Commit b4e4d866 authored by Charles G Waldman's avatar Charles G Waldman
Browse files

Merge branch 'cgw-pdf' into 'main' 

Enable PDF output

See merge request !170
parents 5b828a94 14e57f0e

README.md

+23 −6
Original line number Diff line number Diff line
@@ -34,16 +34,33 @@ can be built locally by: 
> pip install sphinx sphinx_rtd_theme sphinx-tabs sphinxcontrib-bibtex

```



2. Build the documentation:

2. Build the documentation (HTML):



```shell

> mkdir build

> sphinx-build -b html docs/source_docs/ build

$ make  # note, "make html" also works

```



The HTML pages will now be located in the `build` directory. Open the

`index.html` with your favorite browser:

The HTML pages will be located in the `build/html` directory.

Open the `index.html` with your favorite browser:



```shell

> firefox build/index.html

$ firefox build/html/index.html

```



3. Build the documentation (PDF):



You will need xetex.  You should be able to get this from your

distribution's package repository.  On Ubuntu something like

``sudo apt-get install texlive-xetex`` should do the trick.

More info at https://www.tug.org/texlive/



```shell

$ make pdf

```



The output file `mfix.pdf` will be in `build/latex`



4. Cleaning up:

``` shell

$ make clean

```

docs/source_docs/_static/theme_overrides.css

+4 −0
Original line number Diff line number Diff line
@@ -15,3 +15,7 @@ 
.eqno {

    float: right;

}



.wy-nav-content {

    max-width: none;

}

docs/source_docs/conf.py

+22 −0
Original line number Diff line number Diff line
@@ -194,3 +194,25 @@ texinfo_documents = [ 
     author, 'MFIX-Exa Team', "MFIX-Exa, it's MFiX... but now with more Exa!",

     'Miscellaneous Aardvark'),

]



latex_engine = 'xelatex'



latex_elements = {

    'geometry': r'\usepackage[margin=0.75in]{geometry}',

    'preamble': r'''

% Increase minimum column width

\setlength{\tymin}{120pt}

% Allow text to wrap better in table cells

\usepackage{ragged2e}

\RaggedRight

% More vertical space in table rows

\renewcommand{\arraystretch}{1.2}

% Fix for tables with problematic content

\usepackage{ltablex}

\usepackage{tabularx}

% Prevent overfull hbox in tables

\setlength{\emergencystretch}{3em}

''',

}

# Use longtable for better page breaks and wrapping

latex_table_style = ['longtable', 'colorrows']

docs/source_docs/references/size_distributions.rst

+10 −10
Original line number Diff line number Diff line
@@ -233,20 +233,20 @@ The mean of this distribution is computed as 
.. math::

   :label: eq_normal_dist_FN_to_FV_mean



   \begin{align}

   \begin{aligned}

       \mu_V =& \frac{ \int_{-\infty}^{\infty} x \tilde{f}_X^V(x) dx }{\int_{-\infty}^{\infty} \tilde{f}_X^V(x) dx } \\[10pt]

             =& \frac{3\sigma_N^4 + 6\sigma_N^2\mu_N^2 + \mu_N^4}{3\sigma_N^2 \mu_N + \mu_N^3}

   \end{align}

   \end{aligned}



and the variance is given by



.. math::

   :label: eq_normal_dist_FN_to_FV_variance



   \begin{align}

   \begin{aligned}

       \sigma^2_V =& \frac{ \int_{-\infty}^{\infty} (x - \mu_V)^2 \tilde{f}_X^V(x) dx }{\int_{-\infty}^{\infty} \tilde{f}_X^V(x) dx } \\[10pt]

                  =& \frac{3\sigma_N^4 (3\mu_N + 2b) + \sigma^2(\mu_N^3 + 6\mu_N^2 b + 3\mu_Nb^2)+\mu_N^3 b^2}{3\sigma_N^2 \mu_N + \mu_N^3}

   \end{align}

   \end{aligned}



where :math:`b = (\mu_N - \mu_V)`. Because the volume-weighted distribution is normally distributed, the computed

mean and variance can be substituted directly into :eq:`eq_normal_dist`.
@@ -264,10 +264,10 @@ mean and standard deviation, :math:`\mu_V` and :math:`\sigma_V`, by solving the 


.. math::



   \begin{align}

   \begin{aligned}

     f_1(\mu_N,\sigma_N) &= \left( 3\sigma_N^4 + 6\sigma_N^2\mu_N^2 + \mu_N^4 \right) - \mu_V \left( 3\sigma_N^2 \mu_N + \mu_N^3 \right) = 0 \\

     f_2(\mu_N,\sigma_N) &= \left(3\sigma_N^4 (3\mu_N + 2b) + \sigma^2(\mu_N^3 + 6\mu_N^2 b + 3\mu_Nb^2)+\mu_N^3 b^2\right) - \sigma^2_V \left( 3\sigma_N^2 \mu_N + \mu_N^3 \right) = 0

   \end{align}

   \end{aligned}



This system is solved using the homotopy method outlined in :cite:t:`Burden10`. To ensure rapid convergence, initial guesses for

:math:`\mu_N` and :math:`\sigma_N` are calculated from the density function created by dividing :eq:`eq_normal_dist` by :math:`x^3`
@@ -288,11 +288,11 @@ are found by setting the derivative of :eq:`eq_normal_dist_FV_to_FN_initial_expr 
.. math::

   :label: eq_normal_dist_FV_to_FN_discrete_values



   \begin{align}

   \begin{aligned}

     x_{\mathrm{min}} \; =& \; \left( \mu_V - \sqrt{\mu_V^2 -12\sigma_V^2}\right)/2 \\

     x_{\mathrm{mid}} \; =& \; \left(\mu_V + \sqrt{\mu_V^2 -12\sigma_V^2}\right)/2 \\

     x_{\mathrm{max}} \; =& \; 2x_{\mathrm{mid}} - x_{\mathrm{min}}

   \end{align}

   \end{aligned}



.. _fig_normal-dist-pdf-approx_FN:
@@ -464,10 +464,10 @@ while the parameter :math:`\mu` is computed directly from the other distribution 


.. math::



   \begin{align}

   \begin{aligned}

       \mu_V =& \mu_N + 3.0\sigma^2 \\[10pt]

       \mu_N =& \mu_V - 3.0\sigma^2

   \end{align}

   \end{aligned}



.. rubric:: Sampling a log-normal distribution

docs/source_docs/user_guide/inputs/chemical_reactions.rst

+1 −1
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ 
Defining chemical reactions

===========================



.. |tol_eq| replace:: :math:`\left|\sum\text{products - \sum\text{reactants}\right| < \text{tolerance}`

.. |tol_eq| replace:: :math:`\left|\sum \mathrm{products} - \sum \mathrm{reactants}\right| < \mathrm{tolerance}`



The following inputs are defined using the prefix ``chemistry``: