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stammler committed Dec 3, 2023
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31 changes: 6 additions & 25 deletions docs/6_dust_evolution.html
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177 changes: 80 additions & 97 deletions docs/6_dust_evolution.ipynb
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23 changes: 4 additions & 19 deletions docs/7_gas_evolution.html
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Expand Up @@ -155,36 +155,21 @@ <h2>Hydrodynamics<a class="headerlink" href="#Hydrodynamics" title="Link to this
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">dpi</span><span class="o">=</span><span class="mi">150</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">fig</span><span class="o">.</span><span class="n">add_subplot</span><span class="p">(</span><span class="mi">111</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">sim</span><span class="o">.</span><span class="n">gas</span><span class="o">.</span><span class="n">Sigma</span><span class="o">.</span><span class="n">jacobian</span><span class="p">()</span><span class="o">.</span><span class="n">toarray</span><span class="p">()</span> <span class="o">!=</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">),</span> <span class="n">cmap</span><span class="o">=</span><span class="s2">&quot;Blues&quot;</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">hlines</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">)</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">)</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">hlines</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">Nr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">get_xaxis</span><span class="p">()</span><span class="o">.</span><span class="n">set_visible</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">get_yaxis</span><span class="p">()</span><span class="o">.</span><span class="n">set_visible</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="s2">&quot;Structure of Jacobian $\mathbb</span><span class="si">{J}</span><span class="s2">$&quot;</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;Structure of Jacobian $\mathbb</span><span class="si">{J}</span><span class="s2">$&quot;</span><span class="p">)</span>
<span class="n">fig</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
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&lt;&gt;:8: SyntaxWarning: invalid escape sequence &#39;\m&#39;
&lt;&gt;:8: SyntaxWarning: invalid escape sequence &#39;\m&#39;
/tmp/ipykernel_93989/2308441433.py:8: SyntaxWarning: invalid escape sequence &#39;\m&#39;
ax.set_title(&#34;Structure of Jacobian $\mathbb{J}$&#34;)
/tmp/ipykernel_93989/2308441433.py:4: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
ax.hlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=&#34;gray&#34;, alpha=0.5)
/tmp/ipykernel_93989/2308441433.py:5: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
ax.vlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=&#34;gray&#34;, alpha=0.5)
</pre></div></div>
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<img alt="_images/7_gas_evolution_5_1.png" src="_images/7_gas_evolution_5_1.png" />
<img alt="_images/7_gas_evolution_5_0.png" src="_images/7_gas_evolution_5_0.png" />
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<p>Notable exceptions are the first and the last row, which are used to set the boundary conditions. They require up to three elements to set the gradients if needed.</p>
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105 changes: 46 additions & 59 deletions docs/7_gas_evolution.ipynb
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2 changes: 1 addition & 1 deletion docs/B_publications.ipynb
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Expand Up @@ -292,7 +292,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.10.13"
}
},
"nbformat": 4,
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4 changes: 2 additions & 2 deletions docs/E_changelog.html
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Expand Up @@ -128,7 +128,7 @@ <h1>Appendix E: Changelog<a class="headerlink" href="#Appendix-E:-Changelog" tit
<p>This is a list of changes made to <code class="docutils literal notranslate"><span class="pre">DustPy</span></code> since version <code class="docutils literal notranslate"><span class="pre">v1.0.0</span></code> including discussions of their influence on the simulations.</p>
<section id="v1.0.5">
<h2><strong>v1.0.5</strong><a class="headerlink" href="#v1.0.5" title="Link to this heading"></a></h2>
<p><strong>Release date: 2nd December 2023</strong></p>
<p><strong>Release date: 3rd December 2023</strong></p>
<section id="Using-Meson-as-build-system">
<h3>Using Meson as build system<a class="headerlink" href="#Using-Meson-as-build-system" title="Link to this heading"></a></h3>
<p>Due to the deprecation of <code class="docutils literal notranslate"><span class="pre">numpy.distutils</span></code>, <code class="docutils literal notranslate"><span class="pre">DustPy</span></code> is now using Meson as build system.</p>
Expand All @@ -143,7 +143,7 @@ <h3>Bugfix to plotting script<a class="headerlink" href="#Bugfix-to-plotting-scr
</section>
<section id="Preparation-for-the-addition-of-multiple-gas-species">
<h3>Preparation for the addition of multiple gas species<a class="headerlink" href="#Preparation-for-the-addition-of-multiple-gas-species" title="Link to this heading"></a></h3>
<p>In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous model that have not specifically customized the gas Jacobian should be compatible with this version.</p>
<p>In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous models that have not specifically customized the gas Jacobian should be compatible with this version.</p>
</section>
</section>
<section id="v1.0.4">
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"metadata": {},
"source": [
"### **v1.0.5**\n",
"**Release date: 2nd December 2023**\n",
"**Release date: 3rd December 2023**\n",
"\n",
"#### Using Meson as build system\n",
"\n",
Expand All @@ -38,7 +38,7 @@
"\n",
"#### Preparation for the addition of multiple gas species\n",
"\n",
"In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous model that have not specifically customized the gas Jacobian should be compatible with this version."
"In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous models that have not specifically customized the gas Jacobian should be compatible with this version."
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.10.13"
}
},
"nbformat": 4,
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177 changes: 80 additions & 97 deletions docs/_sources/6_dust_evolution.ipynb.txt
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105 changes: 46 additions & 59 deletions docs/_sources/7_gas_evolution.ipynb.txt
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2 changes: 1 addition & 1 deletion docs/_sources/B_publications.ipynb.txt
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Expand Up @@ -292,7 +292,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.10.13"
}
},
"nbformat": 4,
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Expand Up @@ -22,7 +22,7 @@
"metadata": {},
"source": [
"### **v1.0.5**\n",
"**Release date: 2nd December 2023**\n",
"**Release date: 3rd December 2023**\n",
"\n",
"#### Using Meson as build system\n",
"\n",
Expand All @@ -38,7 +38,7 @@
"\n",
"#### Preparation for the addition of multiple gas species\n",
"\n",
"In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous model that have not specifically customized the gas Jacobian should be compatible with this version."
"In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous models that have not specifically customized the gas Jacobian should be compatible with this version."
]
},
{
Expand Down Expand Up @@ -134,7 +134,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.10.13"
}
},
"nbformat": 4,
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