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ecell4
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<li><a class="reference internal" href="#">8. More about 1. Brief Tour of E-Cell4 Simulations</a><ul>
<li><a class="reference internal" href="#8.1.-Creating-ODEWorld">8.1. Creating ODEWorld</a></li>
<li><a class="reference internal" href="#8.2.-How-to-Use-Real3">8.2. How to Use Real3</a></li>
<li><a class="reference internal" href="#8.3.-Creating-and-Running-ODE-Simulator">8.3. Creating and Running ODE Simulator</a></li>
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<p>This page was generated from <a class="reference external" href="https://github.com/kaizu/ecell4_docs/blob/latest/en/tutorials/tutorial08.ipynb">tutorials/tutorial08.ipynb</a>.</p>
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<div class="section" id="8.-More-about-1.-Brief-Tour-of-E-Cell4-Simulations">
<h1>8. More about 1. Brief Tour of E-Cell4 Simulations<a class="headerlink" href="#8.-More-about-1.-Brief-Tour-of-E-Cell4-Simulations" title="Permalink to this headline">¶</a></h1>
<p>Once you read through <a class="reference external" href="tutorial1.ipynb">1. Brief Tour of E-Cell4 Simulations</a>, it is NOT difficult to use <code class="docutils literal notranslate"><span class="pre">World</span></code> and <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>. <code class="docutils literal notranslate"><span class="pre">volume</span></code> and <code class="docutils literal notranslate"><span class="pre">{'C':</span> <span class="pre">60}</span></code> is equivalent of the <code class="docutils literal notranslate"><span class="pre">World</span></code> and solver is the <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> below.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
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<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="o">%</span><span class="k">matplotlib</span> inline
<span class="kn">from</span> <span class="nn">ecell4.prelude</span> <span class="kn">import</span> <span class="o">*</span>
<span class="k">with</span> <span class="n">reaction_rules</span><span class="p">():</span>
<span class="n">A</span> <span class="o">+</span> <span class="n">B</span> <span class="o">==</span> <span class="n">C</span> <span class="o">|</span> <span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">)</span>
<span class="n">run_simulation</span><span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="p">{</span><span class="s1">'C'</span><span class="p">:</span> <span class="mi">60</span><span class="p">},</span> <span class="n">volume</span><span class="o">=</span><span class="mf">1.0</span><span class="p">)</span>
</pre></div>
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<p>Here we give you a breakdown for <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code>. <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code> use ODE simulator by default, so we create <code class="docutils literal notranslate"><span class="pre">ode.World</span></code> step by step.</p>
<div class="section" id="8.1.-Creating-ODEWorld">
<h2>8.1. Creating ODEWorld<a class="headerlink" href="#8.1.-Creating-ODEWorld" title="Permalink to this headline">¶</a></h2>
<p>You can create <code class="docutils literal notranslate"><span class="pre">World</span></code> like this.</p>
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<span></span><span class="kn">from</span> <span class="nn">ecell4_base.core</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">ecell4_base</span> <span class="kn">import</span> <span class="o">*</span>
</pre></div>
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<span></span><span class="n">w</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
</pre></div>
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<p><code class="docutils literal notranslate"><span class="pre">Real3</span></code> is a coordinate vector. In this example, the first argument for <code class="docutils literal notranslate"><span class="pre">ode.World</span></code> constructor is a cube. Note that you can NOT use volume for <code class="docutils literal notranslate"><span class="pre">ode.World</span></code> argument, like <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code> argument.</p>
<p>Now you created a cube box for simulation, next let’s throw molecules into the cube.</p>
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<span></span><span class="n">w</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">w</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s1">'C'</span><span class="p">),</span> <span class="mi">60</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s1">'C'</span><span class="p">)))</span> <span class="c1"># must return (0.0, 60)</span>
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0.0 60
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<p>Use <code class="docutils literal notranslate"><span class="pre">add_molecules</span></code> to add molecules, <code class="docutils literal notranslate"><span class="pre">remove_molecules</span></code> to remove molecules, <code class="docutils literal notranslate"><span class="pre">num_molecules</span></code> to know the number of molecules. First argument for each method is the <code class="docutils literal notranslate"><span class="pre">Species</span></code> you want to know. You can get current time by <code class="docutils literal notranslate"><span class="pre">t</span></code> method. However the number of molecules in ODE solver is real number, in these <code class="docutils literal notranslate"><span class="pre">_molecules</span></code> functions work only for integer number. When you handle real numbers in ODE, use <code class="docutils literal notranslate"><span class="pre">set_value</span></code> and <code class="docutils literal notranslate"><span class="pre">get_value</span></code>.</p>
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<div class="section" id="8.2.-How-to-Use-Real3">
<h2>8.2. How to Use Real3<a class="headerlink" href="#8.2.-How-to-Use-Real3" title="Permalink to this headline">¶</a></h2>
<p>Before the detail of <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>, we explaing more about <code class="docutils literal notranslate"><span class="pre">Real3</span></code>.</p>
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<span></span><span class="n">pos</span> <span class="o">=</span> <span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span> <span class="c1"># must print like <ecell4.core.Real3 object at 0x7f44e118b9c0></span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">pos</span><span class="p">))</span> <span class="c1"># must print (1.0, 2.0, 3.0)</span>
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<ecell4_base.core.Real3 object at 0x151df81bf260>
(1.0, 2.0, 3.0)
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<p>You can not print the contents in <code class="docutils literal notranslate"><span class="pre">Real3</span></code> object directly. You need to convert <code class="docutils literal notranslate"><span class="pre">Real3</span></code> to Python tuple or list once.</p>
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<span></span><span class="n">pos1</span> <span class="o">=</span> <span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">pos2</span> <span class="o">=</span> <span class="n">pos1</span> <span class="o">+</span> <span class="n">pos1</span>
<span class="n">pos3</span> <span class="o">=</span> <span class="n">pos1</span> <span class="o">*</span> <span class="mi">3</span>
<span class="n">pos4</span> <span class="o">=</span> <span class="n">pos1</span> <span class="o">/</span> <span class="mi">5</span>
<span class="nb">print</span><span class="p">(</span><span class="n">length</span><span class="p">(</span><span class="n">pos1</span><span class="p">))</span> <span class="c1"># must print 1.73205080757</span>
<span class="nb">print</span><span class="p">(</span><span class="n">dot_product</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="n">pos3</span><span class="p">))</span> <span class="c1"># must print 9.0</span>
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1.7320508075688772
9.0
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<p>You can use basic function like <code class="docutils literal notranslate"><span class="pre">dot_product</span></code>. Of course, you can convert <code class="docutils literal notranslate"><span class="pre">Real3</span></code> to numpy array too.</p>
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<span></span><span class="kn">import</span> <span class="nn">numpy</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="c1"># must print [ 1. 2. 3.]</span>
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[1. 2. 3.]
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<p><code class="docutils literal notranslate"><span class="pre">Integer3</span></code> represents a triplet of integers.</p>
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<span></span><span class="n">g</span> <span class="o">=</span> <span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">g</span><span class="p">))</span>
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(1, 2, 3)
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<p>Of course, you can also apply simple arithmetics to <code class="docutils literal notranslate"><span class="pre">Integer3</span></code>.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="o">+</span> <span class="n">Integer3</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)))</span> <span class="c1"># => (5, 7, 9)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">Integer3</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span> <span class="o">-</span> <span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)))</span> <span class="c1"># => (3, 3, 3)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mi">2</span><span class="p">))</span> <span class="c1"># => (2, 4, 6)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">dot_product</span><span class="p">(</span><span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">Integer3</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)))</span> <span class="c1"># => 32</span>
<span class="nb">print</span><span class="p">(</span><span class="n">length</span><span class="p">(</span><span class="n">Integer3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)))</span> <span class="c1"># => 3.74165738677</span>
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(5, 7, 9)
(3, 3, 3)
(2, 4, 6)
32
3.7416573867739413
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<div class="section" id="8.3.-Creating-and-Running-ODE-Simulator">
<h2>8.3. Creating and Running ODE Simulator<a class="headerlink" href="#8.3.-Creating-and-Running-ODE-Simulator" title="Permalink to this headline">¶</a></h2>
<p>You can create a <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> with <code class="docutils literal notranslate"><span class="pre">Model</span></code> and <code class="docutils literal notranslate"><span class="pre">World</span></code> like</p>
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<span></span><span class="k">with</span> <span class="n">reaction_rules</span><span class="p">():</span>
<span class="n">A</span> <span class="o">+</span> <span class="n">B</span> <span class="o">></span> <span class="n">C</span> <span class="o">|</span> <span class="mf">0.01</span> <span class="c1"># equivalent to create_binding_reaction_rule</span>
<span class="n">C</span> <span class="o">></span> <span class="n">A</span> <span class="o">+</span> <span class="n">B</span> <span class="o">|</span> <span class="mf">0.3</span> <span class="c1"># equivalent to create_unbinding_reaction_rule</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">get_model</span><span class="p">()</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">10.0</span><span class="p">)</span>
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<p>then call <code class="docutils literal notranslate"><span class="pre">run</span></code> method, the simulation will run. In this example the simulation runs for 10 seconds.</p>
<p>You can check the state of the <code class="docutils literal notranslate"><span class="pre">World</span></code> like this.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s1">'C'</span><span class="p">)))</span> <span class="c1"># must return (10.0, 30)</span>
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10.0 30
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<p>You can see that the number of the <code class="docutils literal notranslate"><span class="pre">Species</span></code> <code class="docutils literal notranslate"><span class="pre">C</span></code> decreases from 60 to 30.</p>
<p><code class="docutils literal notranslate"><span class="pre">World</span></code> describes the state at a timepoint, so you can NOT tack the transition during the simulation with the <code class="docutils literal notranslate"><span class="pre">World</span></code>. To obtain the time-series result, use <code class="docutils literal notranslate"><span class="pre">Observer</span></code>.</p>
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<span></span><span class="n">w</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">w</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s1">'C'</span><span class="p">),</span> <span class="mi">60</span><span class="p">)</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">obs</span> <span class="o">=</span> <span class="n">FixedIntervalNumberObserver</span><span class="p">(</span><span class="mf">0.1</span><span class="p">,</span> <span class="p">(</span><span class="s1">'A'</span><span class="p">,</span> <span class="s1">'C'</span><span class="p">))</span>
<span class="n">sim</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="n">obs</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">data</span><span class="p">())</span> <span class="c1"># must return [[0.0, 0.0, 60.0], ..., [10.0, 29.994446899691276, 30.005553100308752]]</span>
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[[0.0, 0.0, 60.0], [0.1, 1.7722206143224584, 58.22777938567754], [0.2, 3.4860124975248006, 56.51398750247521], [0.30000000000000004, 5.137633294323578, 54.862366705676436], [0.4, 6.7240908315276045, 53.27590916847241], [0.5, 8.2431297778128, 51.75687022218721], [0.6000000000000001, 9.693203786964157, 50.30679621303585], [0.7000000000000001, 11.073435610343822, 48.926564389656185], [0.8, 12.383567710238625, 47.61643228976138], [0.9, 13.623905934263576, 46.37609406573643], [1.0, 14.795258697983998, 45.204741302016004], [1.1, 15.898873915953542, 44.101126084046456], [1.2000000000000002, 16.936375649258018, 43.06362435074198], [1.3, 17.909702127696086, 42.090297872303914], [1.4000000000000001, 18.821046480898254, 41.17895351910174], [1.5, 19.672801194656238, 40.32719880534375], [1.6, 20.467507011344757, 39.532492988655235], [1.7000000000000002, 21.207806726765288, 38.7921932732347], [1.8, 21.896404106006866, 38.10359589399312], [1.9000000000000001, 22.53602795042438, 37.4639720495756], [2.0, 23.129401196247105, 36.87059880375288], [2.1, 23.679214810305954, 36.320785189694035], [2.2, 24.188106166226664, 35.81189383377333], [2.3000000000000003, 24.6586415307847, 35.341358469215294], [2.4000000000000004, 25.093302260285835, 34.906697739714154], [2.5, 25.494474296223075, 34.505525703776904], [2.6, 25.864440553798364, 34.13555944620162], [2.7, 26.205375812342282, 33.7946241876577], [2.8000000000000003, 26.519343739941075, 33.480656260058915], [2.9000000000000004, 26.808295712922448, 33.19170428707754], [3.0, 27.074071122047478, 32.925928877952515], [3.1, 27.318398889554317, 32.68160111044567], [3.2, 27.54289995329749, 32.45710004670249], [3.3000000000000003, 27.749090505157007, 32.250909494842965], [3.4000000000000004, 27.93838580001201, 32.06161419998797], [3.5, 28.11210437846467, 31.887895621535307], [3.6, 28.27147257094361, 31.728527429056367], [3.7, 28.41762917272733, 31.582370827272648], [3.8000000000000003, 28.551630198838193, 31.448369801161785], [3.9000000000000004, 28.674453644762753, 31.325546355237226], [4.0, 28.78700419370472, 31.212995806295257], [4.1000000000000005, 28.890117823751574, 31.109882176248405], [4.2, 28.98456627912797, 31.015433720872007], [4.3, 29.071061378816175, 30.928938621183804], [4.4, 29.150259143439115, 30.849740856560864], [4.5, 29.222763727609138, 30.77723627239084], [4.6000000000000005, 29.289131150117587, 30.71086884988239], [4.7, 29.349872818534465, 30.650127181465514], [4.800000000000001, 29.40545884814348, 30.5945411518565], [4.9, 29.456321177785775, 30.543678822214204], [5.0, 29.502856487234418, 30.49714351276556], [5.1000000000000005, 29.545428922270702, 30.454571077729277], [5.2, 29.584372634768023, 30.415627365231956], [5.300000000000001, 29.619994145881115, 30.380005854118863], [5.4, 29.652574540951854, 30.347425459048125], [5.5, 29.68237150503112, 30.317628494968858], [5.6000000000000005, 29.709621208023663, 30.290378791976316], [5.7, 29.73454004842796, 30.26545995157202], [5.800000000000001, 29.757326264497603, 30.24267373550238], [5.9, 29.77816142142091, 30.22183857857907], [6.0, 29.797211782822988, 30.202788217176995], [6.1000000000000005, 29.814629574557085, 30.185370425442898], [6.2, 29.830554148384813, 30.16944585161517], [6.300000000000001, 29.84511305275851, 30.154886947241472], [6.4, 29.858423017523837, 30.141576982476145], [6.5, 29.870590858963563, 30.12940914103642], [6.6000000000000005, 29.88171431121031, 30.118285688789673], [6.7, 29.891882789671147, 30.108117210328835], [6.800000000000001, 29.901178091733776, 30.098821908266206], [6.9, 29.909675039664805, 30.090324960335177], [7.0, 29.917442070267278, 30.082557929732705], [7.1000000000000005, 29.92454177553783, 30.075458224462153], [7.2, 29.931031398254603, 30.06896860174538], [7.300000000000001, 29.9369632861354, 30.063036713864584], [7.4, 29.942385307931307, 30.057614692068675], [7.5, 29.94734123456418, 30.0526587654358], [7.6000000000000005, 29.951871088176286, 30.048128911823696], [7.7, 29.95601146173637, 30.043988538263612], [7.800000000000001, 29.9597958116382, 30.04020418836178], [7.9, 29.963254725533886, 30.036745274466096], [8.0, 29.966416167464857, 30.033583832535125], [8.1, 29.969305702187025, 30.030694297812957], [8.200000000000001, 29.971946700432824, 30.02805329956716], [8.3, 29.974360526710818, 30.025639473289164], [8.4, 29.976566711112177, 30.023433288887805], [8.5, 29.978583106472595, 30.021416893527388], [8.6, 29.9804260321266, 30.01957396787338], [8.700000000000001, 29.98211040538864, 30.017889594611344], [8.8, 29.98364986180096, 30.016350138199023], [8.9, 29.985056865101367, 30.014943134898616], [9.0, 29.98634280778428, 30.013657192215703], [9.1, 29.987518103055105, 30.012481896944877], [9.200000000000001, 29.988592268910782, 30.0114077310892], [9.3, 29.98957400501743, 30.01042599498255], [9.4, 29.990471262999563, 30.00952873700042], [9.5, 29.9912913107032, 30.008708689296782], [9.600000000000001, 29.9920407909477, 30.00795920905228], [9.700000000000001, 29.992725775237364, 30.007274224762618], [9.8, 29.993351812863917, 30.006648187136065], [9.9, 29.993923975794377, 30.006076024205605], [10.0, 29.994446899704982, 30.005553100295]]
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<p>There are several types of <code class="docutils literal notranslate"><span class="pre">Observer</span></code>s for E-Cell4. <code class="docutils literal notranslate"><span class="pre">FixedIntervalNumberObserver</span></code> is the simplest <code class="docutils literal notranslate"><span class="pre">Observer</span></code> to obtain the time-series result. As its name suggests, this <code class="docutils literal notranslate"><span class="pre">Observer</span></code> records the number of molecules for each time-step. The 1st argument is the time-step, the 2nd argument is the molecule types. You can check the result with <code class="docutils literal notranslate"><span class="pre">data</span></code> method, but there is a shortcut for this.</p>
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<span></span><span class="n">show</span><span class="p">(</span><span class="n">obs</span><span class="p">)</span>
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<p>This plots the time-series result easily.</p>
<p>We explained the internal of <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code> function. When you change the <code class="docutils literal notranslate"><span class="pre">World</span></code> after creating the <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>, you need to indicate it to <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>. So do NOT forget to call <code class="docutils literal notranslate"><span class="pre">sim.initialize()</span></code> after that.</p>
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<div class="section" id="8.4.-Switching-the-Solver">
<h2>8.4. Switching the Solver<a class="headerlink" href="#8.4.-Switching-the-Solver" title="Permalink to this headline">¶</a></h2>
<p>It is NOT difficult to switch the solver to stochastic method, as we showed <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code>.</p>
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<span></span><span class="kn">from</span> <span class="nn">ecell4</span> <span class="kn">import</span> <span class="o">*</span>
<span class="k">with</span> <span class="n">reaction_rules</span><span class="p">():</span>
<span class="n">A</span> <span class="o">+</span> <span class="n">B</span> <span class="o">==</span> <span class="n">C</span> <span class="o">|</span> <span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">)</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">get_model</span><span class="p">()</span>
<span class="c1"># ode.World -> gillespie.World</span>
<span class="n">w</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">w</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s1">'C'</span><span class="p">),</span> <span class="mi">60</span><span class="p">)</span>
<span class="c1"># ode.Simulator -> gillespie.Simulator</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">obs</span> <span class="o">=</span> <span class="n">FixedIntervalNumberObserver</span><span class="p">(</span><span class="mf">0.1</span><span class="p">,</span> <span class="p">(</span><span class="s1">'A'</span><span class="p">,</span> <span class="s1">'C'</span><span class="p">))</span>
<span class="n">sim</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="n">obs</span><span class="p">)</span>
<span class="n">show</span><span class="p">(</span><span class="n">obs</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
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<p><code class="docutils literal notranslate"><span class="pre">World</span></code> and <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> never change the <code class="docutils literal notranslate"><span class="pre">Model</span></code> itself, so you can switch several <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>s for one <code class="docutils literal notranslate"><span class="pre">Model</span></code>.</p>
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