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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<h1>Source code for prms_python.simulation</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">simulation.py -- Contains ``Simulation`` and ``SimulationSeries`` classes and </span>
<span class="sd">associated functions for managing PRMS simulations at a low level.</span>
<span class="sd">"""</span>
<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">print_function</span>
<span class="kn">import</span> <span class="nn">glob</span>
<span class="kn">import</span> <span class="nn">multiprocessing</span> <span class="k">as</span> <span class="nn">mp</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">shutil</span>
<span class="kn">import</span> <span class="nn">subprocess</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="kn">from</span> <span class="nn">.data</span> <span class="k">import</span> <span class="n">Data</span>
<span class="kn">from</span> <span class="nn">.parameters</span> <span class="k">import</span> <span class="n">Parameters</span>
<span class="kn">from</span> <span class="nn">.util</span> <span class="k">import</span> <span class="n">load_statvar</span>
<span class="n">OPJ</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span>
<div class="viewcode-block" id="SimulationSeries"><a class="viewcode-back" href="../../api.html#prms_python.SimulationSeries">[docs]</a><span class="k">class</span> <span class="nc">SimulationSeries</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Series of simulations all to be run through a common interface. </span>
<span class="sd"> </span>
<span class="sd"> Utilizes :class:`multiprocessing.Pool` class to parallelize the </span>
<span class="sd"> execution of series of PRMS simulations. SimulationSeries also</span>
<span class="sd"> allows the user to define the PRMS executable command which is </span>
<span class="sd"> set to "prms" as default. It is best to add the prms executable to </span>
<span class="sd"> your $PATH environment variable. Each simulation that is run through</span>
<span class="sd"> ``SimulationSeries`` will follow the strict file structure as defined</span>
<span class="sd"> by :func:`Simulation.run()`. This class is useful particularly for</span>
<span class="sd"> creating new programatic workflows not provided yet by PRMS-Python.</span>
<span class="sd"> Arguments:</span>
<span class="sd"> simulations (list or tuple): list of :class:`Simulation` objects</span>
<span class="sd"> to be run.</span>
<span class="sd"> Example:</span>
<span class="sd"> Lets say you have already created a series of PRMS models by modifying</span>
<span class="sd"> the input climatic forcing data, e.g. you have 100 *data* files and</span>
<span class="sd"> you want to run each using the same *control* and *parameters* file.</span>
<span class="sd"> For simplicity lets say there is a directory that contains all 100</span>
<span class="sd"> *data* files e.g. data1, data2, ... or whatever they are named and </span>
<span class="sd"> nothing else. This example also assumes that you want each simulation </span>
<span class="sd"> to be run and stored in directories named after the *data* files as </span>
<span class="sd"> shown.</span>
<span class="sd"> >>> data_dir = 'dir_that_contains_all_data_files'</span>
<span class="sd"> >>> params = Parameters('path_to_parameter_file')</span>
<span class="sd"> >>> control_path = 'path_to_control'</span>
<span class="sd"> >>> # a list comprehension to make multiple simulations with</span>
<span class="sd"> >>> # different data files, alternatively you could use a for loop</span>
<span class="sd"> >>> sims = [</span>
<span class="sd"> Simulation.from_data</span>
<span class="sd"> ( </span>
<span class="sd"> Data(data_file),</span>
<span class="sd"> params,</span>
<span class="sd"> control_path,</span>
<span class="sd"> simulation_dir='sim_{}'.format(data_file)</span>
<span class="sd"> )</span>
<span class="sd"> for data_file in os.listdir(data_dir)</span>
<span class="sd"> ]</span>
<span class="sd"> Next we can use ``SimulationSeries`` to run all of these </span>
<span class="sd"> simulations in parrallel. For example we may use 8 logical cores</span>
<span class="sd"> on a common desktop computer.</span>
<span class="sd"> >>> sim_series = SimulationSeries(sims)</span>
<span class="sd"> >>> sim_series.run(nprocs=8)</span>
<span class="sd"> The ``SimulationSeries.run()`` method will run all 100 simulations</span>
<span class="sd"> where chunks of 8 at a time will be run in parrallel. Inputs and </span>
<span class="sd"> outputs of each simulation will be sent to each simulation's</span>
<span class="sd"> ``simulation_dir`` following the file structure of </span>
<span class="sd"> :func:`Simulation.run()`.</span>
<span class="sd"> Note:</span>
<span class="sd"> The :class:`Simulation` and :class:`SimulationSeries` classes</span>
<span class="sd"> are low-level in that they alone do not create metadata for</span>
<span class="sd"> PRMS simulation scenarios. In other words they do not produce</span>
<span class="sd"> any additional files that may help the user know what differs</span>
<span class="sd"> between individual simulations. </span>
<span class="sd"> </span>
<span class="sd"> '''</span>
<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">simulations</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">series</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">simulations</span><span class="p">)</span>
<div class="viewcode-block" id="SimulationSeries.run"><a class="viewcode-back" href="../../api.html#prms_python.SimulationSeries.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="n">prms_exec</span><span class="o">=</span><span class="s1">'prms'</span><span class="p">,</span> <span class="n">nproc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Method to run multiple :class:`Simulation` objects in parrallel.</span>
<span class="sd"> Keyword Arguments:</span>
<span class="sd"> prms_exec (str): name of PRMS executable on $PATH or path to </span>
<span class="sd"> executable</span>
<span class="sd"> nproc (int or None): number of logical or physical processors</span>
<span class="sd"> for parrallel execution of PRMS simulations. </span>
<span class="sd"> Example:</span>
<span class="sd"> see :class:`SimulationSeries`</span>
<span class="sd"> Note:</span>
<span class="sd"> If ``nproc`` is not assigned the deault action is to use half</span>
<span class="sd"> of the available processecors on the machine using the Python</span>
<span class="sd"> :mod:`multiprocessing` module. </span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">nproc</span><span class="p">:</span>
<span class="n">nproc</span> <span class="o">=</span> <span class="n">mp</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span> <span class="o">//</span> <span class="mi">2</span>
<span class="n">pool</span> <span class="o">=</span> <span class="n">mp</span><span class="o">.</span><span class="n">Pool</span><span class="p">(</span><span class="n">processes</span><span class="o">=</span><span class="n">nproc</span><span class="p">)</span>
<span class="n">pool</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">_simulation_runner</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">series</span><span class="p">)</span>
<span class="n">pool</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="SimulationSeries.outputs_iter"><a class="viewcode-back" href="../../api.html#prms_python.SimulationSeries.outputs_iter">[docs]</a> <span class="k">def</span> <span class="nf">outputs_iter</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Return a :class:`generator` of directories with the path to the </span>
<span class="sd"> ``simulation_dir`` as well as paths to the *statvar.dat* output </span>
<span class="sd"> file, and *data* and *parameters* input files used in the simulation.</span>
<span class="sd"> Yields:</span>
<span class="sd"> :obj:`dict`: dictionary of paths to simulation directory,</span>
<span class="sd"> input, and output files.</span>
<span class="sd"> Example:</span>
<span class="sd"> >>> ser = SimulationSeries(simulations)</span>
<span class="sd"> >>> ser.run()</span>
<span class="sd"> >>> g = ser.outputs_iter()</span>
<span class="sd"> Would return something like</span>
<span class="sd"> >>> print(g.next())</span>
<span class="sd"> {</span>
<span class="sd"> 'simulation_dir': 'path/to/sim/', </span>
<span class="sd"> 'statvar': 'path/to/statvar', </span>
<span class="sd"> 'data': 'path/to/data', </span>
<span class="sd"> 'parameters': 'path/to/parameters'</span>
<span class="sd"> }</span>
<span class="sd"> '''</span>
<span class="n">dirs</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">simulation_dir</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">series</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">dirs</span><span class="p">)</span>
<span class="k">return</span> <span class="p">(</span>
<span class="p">{</span>
<span class="s1">'simulation_dir'</span><span class="p">:</span> <span class="n">d</span><span class="p">,</span>
<span class="s1">'statvar'</span><span class="p">:</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="s1">'outputs'</span><span class="p">,</span> <span class="s1">'statvar.dat'</span><span class="p">),</span>
<span class="s1">'data'</span><span class="p">:</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="s1">'inputs'</span><span class="p">,</span> <span class="s1">'data'</span><span class="p">),</span>
<span class="s1">'parameters'</span><span class="p">:</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="s1">'inputs'</span><span class="p">,</span> <span class="s1">'parameters'</span><span class="p">)</span>
<span class="p">}</span>
<span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span>
<span class="p">)</span> </div>
<span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputs_iter</span><span class="p">()))</span></div>
<span class="k">def</span> <span class="nf">_simulation_runner</span><span class="p">(</span><span class="n">sim</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="n">prms_exec</span><span class="o">=</span><span class="s1">'prms'</span><span class="p">)</span>
<div class="viewcode-block" id="Simulation"><a class="viewcode-back" href="../../api.html#prms_python.Simulation">[docs]</a><span class="k">class</span> <span class="nc">Simulation</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Class that runs and manages file structure for a single PRMS simulation.</span>
<span class="sd"> </span>
<span class="sd"> The ``Simulation`` class provides low-level managment of a PRMS simulation</span>
<span class="sd"> by copying model input files from ``input_dir`` argument to an output dir</span>
<span class="sd"> ``simulation_dir``. The file stucture for an individual simulation after</span>
<span class="sd"> calling the ``run`` method is simple, two subdirectories "inputs" and </span>
<span class="sd"> "outputs" are created under ``simulation_dir`` and the respective input</span>
<span class="sd"> and output files from the current PRMS simulation are transfered there after</span>
<span class="sd"> the ``Simulation.run()`` method is called which executes the PRMS model,</span>
<span class="sd"> (see examples below in :func:`Simulation.run`).</span>
<span class="sd"> A ``Simulation`` instance checks that all required PRMS inputs (control, </span>
<span class="sd"> parameters, data) exist in the expected locations. If simulation_dir is </span>
<span class="sd"> provided and does not exist, it will be created. If it does exist it will </span>
<span class="sd"> be overwritten.</span>
<span class="sd"> </span>
<span class="sd"> Keyword Arguments:</span>
<span class="sd"> input_dir (str): path to directory that contains control, parameter, </span>
<span class="sd"> and data files for the simulation</span>
<span class="sd"> simulation_dir (str): directory path to bundle inputs and outputs</span>
<span class="sd"> </span>
<span class="sd"> Example:</span>
<span class="sd"> see :func:`Simulation.run()`</span>
<span class="sd"> Raises:</span>
<span class="sd"> RuntimeError: if input directory does not contain a PRMS *data*,</span>
<span class="sd"> *parameters*, and *control* file.</span>
<span class="sd"> """</span>
<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">input_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">simulation_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="c1"># check if model input paths exist</span>
<span class="n">idir</span> <span class="o">=</span> <span class="n">input_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">input_dir</span> <span class="o">=</span> <span class="n">idir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span> <span class="o">=</span> <span class="n">simulation_dir</span>
<span class="k">if</span> <span class="n">idir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">control_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">idir</span><span class="p">,</span> <span class="s1">'control'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">idir</span><span class="p">,</span> <span class="s1">'parameters'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">idir</span><span class="p">,</span> <span class="s1">'data'</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">control_path</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">'Control file missing from '</span> <span class="o">+</span> <span class="n">idir</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters_path</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">'Parameter file missing from '</span> <span class="o">+</span> <span class="n">idir</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data_path</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">'Data file missing from '</span> <span class="o">+</span> <span class="n">idir</span><span class="p">)</span>
<span class="c1"># build output (simulation_dir) and move input files there</span>
<span class="k">if</span> <span class="n">simulation_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span> <span class="o">=</span> <span class="n">simulation_dir</span>
<span class="k">if</span> <span class="n">simulation_dir</span> <span class="ow">and</span> <span class="n">simulation_dir</span> <span class="o">!=</span> <span class="n">input_dir</span><span class="p">:</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">):</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">control_path</span><span class="p">,</span> <span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data_path</span><span class="p">,</span> <span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters_path</span><span class="p">,</span> <span class="n">simulation_dir</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">control_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">,</span> <span class="s1">'control'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">,</span>
<span class="s1">'parameters'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">,</span> <span class="s1">'data'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">control_path</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters_path</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data_path</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">has_run</span> <span class="o">=</span> <span class="kc">False</span>
<div class="viewcode-block" id="Simulation.from_data"><a class="viewcode-back" href="../../api.html#prms_python.Simulation.from_data">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_data</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">parameters</span><span class="p">,</span> <span class="n">control_path</span><span class="p">,</span> <span class="n">simulation_dir</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Create a ``Simulation`` from a :class:`Data` and :class:`Parameter` object,</span>
<span class="sd"> plus a path to the *control* file, and providing a ``simulation_dir`` </span>
<span class="sd"> where the simulation should be run.</span>
<span class="sd"> Arguments:</span>
<span class="sd"> data (:class:`Data`): ``Data`` object for simulation</span>
<span class="sd"> parameters (:class:`Parameters`): ``Parameters`` object for simulation </span>
<span class="sd"> control_path (str): path to control file</span>
<span class="sd"> simulation_dir (str): path to directory where simulations will be</span>
<span class="sd"> run and where input and output will be stored. If it exists it will </span>
<span class="sd"> be overwritten.</span>
<span class="sd"> Returns:</span>
<span class="sd"> :class:`Simulation` ready to be run using ``simulation_dir`` for</span>
<span class="sd"> inputs and outputs</span>
<span class="sd"> Example:</span>
<span class="sd"> >>> d = Data('path_to_data_file')</span>
<span class="sd"> >>> p = Parameters('path_to_parameters_file')</span>
<span class="sd"> >>> c = 'path_to_control_file'</span>
<span class="sd"> >>> sim_dir = 'path_to_create_simulation'</span>
<span class="sd"> >>> sim = Simulation.from_data(d, p, c, sim_dir)</span>
<span class="sd"> >>> sim.run()</span>
<span class="sd"> Raises:</span>
<span class="sd"> TypeError: if ``data`` and ``parameters`` arguments are not of type</span>
<span class="sd"> :class:`Data` and :class:`Parameters`</span>
<span class="sd"> '''</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">Data</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'data must be instance of Data'</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">parameters</span><span class="p">,</span> <span class="n">Parameters</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'parameters must be instance of Parameters, not '</span>\
<span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">parameters</span><span class="p">)))</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">):</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">simulation_dir</span><span class="p">)</span>
<span class="n">sim</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">()</span>
<span class="n">sim</span><span class="o">.</span><span class="n">simulation_dir</span> <span class="o">=</span> <span class="n">simulation_dir</span>
<span class="n">sd</span> <span class="o">=</span> <span class="n">simulation_dir</span>
<span class="n">data_path</span> <span class="o">=</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="s1">'data'</span><span class="p">)</span>
<span class="n">data</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">data_path</span><span class="p">)</span>
<span class="n">params_path</span> <span class="o">=</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="s1">'parameters'</span><span class="p">)</span>
<span class="n">parameters</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">params_path</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">control_path</span><span class="p">,</span> <span class="n">OPJ</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="s1">'control'</span><span class="p">))</span>
<span class="k">return</span> <span class="n">sim</span></div>
<div class="viewcode-block" id="Simulation.run"><a class="viewcode-back" href="../../api.html#prms_python.Simulation.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="n">prms_exec</span><span class="o">=</span><span class="s1">'prms'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Run a ``Simulation`` instance using PRMS input files from ``input_dir`` </span>
<span class="sd"> and copy to the ``Simulation`` file structure under ``simulation_dir`` if</span>
<span class="sd"> given, otherwise leave PRMS input output unstructured and in ``input_dir``</span>
<span class="sd"> This method runs a single PRMS simulation from a ``Simulation`` instance,</span>
<span class="sd"> waits until the process has completed and then transfers model input and </span>
<span class="sd"> output files to respective newly created directories. See example of the </span>
<span class="sd"> file structure that is created under different workflows of the ``run``</span>
<span class="sd"> method below.</span>
<span class="sd"> Keyword Arguments:</span>
<span class="sd"> prms_exec (str): name of PRMS executable on $PATH or path to executable</span>
<span class="sd"> </span>
<span class="sd"> Examples:</span>
<span class="sd"> If we create a :class:`Simulation` instance by only assigning the </span>
<span class="sd"> ``input_dir`` argument and call its ``run`` method the model will be</span>
<span class="sd"> run in the ``input_dir`` and all model input and output files will</span>
<span class="sd"> remain in ``input_dir``,</span>
<span class="sd"> </span>
<span class="sd"> >>> import os</span>
<span class="sd"> >>> input_dir = os.path.join(</span>
<span class="sd"> 'PRMS-Python',</span>
<span class="sd"> 'prms_python',</span>
<span class="sd"> 'models',</span>
<span class="sd"> 'lbcd'</span>
<span class="sd"> )</span>
<span class="sd"> >>> os.listdir(input_dir)</span>
<span class="sd"> ['data',</span>
<span class="sd"> 'data_3deg_upshift',</span>
<span class="sd"> 'parameters',</span>
<span class="sd"> 'parameters_adjusted',</span>
<span class="sd"> 'control']</span>
<span class="sd"> >>> sim = Simulation(input_dir)</span>
<span class="sd"> >>> sim.run()</span>
<span class="sd"> >>> os.listdir(input_dir) # all input and outputs in input_dir</span>
<span class="sd"> ['data',</span>
<span class="sd"> 'data_3deg_upshift',</span>
<span class="sd"> 'parameters',</span>
<span class="sd"> 'parameters_adjusted',</span>
<span class="sd"> 'control',</span>
<span class="sd"> 'statvar.dat',</span>
<span class="sd"> 'prms_ic.out',</span>
<span class="sd"> 'prms.out' ]</span>
<span class="sd"> </span>
<span class="sd"> Instead if we assigned a path for ``simulation_dir`` keyword </span>
<span class="sd"> argument and then called ``run``, i.e. </span>
<span class="sd"> </span>
<span class="sd"> >>> sim = Simulation(input_dir, 'path_simulation')</span>
<span class="sd"> >>> sim.run()</span>
<span class="sd"> </span>
<span class="sd"> the files structure for the PRMS simulation created by ``Simulation.run()`` </span>
<span class="sd"> would be::</span>
<span class="sd"> </span>
<span class="sd"> path_simulation </span>
<span class="sd"> ├── inputs</span>
<span class="sd"> │ ├── control</span>
<span class="sd"> │ ├── data</span>
<span class="sd"> │ └── parameters</span>
<span class="sd"> └── outputs</span>
<span class="sd"> ├── data_3deg_upshift</span>
<span class="sd"> ├── parameters_adjusted</span>
<span class="sd"> ├── prms_ic.out</span>
<span class="sd"> ├── prms.out</span>
<span class="sd"> └── statvar.dat</span>
<span class="sd"> Note:</span>
<span class="sd"> As shown in the last example, currently the ``Simulation.run`` routine only</span>
<span class="sd"> recognizes the *data*, *parameters*. and *control* file as PRMS inputs,</span>
<span class="sd"> all other files found in ``input_dir`` before *and* after normal completion </span>
<span class="sd"> of the PRMS simulation will be transferred to ``simulation_dir/outputs/``. </span>
<span class="sd"> """</span>
<span class="n">cwd</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_dir</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span>
<span class="n">prms_exec</span> <span class="o">+</span> <span class="s1">' control'</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span>
<span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span>
<span class="p">)</span>
<span class="n">prms_finished</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">checked_once</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">while</span> <span class="ow">not</span> <span class="n">prms_finished</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">checked_once</span><span class="p">:</span>
<span class="n">p</span><span class="o">.</span><span class="n">communicate</span><span class="p">()</span>
<span class="n">checked_once</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">poll</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">poll</span><span class="p">()</span>
<span class="n">prms_finished</span> <span class="o">=</span> <span class="n">poll</span> <span class="o">>=</span> <span class="mi">0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">has_run</span> <span class="o">=</span> <span class="kc">True</span>
<span class="c1"># avoid too many files open error</span>
<span class="n">p</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">p</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">simulation_dir</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="s1">'inputs'</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="s1">'outputs'</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="s1">'data'</span><span class="p">,</span> <span class="s1">'inputs'</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="s1">'parameters'</span><span class="p">,</span> <span class="s1">'inputs'</span><span class="p">)</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="s1">'control'</span><span class="p">,</span> <span class="s1">'inputs'</span><span class="p">)</span>
<span class="c1"># all remaining files are outputs</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s1">'*'</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">g</span><span class="p">):</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="s1">'outputs'</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">cwd</span><span class="p">)</span></div></div>
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