Finishing updates

three_d_viewer/templates/three_d_viewer/erb101/base.html

@@ -21,7 +21,7 @@
 <li><a href="{% url 'three_d_viewer:erb101_theory_structure' %}"><span>Structure of Earth</span></a></li>
 <li><a href="{% url 'three_d_viewer:erb101_theory_pt' %}"><span>Pressure and temperature</span></a></li>
 <li><a href="{% url 'three_d_viewer:erb101_theory_bowen' %}"><span>Bowen's reaction series</span></a></li>
-<li><a href="{% url 'three_d_viewer:theory_classification' %}"><span>Classification of minerals</span></a></li>
+<li><a href="{% url 'three_d_viewer:erb101_theory_classification' %}"><span>Classification of minerals</span></a></li>
 <li><a href="{% url 'three_d_viewer:erb101_theory_silicates' %}"><span>Silicates</span></a></li>
 <li class='last'><a href="{% url 'three_d_viewer:erb101_theory_crystals' %}"><span>Crystals</span></a></li>
 {% endblock %}

three_d_viewer/templates/three_d_viewer/erb101/theory/classification.html

@@ -0,0 +1,32 @@
+{% extends "three_d_viewer/base.html" %}
+{% load static %}
+
+{% block content %}
+    <div id="pushDownTwo"></div>
+        <div id="mainText">
+        <h1 class="subHeadings">Theory</h1>
+        <h2 class="theoryHeadings" id="classification">Classification of Minerals</h2>
+        <p>
+        The classification of minerals is based on their chemistry. The following mineral classes are based on the character of their common anions:</p>
+        <li><p>Silicates (SiO<sub>4</sub><sup>4-</sup>)</p></li>
+        <li><p>Oxides (O<sup>2-</sup>)</p></li>
+        <li><p>Sulfides (S<sup>2-</sup>)</p></li>
+        <li><p>Sulfates (SO<sub>4</sub><sup>2-</sup>)</p></li>
+        <li><p>Halides (Cl<sup>-</sup>)</p></li>
+        <li><p>Fluorites (F<sup>-</sup>)</p></li>
+        <li><p>Phosphates (PO<sub>4</sub><sup>3-</sup>)</p></li>
+        <li><p>Carbonates (CO<sub>3</sub><sup>2-</sup>)</p></li>
+        <li><p>Native elements, e.g. Au.</p></li>
+        <p><br />
+        The relative abundance of elements in the Earth’s crust (? Composition and structure of Earth) determines which minerals form. 
+        As we can see in table x, oxygen is the most abundant anion in the Earth’s crust. 
+        Thus, the crust can be seen as a tight package of oxygen anions (O<sup>2-</sup>), which are bonded by larger cations, 
+        such as Si<sup>4+</sup>, Mg<sup>2+</sup>, or Al<sup>3+</sup>.
+        The way atoms are packed together depends on the cation to anion radius ratio (Rx/Rz). 
+        With oxygen as the major anion, specific coordination and coordination polyhedra can be expected for different cations.
+        <br /><br /><br />
+        <a href="{% url 'three_d_viewer:theory_silicates' %}"><span>Silicate minerals</span></a>
+        </p>
+        <div id="pushDownThree"></div>
+        </div>
+{% endblock %}

three_d_viewer/templates/three_d_viewer/erb101/theory/structure.html

@@ -13,7 +13,7 @@
 	continental environments. Ocean crust is young mafic crust dominated by basalts and gabbros that is recycled regularly(~300Ma) due to subduction processes. 
 	Continental crust is much more varied in structure and composition than oceanic, but has an overall average composition of granodiorite. 
 	<br /><br />
-	The boundary of the crust and mantle is defined by the Mohorovi?i? discontinuity, commonly referred to as the Moho. 
+	The boundary of the crust and mantle is defined by the Mohorovičić discontinuity, commonly referred to as the Moho. 
 	It is defined by a sharp increase in seismic wave velocity, due to a change in material properties between crustal rocks and mantle rocks. The mantle is dominated by 
 	silicate minerals that are rich in iron and magnesium, chiefly pyroxenes and polymorphs of olivine, forming peridotite. The mantle, while solid, behaves plastically, 
 	allowing to flow at very slow rates.

three_d_viewer/templates/three_d_viewer/theory/bowen.html

@@ -7,25 +7,25 @@
         <h1 class="subHeadings">Theory</h1>
         <h2 class="theoryHeadings" id="bowensreactionseries">Bowen's Reaction Series</h2>
         <p>
-	Bowen's Reaction Series arranges the silicate minerals (? Silicate minerals) in the order that they crystallize from magma. The minerals at the 
+	Bowen's Reaction Series arranges the <a href="{% url 'three_d_viewer:theory_silicates' %}"><span>silicate minerals</span></a> in the order that they crystallize from magma. The minerals at the 
     top of the series crystallize from the melt at higher temperature than those lower down. It contains a continuous series, (right hand limb), a 
     discontinuous series (left hand limb), and the residual phases, which are listed in their relative sequence of crystallization. The discontinuous 
     series describes the sequence of minerals that crystallize as the temperature of the magma decreases. The discontinuity of each of the 
     crystallization sequences reflects the different melting/crystallization temperatures of the minerals, and the change in composition of the 
-    residual magma, as the early crystallizing phases are being fractionated from the melt. The continuous series always crystallizes plagioclase, 
+    residual magma, as the early crystallizing phases are being fractionated from the melt. The continuous series always crystallizes <a href={% url 'three_d_viewer:'|add:plag.url plag.id %}>plagioclase</a>, 
     but the composition of the plagioclase changes from more calcic (i.e. anorthite) at higher temperatures to more sodic (i.e. albite) as the 
     temperature decreases. The compositional change during mineral growth can be recorded in compositional zoning of plagioclase 
-    crystals (see ? Solid-solution series). The minerals at the bottom of Bowen’s reaction series crystallize last and are more stable, 
+    crystals. The minerals at the bottom of Bowen’s reaction series crystallize last and are more stable, 
-    and less susceptible to weathering. Thus, Bowen's reaction series also predicts the stability of minerals (? Stability of minerals) in the 
+    and less susceptible to weathering. Thus, Bowen's reaction series also predicts the stability of minerals in the 
     low pressure conditions at the Earth's surface.
 	<br /><br />
 	It should be noted that all reactions do not start crystallizing olivine/anorthite-rich plagioclase and continue through until they 
-    crystallize quartz (? Quartz). Which minerals actually form, depend on many factors, such as the chemical composition of the melt, temperature, 
+    crystallize <a href={% url url_extender|add:quartz.url quartz.id %}>quartz</a>. Which minerals actually form, depend on many factors, such as the chemical composition of the melt, temperature, 
-    pressure, and amount of fractional crystallization. For example, basalts form from the crystallization of olivine, pyroxene and 
+    pressure, and amount of fractional crystallization. For example, basalts form from the crystallization of 
+    <a href={% url url_extender|add:olivine.url olivine.id %}>olivine</a>, 
+    <a href={% url url_extenderadd:diopside.url diopside.id %}>pyroxene</a> and 
     calcic plagioclase, meaning that crystallization stopped without the series progressing. If more fractional crystallization 
-    (? Fractional crystallization) were to occur, more intermediate and felsic minerals can crystallize. Such a differentiation path is 
+    were to occur, more intermediate and felsic minerals can crystallize. 
-    illustrated in the TAS diagram, where primitive igneous rocks (i.e. basaltic) evolve to more felsic 
-    (SiO2-rich; i.e. rhyolite) ones (? TAS diagram).
             <br/>
 	<img src="{% static "three_d_viewer/images/bowen.jpg" %}" style="padding-top:20px; text-align: left;" width="600px" height="auto">
 	</p>

three_d_viewer/templates/three_d_viewer/theory/classification.html

@@ -8,7 +8,7 @@
         <h2 class="theoryHeadings" id="classification">Classification of Minerals</h2>
         <p>
         The classification of minerals is based on their chemistry. The following mineral classes are based on the character of their common anions:</p>
-        <li><p>Silicates (SiO<sub>4</sub><sup>4-</sup>)</p></li>
+        <li><p><a href="{% url 'three_d_viewer:theory_silicates' %}"><span>Silicates</span></a> (SiO<sub>4</sub><sup>4-</sup>)</p></li>
         <li><p>Oxides (O<sup>2-</sup>)</p></li>
         <li><p>Sulfides (S<sup>2-</sup>)</p></li>
         <li><p>Sulfates (SO<sub>4</sub><sup>2-</sup>)</p></li>
@@ -18,14 +18,13 @@
         <li><p>Carbonates (CO<sub>3</sub><sup>2-</sup>)</p></li>
         <li><p>Native elements, e.g. Au.</p></li>
         <p><br />
-        The relative abundance of elements in the Earth’s crust (? Composition and structure of Earth) determines which minerals form. 
+        <img src="{% static "three_d_viewer/images/element abundance.png" %}" align="right" width="412" height="324">
-        As we can see in table x, oxygen is the most abundant anion in the Earth’s crust. 
+        The relative abundance of elements in the Earth’s crust (see <a href="{% url 'three_d_viewer:theory_structure' %}"><span>Structure of Earth</span></a>) determines which minerals form. 
+        Oxygen is the most abundant anion in the Earth’s crust. 
         Thus, the crust can be seen as a tight package of oxygen anions (O<sup>2-</sup>), which are bonded by larger cations, 
         such as Si<sup>4+</sup>, Mg<sup>2+</sup>, or Al<sup>3+</sup>.
         The way atoms are packed together depends on the cation to anion radius ratio (Rx/Rz). 
         With oxygen as the major anion, specific coordination and coordination polyhedra can be expected for different cations.
-        <br /><br /><br />
-        <a href="{% url 'three_d_viewer:theory_silicates' %}"><span>Silicate minerals</span></a>
         </p>
         <div id="pushDownThree"></div>
         </div>

three_d_viewer/templates/three_d_viewer/theory/formationdiff.html

@@ -12,7 +12,9 @@
         gravitational collapse emerged the proto-Sun and a surrounding disk of dust and gas. Attraction forces within this rotating 
         protoplanetary disk that fed the young Sun, led to the accretion of progressively growing objects and planetesimals. 
         Increasing mass and gravitational forces of the growing planetary bodies resulted in interactions and disturbance in their orbits, 
-        ultimately giving rise to larger collisions. Earth, as a terrestrial inner planet formed relatively close to the Sun through the 
+        ultimately giving rise to larger collisions. 
+        <br /><br />
+        Earth, as a terrestrial inner planet formed relatively close to the Sun through the 
         accumulation of rather heavier matter, whereas the outer planets formed from gas that had been blown away in more distal 
         regions of the solar system (solar wind). Continuous bombardment and larger impacts – including one that led to the 
         formation of the Moon -, and the radioactive decay within the Earth heated the planet resulting in partial melting. 
@@ -20,6 +22,7 @@
         silicate mantle. Further chemical differentiation by partial melting of the mantle led to the formation of Earth’s proto-crust. 
         The Earth’s layering into core, mantle and crust due to this early differentiation remains an essential 
         feature of the Earth’s structure.
+        <br /><br />
         </p>
         <figure>
         <a href="{% static "three_d_viewer/images/earth differentiation.png" %}"><img width=600 height=350 src="{% static "three_d_viewer/images/earth differentiation.png" %}">

three_d_viewer/templates/three_d_viewer/theory/pressure_temp.html

@@ -30,7 +30,7 @@
         The method of heat transfer changes throughout the Earth. There are three main mechanisms for heat transfer in the Earth: 
         conduction, convection, and radiation. Starting in the inner core, the main method of heat transfer is by conduction through the 
         solid material. In the liquid, outer core heat transfer is by both conduction and convection. The mantle is dominated by convection, 
-        which is the driver of plate tectonics (? Plate tectonics). The crust is again dominated by conduction, and finally energy escapes the 
+        which is the driver of plate tectonics. The crust is again dominated by conduction, and finally energy escapes the 
         Earth to the atmosphere by radiation. 
         <br /><br />
         Pressure in the Earth continually increases with depth, according to the formula P = gρz, where g is the gravitation field strength, 
@@ -39,7 +39,7 @@
         and increases to about 3.3 g/cm<sup>3</sup> in the mantle. The increase of pressure with depth in the Earth affects the dominant mineralogy, 
         as well as the increase of the melting point of different minerals. 
         <br /><br />
-        The structure of minerals, such as <a href={% url 'three_d_viewer:'|add:olivine.url olivine.id %}>olivine</a> becomes unstable as pressure increases (? Stability of minerals). 
+        The structure of minerals, such as <a href={% url url_extender|add:olivine.url olivine.id %}>olivine</a> becomes unstable as pressure increases. 
         Below about 410 km olivine (Mg<sub>2</sub>SiO<sub>4</sub>) becomes unstable and transforms into wadsleyite (Mg<sub>2</sub>SiO<sub>4</sub>), 
         which has the same chemical composition as olivine, but has a different crystal structure. As depth increases, 
         wadsleyite transforms to ringwoodite (Mg<sub>2</sub>SiO<sub>4</sub>) at ~520 km, which subsequently transforms into silicate perovskite 

three_d_viewer/templates/three_d_viewer/theory/silicates.html

@@ -26,9 +26,10 @@
             <img src="{% static "three_d_viewer/images/inosilicates.png" %}" align="right">
             In the inosilicates, [SiO<sub>4</sub>]<sup>4-</sup> tedrahedra are linked as chains, which in turn are linked together by cations. 
             Single-chain inosilicates form [Si<sub>2</sub>O<sub>6</sub>]<sup>4-</sup> groups, and double-chain inosilicates 
-            form [Si<sub>4</sub>O<sub>11</sub>]<sup>6-</sup> groups. Pyroxenes, e.g. diopside with the chemical formula 
+            form [Si<sub>4</sub>O<sub>11</sub>]<sup>6-</sup> groups. Pyroxenes, e.g.  <a href={% url url_extender|add:diopside.url diopside.id %}>diopside</a> with the chemical formula 
             CaMgSi<sub>2</sub>O<sub>6</sub>, are single-chain, and amphiboles, e.g. hornblende 
-            (Ca<sub>2</sub>(Mg,Fe,Al)<sub>5</sub>(Al,Si)<sub>8</sub>O<sub>22</sub>(OH)), are double-chain inosilicates.
+            (Ca<sub>2</sub>(Mg,Fe,Al)<sub>5</sub>(Al,Si)<sub>8</sub>O<sub>22</sub>(OH)) or <a href={% url url_extender|add:actinolite.url actinolite.id %}>actinolite</a> 
+            (Ca<sub>2</sub>(Fe,Mg)<sub>5</sub>Si<sub>8</sub>O<sub>22</sub>(OH)<sub>2</sub>) are double-chain inosilicates.
             </p>
             </tr></td>
             <tr><td>
@@ -38,7 +39,7 @@
             In the nesosilicate group, [SiO<sub>4</sub>]<sup>4-</sup> tedrahedra are isolated from each other and share their oxygens 
             with octahedral groups, which contain cations, such as Mg<sup>2+</sup>, Fe<sup>2+</sup>, or Ca<sup>2+</sup>.  A common 
             rock-forming mineral of the nesosilicate group is 
-            <a href={% url 'three_d_viewer:'|add:olivine.url olivine.id %}>olivine</a> with the chemical formula 
+            <a href={% url url_extender|add:olivine.url olivine.id %}>olivine</a> with the chemical formula 
             (Mg,Fe)<sub>2</sub>SiO<sub>4</sub>.
             </p>
             </tr></td>
@@ -65,9 +66,9 @@
             <p>
             <img src="{% static "three_d_viewer/images/tectosilicates.png" %}" align="right">            
             Complete linkage of [SiO<sub>4</sub>]<sup>4-</sup> tedrahedra results in the 3-dimensional framework of the tectosilicates. 
-            <a href={% url 'three_d_viewer:'|add:quartz.url quartz.id %}>Quartz</a> (SiO<sub>2</sub>) and the feldspars 
+            <a href={% url url_extender|add:quartz.url quartz.id %}>Quartz</a> (SiO<sub>2</sub>) and the feldspars 
-            (<a href={% url 'three_d_viewer:'|add:plag.url plag.id %}>plagioclase</a>, 
+            (<a href={% url url_extender|add:plag.url plag.id %}>plagioclase</a>, 
-            <a href={% url 'three_d_viewer:'|add:microcline.url microcline.id %}>microcline</a>) 
+            <a href={% url url_extender|add:microcline.url microcline.id %}>microcline</a>) 
             (e.g. anorthite, CaAl<sub>2</sub>Si<sub>2</sub>O<sub>8</sub>) are tectosilicates.
             </p>
             </tr></td>

three_d_viewer/templates/three_d_viewer/theory/structure.html

@@ -6,19 +6,30 @@
         <div id="mainText">
         <h1 class="subHeadings">Theory</h1>
         <h2 class="theoryHeadings" id="structureofearth">Structure of Earth</h2>
-        <p>
+        
-	The Earth's structure is differentiated in three distinct layers: the core, mantle, and crust (? Earth profile). The layers are distinguished 
+    <figure align="left">
-    by a change in the velocity of seismic waves at their boundaries (? Seismic profile). The crust is the upper most part of the earth, with 
+		<img src="{% static "three_d_viewer/images/structure - usgs.gif" %}" >
+		<figcaption align="left"><p>Image sourced from <a href="http://pubs.usgs.gov/gip/dynamic/graphics/FigS1-1.gif">USGS</a>.</p></figcaption>
+	</figure>
+    <br />
+    <p>The Earth's structure is differentiated in three distinct layers: the core, mantle, and crust. The layers are distinguished 
+    by a change in the velocity of seismic waves at their boundaries (? Seismic profile). 
+    The crust is the upper most part of the earth, with 
     depths ranging from an average of 7 km in the oceans, to an average of 38 km in continental crust. The crust thickens underneath mountain 
     ranges, and can reach depths of 90 km underneath the Himalayas. The composition of the crust also differs between oceanic and continental 
     environments. Ocean crust is young mafic crust dominated by basalts and gabbros that is recycled regularly (~300 Ma) due to subduction 
-    processes (? Subduction). Continental crust is much more varied in structure and composition than oceanic, but has an overall average 
+    processes. Continental crust is much more varied in structure and composition than oceanic, but has an overall average 
     composition of granodiorite. 
+    </p>
+    
+    <p>
     <br /><br />
     <img src="{% static "three_d_viewer/images/element abundance.png" %}" align="right" width="412" height="324">
 	The boundary of the crust and mantle is defined by the Mohorovicic discontinuity, commonly referred to as the Moho. It is defined by a 
-    sharp increase in seismic wave velocity, due to a change in material properties between crustal rocks and mantle rocks (? Seismic profile). 
+    sharp increase in seismic wave velocity, due to a change in material properties between crustal rocks and mantle rocks. 
-    The mantle is dominated by silicate minerals that are rich in iron and magnesium, chiefly pyroxenes and polymorphs (? Polymorphs) of olivine, 
+    The mantle is dominated by silicate minerals that are rich in iron and magnesium, chiefly 
+    <a href={% url url_extender|add:diopside.url diopside.id %}>pyroxenes</a> and polymorphs of 
+    <a href={% url url_extender|add:olivine.url olivine.id %}>olivine</a>, 
     forming peridotite. The mantle, while solid, behaves plastically, allowing to flow at very slow rates. 
 	<br /><br />
 	The core is distinguished by the absence of S waves, leading to the inference that the core is liquid. 
@@ -27,15 +38,15 @@
     crystallizing minerals from the liquid part of the core as the Earth cools. 
 	<br /><br />
     The crust and mantle are also further distinguished by material properties into the lithosphere, asthenosphere, and 
-    mesosphere (? Earth profile). The chemical composition is uniform throughout the mantle though, but changes in pressure and temperature 
+    mesosphere. The chemical composition is uniform throughout the mantle though, but changes in pressure and temperature 
     determine which polymorphs will exist at different depths. The lithosphere contains the crust, and the upper part of the mantle down 
     to ~100 km under oceanic crust, and 200-300 km under continental crust (Twiss & Moores, 2007). The lithosphere-asthenosphere boundary 
     is defined by the 1300 K isotherm, which is the temperature where olivine starts to behave viscously. The rocks in the mesosphere are 
     under more pressure than those in the asthenosphere, so no longer behave viscously.
     </p>
-	<figure>
+	<figure align="left" >
-		<img src="{% static "three_d_viewer/images/structure - usgs.gif" %}" style="padding-top:20px;">
+		<a href='{% static "three_d_viewer/images/depth profile.png" %}' align="right"><img height=494 width=412 src='{% static "three_d_viewer/images/depth profile.png" %}'></a>
-		<figcaption><p>Image sourced from <a href="http://pubs.usgs.gov/gip/dynamic/graphics/FigS1-1.gif">USGS</a>.</p></figcaption>
+		<figcaption>The seismic profile of the Earth.</figcaption>
 	</figure>
 </div>
         <div id="pushDownThree"></div>

three_d_viewer/views.py

@@ -284,15 +284,25 @@ class TheoryTemplateView(generic.TemplateView):
     def get_context_data(self, **kwargs):
         context = super(TheoryTemplateView, self).get_context_data(**kwargs)
         context['base_template'] = 'three_d_viewer/base.html'
+        context['url_extender'] = 'three_d_viewer:'
         context['olivine'] = Mineral.objects.filter(name='Olivine')[0]
         context['quartz'] = Mineral.objects.filter(name='Quartz')[0]
         context['microcline'] = Mineral.objects.filter(name='Microcline')[0]
         context['plag'] = Mineral.objects.filter(name='Plagioclase')[0]
+        context['diopside'] = Mineral.objects.filter(name='Diopside')[0]
+        context['actinolite'] = Mineral.objects.filter(name='Actinolite')[0]
         return context
  
 class ERB101TheoryTemplateView(generic.TemplateView):
     def get_context_data(self, **kwargs):
         context = super(ERB101TheoryTemplateView, self).get_context_data(**kwargs)
         context['base_template'] = 'three_d_viewer/erb101/base.html'
+        context['url_extender'] = 'three_d_viewer:erb101_'
+        context['olivine'] = Mineral.objects.filter(name='Olivine')[0]
+        context['quartz'] = Mineral.objects.filter(name='Quartz')[0]
+        context['microcline'] = Mineral.objects.filter(name='Microcline')[0]
+        context['plag'] = Mineral.objects.filter(name='Plagioclase')[0]
+        context['diopside'] = Mineral.objects.filter(name='Diopside')[0]
+        context['actinolite'] = Mineral.objects.filter(name='Actinolite')[0]
         return context