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ecell4
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<li><a class="reference internal" href="#">4. How to Run a Simulation</a><ul>
<li><a class="reference internal" href="#4.1.-How-to-Setup-a-Simulator">4.1. How to Setup a Simulator</a></li>
<li><a class="reference internal" href="#4.2.-Running-Simulations">4.2. Running Simulations</a></li>
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<div class="section" id="4.-How-to-Run-a-Simulation">
<h1>4. How to Run a Simulation<a class="headerlink" href="#4.-How-to-Run-a-Simulation" title="Permalink to this headline">¶</a></h1>
<p>In sections 2 and 3, we explained the way to build a model and to setup the intial state. Now, it is the time to run a simulation. Corresponding to <code class="docutils literal notranslate"><span class="pre">World</span></code> classes, six <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> classes are there: <code class="docutils literal notranslate"><span class="pre">spatiocyte.SpatiocyteSimulator</span></code>, <code class="docutils literal notranslate"><span class="pre">egfrd.EGFRDSimulator</span></code>, <code class="docutils literal notranslate"><span class="pre">bd.BDSimulator</span></code>, <code class="docutils literal notranslate"><span class="pre">meso.MesoscopicSimulator</span></code>, <code class="docutils literal notranslate"><span class="pre">gillespie.GillespieSimulator</span></code>, and <code class="docutils literal notranslate"><span class="pre">ode.ODESimulator</span></code>. Each <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> class only accepts the corresponding type of <code class="docutils literal notranslate"><span class="pre">World</span></code>, but all of them allow the same <code class="docutils literal notranslate"><span class="pre">Model</span></code>.</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>
</pre></div>
</div>
</div>
<div class="section" id="4.1.-How-to-Setup-a-Simulator">
<h2>4.1. How to Setup a Simulator<a class="headerlink" href="#4.1.-How-to-Setup-a-Simulator" title="Permalink to this headline">¶</a></h2>
<p>Except for the initialization (so-called constructor function) with arguments specific to the algorithm, all <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>s have the same APIs.</p>
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<span></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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<p>Before constructing a <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>, parepare a <code class="docutils literal notranslate"><span class="pre">Model</span></code> and a <code class="docutils literal notranslate"><span class="pre">World</span></code> corresponding to the type of <code class="docutils literal notranslate"><span class="pre">Simulator</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="n">species_attributes</span><span class="p">,</span> <span class="n">reaction_rules</span><span class="p">,</span> <span class="n">get_model</span>
<span class="k">with</span> <span class="n">species_attributes</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="s1">'D'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'radius'</span><span class="p">:</span> <span class="mf">0.005</span><span class="p">}</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>
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<span></span><span class="n">w1</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">w2</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">w3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
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<p><code class="docutils literal notranslate"><span class="pre">Simulator</span></code> requires both <code class="docutils literal notranslate"><span class="pre">Model</span></code> and <code class="docutils literal notranslate"><span class="pre">World</span></code> in this order at the construction.</p>
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<span></span><span class="n">sim1</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">w1</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim2</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">w2</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w3</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w4</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w5</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
<span class="n">sim6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w6</span><span class="p">,</span> <span class="n">m</span><span class="p">)</span>
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<p>If you bind the <code class="docutils literal notranslate"><span class="pre">Model</span></code> to the <code class="docutils literal notranslate"><span class="pre">World</span></code>, you need only the <code class="docutils literal notranslate"><span class="pre">World</span></code> to create a <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>.</p>
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<span></span><span class="n">w1</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
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<span></span><span class="n">sim1</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">w1</span><span class="p">)</span>
<span class="n">sim2</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">w2</span><span class="p">)</span>
<span class="n">sim3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w3</span><span class="p">)</span>
<span class="n">sim4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w4</span><span class="p">)</span>
<span class="n">sim5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w5</span><span class="p">)</span>
<span class="n">sim6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">Simulator</span><span class="p">(</span><span class="n">w6</span><span class="p">)</span>
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<p>Of course, the <code class="docutils literal notranslate"><span class="pre">Model</span></code> and <code class="docutils literal notranslate"><span class="pre">World</span></code> bound to a <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> can be drawn from <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> in the way below:</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim1</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim2</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim3</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim4</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim5</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">model</span><span class="p">(),</span> <span class="n">sim6</span><span class="o">.</span><span class="n">world</span><span class="p">())</span>
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<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.gillespie.GillespieWorld object at 0x14882cdae768>
<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.ode.ODEWorld object at 0x14882cdae6f8>
<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.spatiocyte.SpatiocyteWorld object at 0x14882cdae688>
<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.bd.BDWorld object at 0x14882cdae650>
<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.meso.MesoscopicWorld object at 0x14882cdae7a0>
<ecell4_base.core.NetworkModel object at 0x14882cdd8730> <ecell4_base.egfrd.EGFRDWorld object at 0x14882cdae7d8>
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<p>After updating the <code class="docutils literal notranslate"><span class="pre">World</span></code> by yourself, you must initialize the internal state of a <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> before running simulation.</p>
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<span></span><span class="n">w1</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">w2</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">w3</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">w4</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">w5</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">w6</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>
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<span></span><span class="n">sim1</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
<span class="n">sim2</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
<span class="n">sim3</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
<span class="n">sim4</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
<span class="n">sim5</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
<span class="n">sim6</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
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<p>For algorithms with a fixed step interval, the <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> also requires <code class="docutils literal notranslate"><span class="pre">dt</span></code>.</p>
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<span></span><span class="n">sim2</span><span class="o">.</span><span class="n">set_dt</span><span class="p">(</span><span class="mf">1e-6</span><span class="p">)</span> <span class="c1"># ode.Simulator. This is optional</span>
<span class="n">sim4</span><span class="o">.</span><span class="n">set_dt</span><span class="p">(</span><span class="mf">1e-6</span><span class="p">)</span> <span class="c1"># bd.Simulator</span>
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<div class="section" id="4.2.-Running-Simulations">
<h2>4.2. Running Simulations<a class="headerlink" href="#4.2.-Running-Simulations" title="Permalink to this headline">¶</a></h2>
<p>For running simulations, <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> provides two APIs, <code class="docutils literal notranslate"><span class="pre">step</span></code> and <code class="docutils literal notranslate"><span class="pre">run</span></code>.</p>
<p><code class="docutils literal notranslate"><span class="pre">step()</span></code> advances a simulation for the time that the <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> expects, <code class="docutils literal notranslate"><span class="pre">next_time()</span></code>.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim1</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim1</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim2</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim2</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span> <span class="c1"># => (0.0, 1e-6, 1e-6)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim3</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim3</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim4</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim4</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span> <span class="c1"># => (0.0, 1e-6, 1e-6)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim5</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim5</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">sim6</span><span class="o">.</span><span class="n">next_time</span><span class="p">(),</span> <span class="n">sim6</span><span class="o">.</span><span class="n">dt</span><span class="p">())</span> <span class="c1"># => (0.0, 0.0, 0.0)</span>
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0.0 0.03782982587603311 0.03782982587603311
0.0 1e-06 1e-06
0.0 6.666666666666667e-05 6.666666666666667e-05
0.0 1e-06 1e-06
0.0 0.0025188519074043213 0.0025188519074043213
0.0 0.0 0.0
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<span></span><span class="n">sim1</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="n">sim2</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="n">sim3</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="n">sim4</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="n">sim5</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="n">sim6</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 1e-6</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 1e-6</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.0</span>
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0.03782982587603311
1e-06
6.666666666666667e-05
1e-06
0.0025188519074043213
0.0
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<p><code class="docutils literal notranslate"><span class="pre">last_reactions()</span></code> returns a list of pairs of <code class="docutils literal notranslate"><span class="pre">ReactionRule</span></code> and <code class="docutils literal notranslate"><span class="pre">ReactionInfo</span></code> which occurs at the last step. Each algorithm have its own implementation of <code class="docutils literal notranslate"><span class="pre">ReactionInfo</span></code>. See <code class="docutils literal notranslate"><span class="pre">help(module.ReactionInfo)</span></code> for details.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">last_reactions</span><span class="p">())</span>
<span class="c1"># print(sim2.last_reactions())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">last_reactions</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">last_reactions</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">last_reactions</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">last_reactions</span><span class="p">())</span>
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[(<ecell4_base.core.ReactionRule object at 0x148858eaf5e0>, <ecell4_base.gillespie.ReactionInfo object at 0x148858eaf618>)]
[]
[]
[]
[]
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<p><code class="docutils literal notranslate"><span class="pre">step(upto)</span></code> advances a simulation for <code class="docutils literal notranslate"><span class="pre">next_time</span></code> if <code class="docutils literal notranslate"><span class="pre">next_time</span></code> is less than <code class="docutils literal notranslate"><span class="pre">upto</span></code>, or for <code class="docutils literal notranslate"><span class="pre">upto</span></code> otherwise. <code class="docutils literal notranslate"><span class="pre">step(upto)</span></code> returns whether the time does <strong>NOT</strong> reach the limit, <code class="docutils literal notranslate"><span class="pre">upto</span></code>.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim1</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim2</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim3</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim4</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim5</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">),</span> <span class="n">sim6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
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True 0.1531251186177207
True 2e-06
True 0.00013333333333333334
True 2e-06
True 0.003502192717675309
True 0.0
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<p>To run a simulation just until the time, <code class="docutils literal notranslate"><span class="pre">upto</span></code>, call <code class="docutils literal notranslate"><span class="pre">step(upto)</span></code> while it returns <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p>
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<span></span><span class="k">while</span> <span class="n">sim1</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">):</span> <span class="k">pass</span>
<span class="k">while</span> <span class="n">sim2</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">0.001</span><span class="p">):</span> <span class="k">pass</span>
<span class="k">while</span> <span class="n">sim3</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">0.001</span><span class="p">):</span> <span class="k">pass</span>
<span class="k">while</span> <span class="n">sim4</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">0.001</span><span class="p">):</span> <span class="k">pass</span>
<span class="k">while</span> <span class="n">sim5</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">1.0</span><span class="p">):</span> <span class="k">pass</span>
<span class="k">while</span> <span class="n">sim6</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="mf">0.001</span><span class="p">):</span> <span class="k">pass</span>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 1.0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.001</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.001</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.001</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 1.0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.001</span>
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1.0
0.001
0.001
0.001
1.0
0.001
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<p>This is just what <code class="docutils literal notranslate"><span class="pre">run</span></code> does. <code class="docutils literal notranslate"><span class="pre">run(tau)</span></code> advances a simulation upto <code class="docutils literal notranslate"><span class="pre">t()+tau</span></code>.</p>
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<span></span><span class="n">sim1</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">sim2</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">0.001</span><span class="p">)</span>
<span class="n">sim3</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">0.001</span><span class="p">)</span>
<span class="n">sim4</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">0.001</span><span class="p">)</span>
<span class="n">sim5</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">sim6</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">0.001</span><span class="p">)</span>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 2.0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.002</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.002</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.002</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 2.0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span> <span class="c1"># => 0.02</span>
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2.0
0.002
0.002
0.002
2.0
0.002
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<p><code class="docutils literal notranslate"><span class="pre">num_steps</span></code> returns the number of steps during the simulation.</p>
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<span></span><span class="nb">print</span><span class="p">(</span><span class="n">sim1</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim2</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim3</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim4</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim5</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim6</span><span class="o">.</span><span class="n">num_steps</span><span class="p">())</span>
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28
2001
28
2001
835
738
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<div class="section" id="4.3.-Capsulizing-Algorithm-into-a-Factory-Class">
<h2>4.3. Capsulizing Algorithm into a Factory Class<a class="headerlink" href="#4.3.-Capsulizing-Algorithm-into-a-Factory-Class" title="Permalink to this headline">¶</a></h2>
<p>Owing to the portability of a <code class="docutils literal notranslate"><span class="pre">Model</span></code> and consistent APIs of <code class="docutils literal notranslate"><span class="pre">World</span></code>s and <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>s, it is very easy to write a script common in algorithms. However, when switching the algorithm, still we have to rewrite the name of classes in the code, one by one.</p>
<p>To avoid the trouble, E-Cell4 also provides a <code class="docutils literal notranslate"><span class="pre">Factory</span></code> class for each algorithm. <code class="docutils literal notranslate"><span class="pre">Factory</span></code> encapsulates <code class="docutils literal notranslate"><span class="pre">World</span></code> and <code class="docutils literal notranslate"><span class="pre">Simulator</span></code> with their arguments needed for the construction. By using <code class="docutils literal notranslate"><span class="pre">Factory</span></code> class, your script could be portable and robust agaist changes in the algorithm.</p>
<p><code class="docutils literal notranslate"><span class="pre">Factory</span></code> just provides two functions, <code class="docutils literal notranslate"><span class="pre">world</span></code> and <code class="docutils literal notranslate"><span class="pre">simulator</span></code>.</p>
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<span></span><span class="k">def</span> <span class="nf">singlerun</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">m</span><span class="p">):</span>
<span class="n">w</span> <span class="o">=</span> <span class="n">f</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">bind_to</span><span class="p">(</span><span class="n">m</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">f</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">sim</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mf">0.01</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sim</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>
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<p><code class="docutils literal notranslate"><span class="pre">singlerun</span></code> above is free from the algorithm. Thus, by just switching <code class="docutils literal notranslate"><span class="pre">Factory</span></code>, you can easily compare the results.</p>
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<span></span><span class="n">singlerun</span><span class="p">(</span><span class="n">gillespie</span><span class="o">.</span><span class="n">Factory</span><span class="p">(),</span> <span class="n">m</span><span class="p">)</span>
<span class="n">singlerun</span><span class="p">(</span><span class="n">ode</span><span class="o">.</span><span class="n">Factory</span><span class="p">(),</span> <span class="n">m</span><span class="p">)</span>
<span class="n">singlerun</span><span class="p">(</span><span class="n">spatiocyte</span><span class="o">.</span><span class="n">Factory</span><span class="p">(),</span> <span class="n">m</span><span class="p">)</span>
<span class="n">singlerun</span><span class="p">(</span><span class="n">bd</span><span class="o">.</span><span class="n">Factory</span><span class="p">(</span><span class="n">bd_dt_factor</span><span class="o">=</span><span class="mi">1</span><span class="p">),</span> <span class="n">m</span><span class="p">)</span>
<span class="n">singlerun</span><span class="p">(</span><span class="n">meso</span><span class="o">.</span><span class="n">Factory</span><span class="p">(),</span> <span class="n">m</span><span class="p">)</span>
<span class="n">singlerun</span><span class="p">(</span><span class="n">egfrd</span><span class="o">.</span><span class="n">Factory</span><span class="p">(),</span> <span class="n">m</span><span class="p">)</span>
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0.01 60
0.01 59
0.01 60
0.01 60
0.01 60
0.01 60
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<p>When you need to provide several parameters to initialize <code class="docutils literal notranslate"><span class="pre">World</span></code> or <code class="docutils literal notranslate"><span class="pre">Simulator</span></code>, <code class="docutils literal notranslate"><span class="pre">run_simulation</span></code> also accepts <code class="docutils literal notranslate"><span class="pre">Factory</span></code> instead of <code class="docutils literal notranslate"><span class="pre">solver</span></code>.</p>
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<span></span><span class="kn">from</span> <span class="nn">ecell4.util</span> <span class="kn">import</span> <span class="n">run_simulation</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">gillespie</span><span class="o">.</span><span class="n">Factory</span><span class="p">())[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">ode</span><span class="o">.</span><span class="n">Factory</span><span class="p">())[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">spatiocyte</span><span class="o">.</span><span class="n">Factory</span><span class="p">())[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">bd</span><span class="o">.</span><span class="n">Factory</span><span class="p">(</span><span class="n">bd_dt_factor</span><span class="o">=</span><span class="mi">1</span><span class="p">))[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">meso</span><span class="o">.</span><span class="n">Factory</span><span class="p">())[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">run_simulation</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">y0</span><span class="o">=</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">return_type</span><span class="o">=</span><span class="s1">'array'</span><span class="p">,</span> <span class="n">solver</span><span class="o">=</span><span class="n">egfrd</span><span class="o">.</span><span class="n">Factory</span><span class="p">())[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
</pre></div>
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<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
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<div class="output_area docutils container">
<div class="highlight"><pre>
[0.01, 0.0, 0.0, 60.0]
[0.01, 0.17972919304002502, 0.17972919304002502, 59.820270806960046]
[0.01, 1.0, 1.0, 59.0]
[0.01, 0.0, 0.0, 60.0]
[0.01, 1.0, 1.0, 59.0]
[0.01, 1.0, 1.0, 59.0]
</pre></div></div>
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