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jail.html
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<!DOCTYPE html>
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<title>jail — Cortix 0.1.0 documentation</title>
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<h1>Source code for jail</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1"># This file is part of the Cortix toolkit environment.</span>
<span class="c1"># https://cortix.org</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">scipy.constants</span> <span class="k">as</span> <span class="nn">const</span>
<span class="kn">from</span> <span class="nn">scipy.integrate</span> <span class="k">import</span> <span class="n">odeint</span>
<span class="kn">from</span> <span class="nn">cortix</span> <span class="k">import</span> <span class="n">Module</span>
<span class="kn">from</span> <span class="nn">cortix</span> <span class="k">import</span> <span class="n">Phase</span>
<span class="kn">from</span> <span class="nn">cortix</span> <span class="k">import</span> <span class="n">Quantity</span>
<div class="viewcode-block" id="Jail"><a class="viewcode-back" href="../examples_rst/city_justice_rst/jail.html#jail.Jail">[docs]</a><span class="k">class</span> <span class="nc">Jail</span><span class="p">(</span><span class="n">Module</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Jail Cortix module used to model criminal group population in a jail.</span>
<span class="sd"> Notes</span>
<span class="sd"> -----</span>
<span class="sd"> These are the `port` names available in this module to connect to respective</span>
<span class="sd"> modules: `probation`, `adjudication`, `arrested`, `prison`, and `community`.</span>
<span class="sd"> See instance attribute `port_names_expected`.</span>
<span class="sd"> '''</span>
<div class="viewcode-block" id="Jail.__init__"><a class="viewcode-back" href="../examples_rst/city_justice_rst/jail.html#jail.Jail.__init__">[docs]</a> <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n_groups</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">pool_size</span><span class="o">=</span><span class="mf">0.0</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> n_groups: int</span>
<span class="sd"> Number of groups in the population.</span>
<span class="sd"> pool_size: float</span>
<span class="sd"> Upperbound on the range of the existing population groups. A random value</span>
<span class="sd"> from 0 to the upperbound value will be assigned to each group.</span>
<span class="sd"> '''</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">port_names_expected</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'probation'</span><span class="p">,</span><span class="s1">'adjudication'</span><span class="p">,</span><span class="s1">'arrested'</span><span class="p">,</span><span class="s1">'prison'</span><span class="p">,</span>
<span class="s1">'community'</span><span class="p">]</span>
<span class="n">quantities</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">initial_time</span> <span class="o">=</span> <span class="mf">0.0</span> <span class="o">*</span> <span class="n">const</span><span class="o">.</span><span class="n">day</span>
<span class="bp">self</span><span class="o">.</span><span class="n">end_time</span> <span class="o">=</span> <span class="mi">100</span> <span class="o">*</span> <span class="n">const</span><span class="o">.</span><span class="n">day</span>
<span class="bp">self</span><span class="o">.</span><span class="n">time_step</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">const</span><span class="o">.</span><span class="n">day</span>
<span class="c1"># Population groups</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span> <span class="o">=</span> <span class="n">n_groups</span>
<span class="c1"># Jail population groups</span>
<span class="n">fjg_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span> <span class="o">*</span> <span class="n">pool_size</span>
<span class="n">fjg</span> <span class="o">=</span> <span class="n">Quantity</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'fjg'</span><span class="p">,</span> <span class="n">formalName</span><span class="o">=</span><span class="s1">'jail-pop-grps'</span><span class="p">,</span>
<span class="n">unit</span><span class="o">=</span><span class="s1">'individual'</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">fjg_0</span><span class="p">)</span>
<span class="n">quantities</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fjg</span><span class="p">)</span>
<span class="c1"># Model parameters: commitment coefficients and their modifiers</span>
<span class="c1"># Jail to community</span>
<span class="n">cj0g_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span> <span class="o">/</span> <span class="n">const</span><span class="o">.</span><span class="n">day</span>
<span class="n">cj0g</span> <span class="o">=</span> <span class="n">Quantity</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'cj0g'</span><span class="p">,</span> <span class="n">formalName</span><span class="o">=</span><span class="s1">'commit-community-coeff-grps'</span><span class="p">,</span>
<span class="n">unit</span><span class="o">=</span><span class="s1">'individual'</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">cj0g_0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">cj0g_0</span>
<span class="n">quantities</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cj0g</span><span class="p">)</span>
<span class="n">mj0g_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="n">mj0g</span> <span class="o">=</span> <span class="n">Quantity</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'mj0g'</span><span class="p">,</span> <span class="n">formalName</span><span class="o">=</span><span class="s1">'commit-community-coeff-mod-grps'</span><span class="p">,</span>
<span class="n">unit</span><span class="o">=</span><span class="s1">'individual'</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">mj0g_0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-mod-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mj0g_0</span>
<span class="n">quantities</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mj0g</span><span class="p">)</span>
<span class="c1"># Jail to prison </span>
<span class="n">cjpg_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span> <span class="o">/</span> <span class="n">const</span><span class="o">.</span><span class="n">day</span>
<span class="n">cjpg</span> <span class="o">=</span> <span class="n">Quantity</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'cjpg'</span><span class="p">,</span> <span class="n">formalName</span><span class="o">=</span><span class="s1">'commit-prison-coeff-grps'</span><span class="p">,</span>
<span class="n">unit</span><span class="o">=</span><span class="s1">'individual'</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">cjpg_0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">cjpg_0</span>
<span class="n">quantities</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cjpg</span><span class="p">)</span>
<span class="n">mjpg_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="n">mjpg</span> <span class="o">=</span> <span class="n">Quantity</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'mjpg'</span><span class="p">,</span> <span class="n">formalName</span><span class="o">=</span><span class="s1">'commit-prison-coeff-mod-grps'</span><span class="p">,</span>
<span class="n">unit</span><span class="o">=</span><span class="s1">'individual'</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">mjpg_0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-mod-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mjpg_0</span>
<span class="n">quantities</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mjpg</span><span class="p">)</span>
<span class="c1"># Death term</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'jail-death-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="c1"># Phase state</span>
<span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span> <span class="o">=</span> <span class="n">Phase</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">initial_time</span><span class="p">,</span> <span class="n">time_unit</span><span class="o">=</span><span class="s1">'s'</span><span class="p">,</span>
<span class="n">quantities</span><span class="o">=</span><span class="n">quantities</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">SetValue</span><span class="p">(</span><span class="s1">'fjg'</span><span class="p">,</span> <span class="n">fjg_0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">initial_time</span><span class="p">)</span>
<span class="c1"># Initialize inflows to zero</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'arrested-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'probation-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'adjudication-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="k">return</span></div>
<div class="viewcode-block" id="Jail.run"><a class="viewcode-back" href="../examples_rst/city_justice_rst/jail.html#jail.Jail.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__zero_ode_parameters</span><span class="p">()</span>
<span class="n">time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">initial_time</span>
<span class="k">while</span> <span class="n">time</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">end_time</span><span class="p">:</span>
<span class="c1"># Interactions in the prison port</span>
<span class="c1">#--------------------------------</span>
<span class="c1"># one way "to" prison</span>
<span class="n">message_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recv</span><span class="p">(</span><span class="s1">'prison'</span><span class="p">)</span>
<span class="n">outflow_rates</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__compute_outflow_rates</span><span class="p">(</span> <span class="n">message_time</span><span class="p">,</span> <span class="s1">'prison'</span> <span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">send</span><span class="p">(</span> <span class="p">(</span><span class="n">message_time</span><span class="p">,</span> <span class="n">outflow_rates</span><span class="p">),</span> <span class="s1">'prison'</span> <span class="p">)</span>
<span class="c1"># Interactions in the adjudication port</span>
<span class="c1">#------------------------------------</span>
<span class="c1"># one way "from" adjudication</span>
<span class="bp">self</span><span class="o">.</span><span class="n">send</span><span class="p">(</span> <span class="n">time</span><span class="p">,</span> <span class="s1">'adjudication'</span> <span class="p">)</span>
<span class="p">(</span><span class="n">check_time</span><span class="p">,</span> <span class="n">adjudication_inflow_rates</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recv</span><span class="p">(</span><span class="s1">'adjudication'</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">abs</span><span class="p">(</span><span class="n">check_time</span><span class="o">-</span><span class="n">time</span><span class="p">)</span> <span class="o"><=</span> <span class="mf">1e-6</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'adjudication-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">adjudication_inflow_rates</span>
<span class="c1"># Interactions in the arrested port</span>
<span class="c1">#----------------------------------</span>
<span class="c1"># one way "from" arrested</span>
<span class="bp">self</span><span class="o">.</span><span class="n">send</span><span class="p">(</span> <span class="n">time</span><span class="p">,</span> <span class="s1">'arrested'</span> <span class="p">)</span>
<span class="p">(</span><span class="n">check_time</span><span class="p">,</span> <span class="n">arrested_inflow_rates</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recv</span><span class="p">(</span><span class="s1">'arrested'</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">abs</span><span class="p">(</span><span class="n">check_time</span><span class="o">-</span><span class="n">time</span><span class="p">)</span> <span class="o"><=</span> <span class="mf">1e-6</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'arrested-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">arrested_inflow_rates</span>
<span class="c1"># Interactions in the probation port</span>
<span class="c1">#-----------------------------------</span>
<span class="c1"># one way "from" probation</span>
<span class="bp">self</span><span class="o">.</span><span class="n">send</span><span class="p">(</span> <span class="n">time</span><span class="p">,</span> <span class="s1">'probation'</span> <span class="p">)</span>
<span class="p">(</span><span class="n">check_time</span><span class="p">,</span> <span class="n">probation_inflow_rates</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recv</span><span class="p">(</span><span class="s1">'probation'</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">abs</span><span class="p">(</span><span class="n">check_time</span><span class="o">-</span><span class="n">time</span><span class="p">)</span> <span class="o"><=</span> <span class="mf">1e-6</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'probation-inflow-rates'</span><span class="p">]</span> <span class="o">=</span> <span class="n">probation_inflow_rates</span>
<span class="c1"># Interactions in the community port</span>
<span class="c1">#------------------------------</span>
<span class="c1"># one way "to" community</span>
<span class="n">message_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recv</span><span class="p">(</span><span class="s1">'community'</span><span class="p">)</span>
<span class="n">outflow_rates</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__compute_outflow_rates</span><span class="p">(</span> <span class="n">message_time</span><span class="p">,</span> <span class="s1">'community'</span> <span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">send</span><span class="p">(</span> <span class="p">(</span><span class="n">message_time</span><span class="p">,</span> <span class="n">outflow_rates</span><span class="p">),</span> <span class="s1">'community'</span> <span class="p">)</span>
<span class="c1"># Evolve jail group population to the next time stamp</span>
<span class="c1">#----------------------------------------------------</span>
<span class="n">time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__step</span><span class="p">(</span> <span class="n">time</span> <span class="p">)</span></div>
<span class="k">def</span> <span class="nf">__rhs_fn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">u_vec</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
<span class="n">fjg</span> <span class="o">=</span> <span class="n">u_vec</span> <span class="c1"># jail population groups</span>
<span class="n">arrested_inflow_rates</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'arrested-inflow-rates'</span><span class="p">]</span>
<span class="n">probation_inflow_rates</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'probation-inflow-rates'</span><span class="p">]</span>
<span class="n">adjudication_inflow_rates</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'adjudication-inflow-rates'</span><span class="p">]</span>
<span class="n">inflow_rates</span> <span class="o">=</span> <span class="n">arrested_inflow_rates</span> <span class="o">+</span> <span class="n">probation_inflow_rates</span> <span class="o">+</span> \
<span class="n">adjudication_inflow_rates</span>
<span class="n">cj0g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-grps'</span><span class="p">]</span>
<span class="n">mj0g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-mod-grps'</span><span class="p">]</span>
<span class="n">cjpg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-grps'</span><span class="p">]</span>
<span class="n">mjpg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-mod-grps'</span><span class="p">]</span>
<span class="n">outflow_rates</span> <span class="o">=</span> <span class="p">(</span> <span class="n">cj0g</span> <span class="o">*</span> <span class="n">mj0g</span> <span class="o">+</span> <span class="n">cjpg</span> <span class="o">*</span> <span class="n">mjpg</span> <span class="p">)</span> <span class="o">*</span> <span class="n">fjg</span>
<span class="n">death_rates</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'jail-death-rates'</span><span class="p">]</span>
<span class="n">dt_fjg</span> <span class="o">=</span> <span class="n">inflow_rates</span> <span class="o">-</span> <span class="n">outflow_rates</span> <span class="o">-</span> <span class="n">death_rates</span>
<span class="k">return</span> <span class="n">dt_fjg</span>
<span class="k">def</span> <span class="nf">__step</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">time</span><span class="o">=</span><span class="mf">0.0</span><span class="p">):</span>
<span class="sa">r</span><span class="sd">'''</span>
<span class="sd"> ODE IVP problem:</span>
<span class="sd"> Given the initial data at :math:`t=0`,</span>
<span class="sd"> :math:`u = (u_1(0),u_2(0),\ldots)`</span>
<span class="sd"> solve :math:`\frac{\text{d}u}{\text{d}t} = f(u)` in the interval</span>
<span class="sd"> :math:`0\le t \le t_f`.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> time: float</span>
<span class="sd"> Time in SI unit.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None</span>
<span class="sd"> '''</span>
<span class="n">u_vec_0</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">GetValue</span><span class="p">(</span><span class="s1">'fjg'</span><span class="p">,</span> <span class="n">time</span><span class="p">)</span>
<span class="n">t_interval_sec</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">time_step</span><span class="p">,</span> <span class="n">num</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="p">(</span><span class="n">u_vec_hist</span><span class="p">,</span> <span class="n">info_dict</span><span class="p">)</span> <span class="o">=</span> <span class="n">odeint</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__rhs_fn</span><span class="p">,</span>
<span class="n">u_vec_0</span><span class="p">,</span> <span class="n">t_interval_sec</span><span class="p">,</span>
<span class="n">args</span><span class="o">=</span><span class="p">(</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">,</span> <span class="p">),</span>
<span class="n">rtol</span><span class="o">=</span><span class="mf">1e-4</span><span class="p">,</span> <span class="n">atol</span><span class="o">=</span><span class="mf">1e-8</span><span class="p">,</span> <span class="n">mxstep</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span>
<span class="n">full_output</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">info_dict</span><span class="p">[</span><span class="s1">'message'</span><span class="p">]</span> <span class="o">==</span><span class="s1">'Integration successful.'</span><span class="p">,</span> <span class="n">info_dict</span><span class="p">[</span><span class="s1">'message'</span><span class="p">]</span>
<span class="n">u_vec</span> <span class="o">=</span> <span class="n">u_vec_hist</span><span class="p">[</span><span class="mi">1</span><span class="p">,:]</span> <span class="c1"># solution vector at final time step</span>
<span class="n">values</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">GetRow</span><span class="p">(</span><span class="n">time</span><span class="p">)</span> <span class="c1"># values at previous time</span>
<span class="n">time</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">time_step</span>
<span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">AddRow</span><span class="p">(</span><span class="n">time</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
<span class="c1"># Update current values</span>
<span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">SetValue</span><span class="p">(</span><span class="s1">'fjg'</span><span class="p">,</span> <span class="n">u_vec</span><span class="p">,</span> <span class="n">time</span><span class="p">)</span>
<span class="k">return</span> <span class="n">time</span>
<span class="k">def</span> <span class="nf">__compute_outflow_rates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">time</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="n">fjg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">population_phase</span><span class="o">.</span><span class="n">GetValue</span><span class="p">(</span><span class="s1">'fjg'</span><span class="p">,</span><span class="n">time</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">fjg</span><span class="o">>=</span><span class="mf">0.0</span><span class="p">),</span> <span class="s1">'values: </span><span class="si">%r</span><span class="s1">'</span><span class="o">%</span><span class="n">fjg</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s1">'prison'</span><span class="p">:</span>
<span class="n">cjpg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-grps'</span><span class="p">]</span>
<span class="n">mjpg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-mod-grps'</span><span class="p">]</span>
<span class="n">outflow_rates</span> <span class="o">=</span> <span class="n">cjpg</span> <span class="o">*</span> <span class="n">mjpg</span> <span class="o">*</span> <span class="n">fjg</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s1">'community'</span><span class="p">:</span>
<span class="n">cj0g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-grps'</span><span class="p">]</span>
<span class="n">mj0g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-mod-grps'</span><span class="p">]</span>
<span class="n">outflow_rates</span> <span class="o">=</span> <span class="n">cj0g</span> <span class="o">*</span> <span class="n">mj0g</span> <span class="o">*</span> <span class="n">fjg</span>
<span class="k">return</span> <span class="n">outflow_rates</span>
<span class="k">def</span> <span class="nf">__zero_ode_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> If ports are not connected the corresponding outflows must be zero.</span>
<span class="sd"> '''</span>
<span class="n">zeros</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_groups</span><span class="p">)</span>
<span class="n">p_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ports</span><span class="p">]</span>
<span class="k">if</span> <span class="s1">'community'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">p_names</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">zeros</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-community-coeff-mod-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">zeros</span>
<span class="k">if</span> <span class="s1">'prison'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">p_names</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">zeros</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ode_params</span><span class="p">[</span><span class="s1">'commit-to-prison-coeff-mod-grps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">zeros</span>
<span class="k">return</span></div>
</pre></div>
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<a href="https://github.com/dpploy/cortix"><img src="https://cortix.org/logo.jpg" alt="Cortix" style="border:none;"></a>
<h3>About Cortix</h3>
<p>
Cortix is a Python library for network modeling and HPC simulation.
</p>
<p>
Cortix Group <br>
c/o <a href="https://www.uml.edu/innovation-hub">UMass Innovation Hub</a> <br>
110 Canal St., 3rd Floor <br>
Lower, MA 01852
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<p>
<a href="https://www.uml.edu/Engineering/Chemical/faculty/de-Almeida-Valmor.aspx">Prof. V. F. de Almeida, Ph.D.</a></br>
Group Leader <br>
<a href="https://www.uml.edu/Engineering/Chemical">Dept. of Chemical Engineering (Nuclear Program)</a></br>
<a href="https://www.uml.edu/">UMass Lowell</a><br>
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<li><a href="https://hpc.inl.gov/SitePages/Home.aspx">Idaho National Laboratory HPC</a></li>
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