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github-actions[bot] committed Aug 8, 2023
1 parent babe966 commit 5413d97
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2 changes: 1 addition & 1 deletion _modules/mici/adapters.html
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Expand Up @@ -185,7 +185,7 @@ <h1>Source code for mici.adapters</h1><div class="highlight"><pre>
<span class="sd"> An adapter which requires only local information to adapt the transition</span>
<span class="sd"> parameters should be classified as fast while one which requires more global</span>
<span class="sd"> information and so more chain iterations should be classified as slow i.e.</span>
<span class="sd"> `is_fast == False`.</span>
<span class="sd"> :code:`is_fast == False`.</span>
<span class="sd"> &quot;&quot;&quot;</span></div>


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228 changes: 133 additions & 95 deletions _modules/mici/integrators.html
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36 changes: 26 additions & 10 deletions _modules/mici/samplers.html
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Expand Up @@ -877,8 +877,18 @@ <h1>Source code for mici.samplers</h1><div class="highlight"><pre>
<span class="ne">DeprecationWarning</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">rng</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">Generator</span><span class="p">(</span><span class="n">rng</span><span class="o">.</span><span class="n">_bit_generator</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rng</span> <span class="o">=</span> <span class="n">rng</span>
<span class="bp">self</span><span class="o">.</span><span class="n">transitions</span> <span class="o">=</span> <span class="n">transitions</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_rng</span> <span class="o">=</span> <span class="n">rng</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_transitions</span> <span class="o">=</span> <span class="n">transitions</span>

<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">transitions</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Transition</span><span class="p">]:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Dictionary of transition kernels sampled from in each chain iteration.&quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_transitions</span>

<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">rng</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Generator</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;NumPy random number generator object.&quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rng</span>

<div class="viewcode-block" id="MarkovChainMonteCarloMethod.sample_chains"><a class="viewcode-back" href="../../mici.samplers.html#mici.samplers.MarkovChainMonteCarloMethod.sample_chains">[docs]</a> <span class="k">def</span> <span class="nf">sample_chains</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
Expand Down Expand Up @@ -1164,21 +1174,22 @@ <h1>Source code for mici.samplers</h1><div class="highlight"><pre>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Args:</span>
<span class="sd"> system Hamiltonian system to be simulated.</span>
<span class="sd"> system Hamiltonian system to be simulated, corresponding to joint</span>
<span class="sd"> distribution on augmented space.</span>
<span class="sd"> rng: Numpy random number generator.</span>
<span class="sd"> integration_transition: Markov transition kernel which leaves canonical</span>
<span class="sd"> integration_transition: Markov transition kernel which leaves joint</span>
<span class="sd"> distribution invariant and jointly updates the position and momentum</span>
<span class="sd"> components of the chain state by integrating the Hamiltonian dynamics of</span>
<span class="sd"> the system to propose new values for the state.</span>
<span class="sd"> momentum_transition: Markov transition kernel which leaves the conditional</span>
<span class="sd"> distribution on the momentum under the canonical distribution invariant,</span>
<span class="sd"> distribution on the momentum under the join distribution invariant,</span>
<span class="sd"> updating only the momentum component of the chain state. If set to</span>
<span class="sd"> `None` the momentum transition operator</span>
<span class="sd"> `mici.transitions.IndependentMomentumTransition` will be used, which</span>
<span class="sd"> independently samples the momentum from its conditional distribution.</span>
<span class="sd"> :py:const:`None` the momentum transition operator</span>
<span class="sd"> :py:class:`mici.transitions.IndependentMomentumTransition` will be used,</span>
<span class="sd"> which independently samples the momentum from its conditional</span>
<span class="sd"> distribution.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">system</span> <span class="o">=</span> <span class="n">system</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rng</span> <span class="o">=</span> <span class="n">rng</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_system</span> <span class="o">=</span> <span class="n">system</span>
<span class="k">if</span> <span class="n">momentum_transition</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">momentum_transition</span> <span class="o">=</span> <span class="n">IndependentMomentumTransition</span><span class="p">(</span><span class="n">system</span><span class="p">)</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
Expand All @@ -1189,6 +1200,11 @@ <h1>Source code for mici.samplers</h1><div class="highlight"><pre>
<span class="p">},</span>
<span class="p">)</span>

<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">system</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">System</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Hamiltonian system corresponding to joint distribution on augmented space.&quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_system</span>

<span class="k">def</span> <span class="nf">_preprocess_init_state</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span> <span class="n">init_state</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">NDArray</span><span class="p">,</span> <span class="n">ChainState</span><span class="p">,</span> <span class="nb">dict</span><span class="p">]</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">ChainState</span><span class="p">:</span>
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