody>
<tr>
<td> Cl's</td>
<td>Scalar</td>
<td> get_transfer</td>
<td> TRUE</td>
<td> accurate_reionization</td>
<td>TRUE</td>
</tr>
<tr>
<td> Do lensing</td>
<td> FALSE</td>
<td> do_nonlinear</td>
<td>Linear</td>
<td> re_ionization_frac</td>
<td>-1</td>
</tr>
<tr>
<td> do_tensor_neutrinos</td>
<td>TRUE</td>
<td> Scalar l_max</td>
<td> 2000</td>
<td> RECFAST_fudge</td>
<td>1.14</td>
</tr>
<tr>
<td> initial_ratio</td>
<td>1</td>
<td> Scalar k*eta_max</td>
<td> 4000</td>
<td> RECFAST_fudge_He</td>
<td>0.86</td>
</tr>
<tr>
<td> Do_late_rad_truncation</td>
<td>TRUE</td>
<td> Use Physical Parameters</td>
<td> FALSE</td>
<td> RECFAST_Heswitch</td>
<td>6</td>
</tr>
<tr>
<td> reionization</td>
<td>True</td>
<td> cs2_lam</td>
<td> 0</td>
<td> RECFAST_Hswitch</td>
<td>TRUE</td>
</tr>
<tr>
<td> high_accuracy_default</td>
<td>1</td>
<td> temp_cmb</td>
<td>2.725</td>
<td> Initial scalar Perturbation Mode</td>
<td>Adiabatic</td>
<tr>
<td> helium_fraction</td>
<td>0.24</td>
<td> vector_mode</td>
<td>0</td>
<td> l_accuracy_boost</td>
<td>1</td>
<tr>
<td> massless_neutrinos</td>
<td>3.04</td>
<td> COBE_normalize</td>
<td>FALSE</td>
<td> l_sample_boost</td>
<td>2.725</td>
<tr>
<td> massive_neutrinos</td>
<td>0</td>
<td> CMB_outputscale</td>
<td>1</td>
<td> massive_nu_approx</td>
<td>1</td>
<tr>
<td> nu_mass_eigenstates</td>
<td>1</td>
<td> transfer_high_precision</td>
<td>TRUE</td>
<td> Lensing Method</td>
<td>Curved Correlation Funtion</td>
<tr>
<td> nu_mass_degeneracies</td>
<td>0</td>
<td> Transfer_kmax</td>
<td>2000</td>
<td> accurate_polarization</td>
<td>TRUE</td>
<tr>
<td> nu_mass_fractions</td>
<td>1</td>
<td> transfer_k_per_logint</td>
<td>100</td>
<td> accurate_BB</td>
<td>FALSE</td>
<tr>
<td> scalar_amp</td>
<td>1</td>
<td>accuracy_boost</td>
<td>1</td>
</tbody>
</table>
</div>
</div>
-->
<!--
<h5>User-Uploaded Transfer</h5>
<p>
To select this option, choose "Custom Transfer" from the "Transfer Function" drop-down list and then upload a
file using the "Upload Transfer Function"
tool. The user must be careful using this option. There is no way for HMF<em>calc</em> to know what cosmology
the uploaded transfer function was
calculated with. The user must therefore be careful to set the correct corresponding parameters. Note that only
parameters that affect both transfer
and the mass function explicitly (see cosmological parameter table) need to be set accurately. Parameters
affecting only the transfer function will not
be used within HMF<em>calc</em>, and parameters used only in HMF<em>calc</em> will not be at odds with the
transfer function. However, for later reference
it is still better to set every parameter properly, as the parameters are written to file which may later be
read.
The file uploaded in this manner should be in the same format as a transfer function produced by CAMB. That is,
it should consist of one column of <em>k/h</em>
values, followed by 6 columns of transfer function values. The last column should be the total transfer
function.
</p>
<h5>On-The-Fly Transfer</h5>
<p>This option is selected if a custom transfer function is chosen, but
no file is uploaded. In this case the user may choose a calculator to use.
Currently only two options are available - CAMB and the Eisenstein-Hu transfer function (which is
calculated using the cosmolopy package).
</p>
<p>
If CAMB is chosen as the calculator, HMF<em>calc</em> only offers the cosmological parameters
as input parameters to CAMB. All other parameters are taken as the defaults from the backend hmf package (listed
in the camb parameters table).
This is both to save computation time (the defaults are the most efficient to achieve requisite accuracy at high
mass, see the linked article),
and to avoid unnecessary clutter in the options.
</p>
<h3>Parameters</h3>
<p>
We have discussed already that the options and parameters of HMF<em>calc</em> are split across two categories:
run parameters and cosmological parameters.
</p>
<p>
We first have the run parameters. In this table, the "Mult?" column specifies whether the given parameter
accepts multiple entries (separated by commas).
<img src="http://hmfstatic.appspot.com/img/runparams.png">
</p>
<p>
Secondly we have the cosmological parameters. The "Affects" column specifies whether the parameter affects the
transfer function (T), the HMF (H) or both (B).
<img src="http://hmfstatic.appspot.com/img/cosmoparams.png">
<h3>Fitting Functions</h3>
<p>
One of the features of HMF<em>calc</em> is its wide array of fitting functions from the literature. We aim to
include any fit from the published literature
that we find, and encourage you to contact us if you know of a fit which we have not included.
</p>
<p>
With such a list of available fits, it is perhaps useful to provide some short commentary on how to best choose
among them for a specific purpose. We note
that each fitting function is a fit to the distribution of halo masses found in a simulation (or set of
simulations) with a particular cosmology, and using
a particular halo-finder. Thus differences between fits can naturally arise from these choices, along with the
evolution of resolution and size with time.
Given these considerations, we give a few suggestions for choosing a fitting function:
<ul>
<li>Prefer functions measured at a similar cosmology to the one you employ</li>
<li>Generally choose a later function over an earlier one</li>
<li>If you are using a wide range of cosmologies, or want to remain as general as possible, prefer a function
fitted over several cosmologies
</li>
<li>Generally, for observational purposes, choose an SO fit, but for halo-model calculations choose an FOF
fit.
</li>
</ul>
</p>
<p>
To help weigh these considerations, we here provide the list of references for all fitting functions found in
HMF<em>calc</em>:
<ul>
<li><a href='http://iopscience.iop.org/0004-637X/671/2/1160/'>Press, Schechter, 1974 </a></li>
<li><a href='http://doi.wiley.com/10.1046/j.1365-8711.2001.04006.x'>Sheth, Mo, Tormen, 2001 </a></li>
<li><a href='http://adsabs.harvard.edu/abs/2001MNRAS.321..372J'>Jenkins et. al. 2001 </a></li>
<li><a href="http://arxiv.org/abs/astro-ph/0301270">Reed et. al., 2003</a></li>
<li><a href='http://adsabs.harvard.edu/abs/2006ApJ...646..881W'>Warren et. al., 2006 </a></li>
<li><a href="http://arxiv.org/abs/0705.0898">Peacock, 2007</a></li>
<li><a href='http://adsabs.harvard.edu/abs/2007MNRAS.374....2R'>Reed et. al., 2007 </a></li>
<li><a href="http://arxiv.org/abs/0803.2706">Tinker et. al., 2008 </a></li>
<li><a href='http://doi.wiley.com/10.1111/j.1365-2966.2009.16194.x'>Crocce et. al., 2010 </a></li>
<li><a href="http://arxiv.org/abs/1001.3425">Courtin et. al., 2010 </a></li>
<li><a href="http://arxiv.org/abs/1005.2239">Bhattacharya et. al., 2011</a></li>
<li><a href="arXiv:1203.3216v1">Angulo et. al., 2012 </a></li>
<li><a href="http://arxiv.org/abs/1212.0095">Watson et. al., 2012 </a></li>
<li><a href="http://arxiv.org/abs/1207.6105">Behroozi, Weschler, Conroy, 2013</a></li>
</ul>
</p>
For a concise summary of the functional forms and respective properties of each fit, download
<a href="/downloads/fitting_functions.pdf">this table</a>,
which will remain a standalone, updated version of Table 3 in the article describing HMF<em>calc</em>.
-->
</div>
{% endblock %}