add references to tutorials

paper/paper.md

@@ -96,7 +96,9 @@ seismological and geodynamic software, including: Mineos [@Masters:2011],
 AxiSEM [@NissenMeyer:2014] and
 ASPECT [@Kronbichler:2012;@aspect-doi-v2.4.0;@aspectmanual]
 
-The project also includes a tutorial, a large collection of annotated examples,
+The project also includes a multipart tutorial
+(\url{https://burnman.readthedocs.io/en/latest/tutorial.html}),
+a large collection of annotated examples,
 an extensive suite of unit tests and benchmarks, and 
 a directory containing user-contributed code from published papers.
 Use of the code requires only moderate Python skills, and its modular nature
@@ -131,7 +133,9 @@ access to many thermodynamic properties
 
 ![Heat capacity and bulk sound velocities of quartz through the alpha-beta
 quartz transition as found in [@Stixrude:2011]. This transition is modelled
-via a Landau-type model.
+via a Landau-type model. 
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_01_material_classes.html#}
+for more details and the code required to make this plot.
 \label{fig:qtzproperties}](figures/quartz_properties.png)
 
 Several other object classes in `BurnMan` build on the endmember
@@ -148,6 +152,8 @@ model [@Jennings:2015], as output by `BurnMan`.
 The excess Gibbs energy is useful for calculating phase equilibria by
 Gibbs minimization, while the endmember activities can be used to
 determine equilibrium via the equilibrium relations [@Holland:1998].
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_01_material_classes.html#}
+for more details and the code required to make this plot.
 \label{fig:garnetsolution}](figures/mg_ca_gt_properties.png)
 
 `BurnMan` includes many higher level functions that use
@@ -164,6 +170,8 @@ AxiSEM [@NissenMeyer:2014] and Mineos [@Woodhouse:1988;@Masters:2011].
 ![Optimized fit of a PV equation of state [@Holland:2011] to
 stishovite data [@Andrault:2003], including 95% confidence intervals
 on both the volume and the bulk modulus.
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_04_fitting.html#}
+for more details and the code required to make this plot.
 \label{fig:fit}](figures/stishovite_fitting.png)
 
 ![A 1D profile through Planet Zog, a planet much like Earth, with an
@@ -180,17 +188,28 @@ with thermal boundary layers
 The computed geotherm is compared to several from the literature
 [@Stacey:1977;@Brown:1981;@Anderson:1982;@Alfe:2007;@Anzellini:2013].
 The other properties are compared to the PREM [@Dziewonski:1981].
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_03_layers_and_planets.html}
+for more details and the code required to make this plot.
 \label{fig:zog}](figures/zog.png)
 
 `BurnMan` also provides many utility classes and functions, including
 those required to undertake bulk and phase chemical calculations,
 to aid preparation and analysis of laboratory experiments.
-One example is a utility function, `fit_phase_proportions_to_bulk_composition()`,
-that uses constrained least squares to estimate phase proportions
-and their corresponding covariances. The fitting applies appropriate
-non-negativity constraints (i.e. no phase can have a negative abundance
-in the bulk). An example that uses real
-experimental data [@Bertka:1997] is shown in \autoref{fig:mars_fit}.
+The `Composition` class provides a high level framework to 
+convert between mass, molar, and elemental compositions, convert
+to different component systems, and add or subtract chemical
+components (see
+\url{https://burnman.readthedocs.io/en/latest/tutorial_02_composition_class.html#}). 
+The utility functions `fit_composition_to_solution()` and
+`fit_phase_proportions_to_bulk_composition()`
+use weighted constrained least squares to estimate endmember or
+phase proportions and their corresponding covariances, given a bulk composition.
+The fitting functions apply appropriate
+non-negativity constraints 
+(i.e. that no species can have negative proportions on a site, 
+and that no phase can have a negative abundance
+in the bulk). An example of `fit_phase_proportions_to_bulk_composition()`
+that uses real experimental data [@Bertka:1997] is shown in \autoref{fig:mars_fit}.
 Loss of an independent component from the bulk composition
 can be tested by adding another phase with the composition of
 that component (e.g. Fe) and checking that the amount of that phase
@@ -202,17 +221,14 @@ $$C_{im} = (A_{ji} K^{-1}_{jk} A_{km})^{-1}.$$
 The weighted residuals are calculated
 using the phase proportions $x$ and the bulk composition $b$:
 $$\chi^2 = (K^{-0.5}_{ij} A_{jk} x_k - K^{-0.5}_{ik} b_k)(K^{-0.5}_{ip} A_{pq} x_q - K^{-0.5}_{iq} b_q).$$
-A related function is `fit_composition_to_solution()`,
-that uses weighted constrained least squares to fit a phase composition
-(calculated, for example, by EPMA) to a solution model. In this case,
-non-negativity constraints are applied such that no site may have a
-negative species occupancy.
 
 ![Mineral phase proportions in the mantle of Mars, estimated by using 
 the method of constrained least squares on high pressure experimental
 data [@Bertka:1997]. Weighted residuals
 (misfits) are also shown, indicating that the majority of experimental
 run products are consistent with the reported starting composition.
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_04_fitting.html#}
+for more details and the code required to make this plot.
 \label{fig:mars_fit}](figures/fit_mars_experiments.png)
 
 `BurnMan` does not attempt to replicate Gibbs minimization codes,
@@ -237,6 +253,8 @@ The equilibrate function is similar to that implemented in THERMOCALC
 ![The olivine phase diagram at three different temperatures as computed
 using the equilibrate routines in `BurnMan`. The solution model properties
 are taken from the literature [@Stixrude:2011].
+See \url{https://burnman.readthedocs.io/en/latest/tutorial_05_equilibrium.html#}
+for more details and the code required to make this plot.
 \label{fig:eqm}](figures/olivine_equilibrium.png)
 
 The features used in `BurnMan` are documented in the codebase