diff --git a/docs/build/doctrees/binary_c_parameters.doctree b/docs/build/doctrees/binary_c_parameters.doctree
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diff --git a/docs/build/doctrees/population_example.doctree b/docs/build/doctrees/population_example.doctree
new file mode 100644
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diff --git a/docs/build/doctrees/useful_funcs.doctree b/docs/build/doctrees/useful_funcs.doctree
index 63a62a9c6af39e9c77b2d4b2f399694c15cba313..2cbfcec94ca9ce3fc83e173d4c6706d5c9edfe15 100644
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diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
index 3c9900c225d9c690e37b1ed9d2f6e5590c46de8e..0fef865eb8bf85eda5e675e928067129120fc8c0 100644
--- a/docs/build/html/.buildinfo
+++ b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6900461cb9d4573b7ee9d2e352bd1545
+config: f4e8f1e1d66809b0bdafd78f415a24e8
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
index 59553cab465cb591625af82bb290feeba5589507..4e934288308f3ab578cdd2f5cbba552e50231364 100644
--- a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
@@ -597,7 +597,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html b/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
index 99427b225e38d67586ed779962e41ed04a0a4b51..57b7d0e499c418c39e1a1c007f0d729e5ba17542 100644
--- a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
@@ -1084,7 +1084,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/functions.html b/docs/build/html/_modules/binarycpython/utils/functions.html
index 4e74cc1d57df072224212f9d6cfd5375983d42ce..3f083c3256a1ccd9c95b561e397cf9ed5181bc85 100644
--- a/docs/build/html/_modules/binarycpython/utils/functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/functions.html
@@ -1527,7 +1527,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/grid.html b/docs/build/html/_modules/binarycpython/utils/grid.html
index 9a78a9eaf317b52482b30178766274bb1e40d43a..22e2ce4ca80215568065f514fce46637181c4ad8 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid.html
@@ -174,6 +174,7 @@
<span class="sd"> - TODO: uncomment and implement the HPC functionality</span>
<span class="sd"> - TODO: think of a clean and nice way to unload and remove the custom_logging_info library from memory (and from disk)</span>
<span class="sd"> - TODO: think of a nice way to remove the loaded grid_code/ generator from memory. </span>
+<span class="sd"> - TODO: Create a designated dict for results</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">os</span>
@@ -264,6 +265,12 @@
<span class="c1">#</span>
<span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="c1"># Create location to store results. Users should write to this dictionary. </span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># Create location where ensemble results are written to</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span> <span class="o">=</span> <span class="p">{}</span>
+
<span class="c1">###################################################</span>
<span class="c1"># Argument functions</span>
<span class="c1">###################################################</span>
@@ -871,8 +878,9 @@
<span class="c1"># Log and print some information</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Population-</span><span class="si">{}</span><span class="s2"> finished! It took a total of </span><span class="si">{}</span><span class="s2">s to run </span><span class="si">{}</span><span class="s2"> systems on </span><span class="si">{}</span><span class="s2"> cores"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"Population-</span><span class="si">{}</span><span class="s2"> finished! The total probability was: </span><span class="si">{}</span><span class="s2">. It took a total of </span><span class="si">{}</span><span class="s2">s to run </span><span class="si">{}</span><span class="s2"> systems on </span><span class="si">{}</span><span class="s2"> cores"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_population_id"</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_probtot"</span><span class="p">],</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_end_time_evolution"</span><span class="p">]</span>
<span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_start_time_evolution"</span><span class="p">],</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_total_starcount"</span><span class="p">],</span>
@@ -973,10 +981,8 @@
<span class="n">combined_output_dict</span> <span class="o">=</span> <span class="n">merge_dicts</span><span class="p">(</span><span class="n">combined_output_dict</span><span class="p">,</span> <span class="n">output_dict</span><span class="p">)</span>
<span class="c1"># Put the values back as object properties</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"results"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"results"</span><span class="p">]</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"ensemble_results"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span>
- <span class="s2">"ensemble_results"</span>
- <span class="p">]</span> <span class="c1"># Ensemble results are also passed as output from that dictionary</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"results"</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s1">'ensemble_results'</span><span class="p">]</span> <span class="c1"># Ensemble results are also passed as output from that dictionary</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_prob"</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined_output_dict</span><span class="p">[</span><span class="s2">"_failed_prob"</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_systems_error_codes"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
@@ -995,6 +1001,7 @@
<span class="sd"> """</span>
<span class="n">binary_cmdline_string</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_return_argline</span><span class="p">(</span><span class="n">full_system_dict</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">binary_cmdline_string</span><span class="p">)</span>
<span class="n">persistent_data_memaddr</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -1036,17 +1043,27 @@
<span class="n">ID</span> <span class="c1"># Store the ID as a object property again, lets see if that works.</span>
<span class="p">)</span>
+ <span class="c1"># lets try out making stores for all the grids:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">]</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_store_memaddr</span><span class="p">()</span>
+
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> started at </span><span class="si">{}</span><span class="s2">.</span><span class="se">\t</span><span class="s2">Using store memaddr </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">,</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">isoformat</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">0</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Set the ensemble memaddr</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># set persistent data memaddr if necessary.</span>
<span class="n">persistent_data_memaddr</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_persistent_data_memaddr</span><span class="p">()</span>
<span class="p">)</span>
+
<span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span> <span class="o">=</span> <span class="p">{</span>
<span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">:</span> <span class="n">persistent_data_memaddr</span>
<span class="p">}</span>
- <span class="c1"># lets try out making stores for all the grids:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">]</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_store_memaddr</span><span class="p">()</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"</span><span class="se">\t</span><span class="s2">Using persistent_data memaddr: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">persistent_data_memaddr</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">0</span>
+ <span class="p">)</span>
<span class="c1"># apparently we have to re-load this for every process, otherwise NameErrors arise (seems like a bug but I'm not sure)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_load_grid_function</span><span class="p">()</span>
@@ -1066,11 +1083,9 @@
<span class="mi">0</span> <span class="c1"># counter for the actual amt of systems this thread ran</span>
<span class="p">)</span>
- <span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> started at </span><span class="si">{}</span><span class="s2">. Using store memaddr </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">,</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">isoformat</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">0</span>
- <span class="p">)</span>
+ <span class="n">round_number_mod</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># rotating modulo</span>
- <span class="n">round_number_mod</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">total_time_calling_binary_c</span> <span class="o">=</span> <span class="mi">0</span>
<span class="c1"># Go over the generator</span>
<span class="k">while</span> <span class="n">running</span><span class="p">:</span>
@@ -1081,7 +1096,7 @@
<span class="n">system</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">generator</span><span class="p">)</span>
<span class="c1"># Check if the ID is the correct one for this process</span>
- <span class="k">if</span> <span class="p">(</span><span class="n">localcounter</span> <span class="o">+</span> <span class="p">(</span><span class="n">ID</span><span class="o">+</span><span class="n">round_number_mod</span><span class="p">))</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">localcounter</span> <span class="o">+</span> <span class="p">(</span><span class="n">ID</span> <span class="o">+</span> <span class="n">round_number_mod</span><span class="p">))</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># Combine that with the other settings</span>
<span class="n">full_system_dict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
@@ -1108,6 +1123,8 @@
<span class="n">end_runtime_binary_c</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+ <span class="n">total_time_calling_binary_c</span> <span class="o">+=</span> <span class="n">end_runtime_binary_c</span> <span class="o">-</span> <span class="n">start_runtime_binary_c</span> <span class="c1"># keep track of total binary_c call time</span>
+
<span class="c1"># Debug line: logging all the lines</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s1">'log_runtime_systems'</span><span class="p">]</span><span class="o">==</span><span class="mi">1</span><span class="p">:</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</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="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"tmp_dir"</span><span class="p">],</span> <span class="s2">"thread_</span><span class="si">{}</span><span class="s2">_runtime_systems.txt"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">)),</span> <span class="s1">'a+'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
@@ -1123,7 +1140,7 @@
<span class="k">if</span> <span class="p">(</span><span class="n">localcounter</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span><span class="o">%</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"amt_cores"</span><span class="p">]</span><span class="o">==</span><span class="mi">0</span><span class="p">:</span>
<span class="n">round_number_mod</span> <span class="o">+=</span> <span class="mi">1</span>
- <span class="c1"># round_number_mod = (localcounter+1)%self.grid_options["amt_cores"]</span>
+
<span class="c1"># print("thread {} round_nr_mod {}. localcounter {}".format(ID, round_number_mod, localcounter))</span>
<span class="c1"># Has to be here because this one is used for the (localcounter+ID) % (self..)</span>
@@ -1132,15 +1149,27 @@
<span class="c1"># Handle ensemble output: is ensemble==1, then either directly write that data to a file, or combine everything into 1 file.</span>
<span class="n">ensemble_json</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Make sure it exists already</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2">: is freeing ensemble output (using persisten_data memaddr </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">]),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">2</span>
+ <span class="p">)</span>
+
<span class="n">ensemble_raw_output</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">free_persistent_data_memaddr_and_return_json_output</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">]</span>
<span class="p">)</span>
<span class="p">)</span>
+ <span class="k">if</span> <span class="n">ensemble_raw_output</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2">: Warning! Ensemble output is empty. "</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">2</span>
+ <span class="p">)</span>
<span class="c1">#</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"combine_ensemble_with_thread_joining"</span><span class="p">]</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>
- <span class="n">ensemble_json</span> <span class="o">=</span> <span class="n">extract_ensemble_json_from_string</span><span class="p">(</span>
+ <span class="n">verbose_print</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2">: Extracting ensemble info from raw string"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ID</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">2</span>
+ <span class="p">)</span>
+
+ <span class="n">ensemble_json</span><span class="p">[</span><span class="s1">'ensemble'</span><span class="p">]</span> <span class="o">=</span> <span class="n">extract_ensemble_json_from_string</span><span class="p">(</span>
<span class="n">ensemble_raw_output</span>
<span class="p">)</span> <span class="c1"># Load this into a dict so that we can combine it later</span>
@@ -1152,23 +1181,24 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_population_id"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span>
<span class="p">),</span>
<span class="p">)</span>
- <span class="nb">print</span><span class="p">(</span>
- <span class="s2">"Thread </span><span class="si">{}</span><span class="s2">: Chosen to output the ensemble results directly to file: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">,</span> <span class="n">output_file</span>
- <span class="p">)</span>
- <span class="p">)</span>
<span class="c1"># Write to file</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">ensemble_raw_output</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span>
+ <span class="s2">"Thread </span><span class="si">{}</span><span class="s2">: Wrote ensemble results directly to file: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">process_ID</span><span class="p">,</span> <span class="n">output_file</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
+
<span class="c1"># free store mem:</span>
<span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">free_store_memaddr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_store_memaddr"</span><span class="p">])</span>
<span class="c1"># Return a set of results and errors</span>
<span class="n">output_dict</span> <span class="o">=</span> <span class="p">{</span>
- <span class="s2">"results"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"results"</span><span class="p">],</span>
+ <span class="s2">"results"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_results</span><span class="p">,</span>
<span class="s2">"ensemble_results"</span><span class="p">:</span> <span class="n">ensemble_json</span><span class="p">,</span>
<span class="s2">"_failed_count"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">],</span>
<span class="s2">"_failed_prob"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_prob"</span><span class="p">],</span>
@@ -1184,11 +1214,12 @@
<span class="n">end_process_time</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> finished:</span><span class="se">\n\t</span><span class="s2">generator started at </span><span class="si">{}</span><span class="s2">, done at </span><span class="si">{}</span><span class="s2"> (total: </span><span class="si">{}</span><span class="s2">s).</span><span class="se">\n\t</span><span class="s2">Ran </span><span class="si">{}</span><span class="s2"> systems with a total probability of </span><span class="si">{}</span><span class="s2">.</span><span class="se">\n\t</span><span class="s2">This thread had </span><span class="si">{}</span><span class="s2"> failing systems with a total probability of </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"Process </span><span class="si">{}</span><span class="s2"> finished:</span><span class="se">\n\t</span><span class="s2">generator started at </span><span class="si">{}</span><span class="s2">, done at </span><span class="si">{}</span><span class="s2"> (total: </span><span class="si">{}</span><span class="s2">s of which </span><span class="si">{}</span><span class="s2">s interfacing with binary_c).</span><span class="se">\n\t</span><span class="s2">Ran </span><span class="si">{}</span><span class="s2"> systems with a total probability of </span><span class="si">{}</span><span class="s2">.</span><span class="se">\n\t</span><span class="s2">This thread had </span><span class="si">{}</span><span class="s2"> failing systems with a total probability of </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">ID</span><span class="p">,</span>
<span class="n">start_process_time</span><span class="o">.</span><span class="n">isoformat</span><span class="p">(),</span>
<span class="n">end_process_time</span><span class="o">.</span><span class="n">isoformat</span><span class="p">(),</span>
<span class="p">(</span><span class="n">end_process_time</span><span class="o">-</span><span class="n">start_process_time</span><span class="p">)</span><span class="o">.</span><span class="n">total_seconds</span><span class="p">(),</span>
+ <span class="n">total_time_calling_binary_c</span><span class="p">,</span>
<span class="n">number_of_systems_run</span><span class="p">,</span>
<span class="n">probability_of_systems_run</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_failed_count"</span><span class="p">],</span>
@@ -1271,7 +1302,7 @@
<span class="c1">### ensemble: make some checks for this</span>
<span class="c1">## check the settings and set all the warnings.</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">[</span><span class="s2">"ensemble_defer"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble_defer"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Error, if you want to run an ensemble in a population, the output needs to be deferred. Please set 'ensemble_defer' to 1"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
@@ -1279,31 +1310,22 @@
<span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"ensemble_output_name"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span>
+ <span class="p">[</span><span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"ensemble_filter_"</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">]</span>
+ <span class="p">):</span>
<span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Error: if you want to run an ensemble in a population, please set set 'ensemble_output_name'. It will be combined with 'data_dir' to write the output of the ensembles to"</span><span class="p">,</span>
+ <span class="s2">"Warning: Running the ensemble without any filter requires alot of available RAM"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
<span class="mi">0</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">raise</span> <span class="ne">ValueError</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span>
- <span class="p">[</span><span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"ensemble_filter_"</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">]</span>
- <span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble_filters_off"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Warning: Running the ensemble without any filter requires alot of available RAM"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
<span class="mi">0</span><span class="p">,</span>
<span class="p">)</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble_filters_off"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">[</span><span class="s2">"ensemble_filters_off"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">verbose_print</span><span class="p">(</span>
- <span class="s2">"Warning: Running the ensemble without any filter requires alot of available RAM"</span><span class="p">,</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
- <span class="mi">0</span><span class="p">,</span>
- <span class="p">)</span>
-
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"combine_ensemble_with_thread_joining"</span><span class="p">]</span> <span class="o">==</span> <span class="kc">False</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"data_dir"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="n">verbose_print</span><span class="p">(</span>
@@ -1311,6 +1333,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
<span class="mi">0</span><span class="p">,</span>
<span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span>
<span class="c1"># Check which type of population generation</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"evolution_type"</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"grid"</span><span class="p">:</span>
@@ -2530,7 +2553,7 @@
<span class="c1">## check the settings:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">[</span><span class="s2">"ensemble"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="p">[</span><span class="s2">"ensemble_defer"</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">bse_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ensemble_defer"</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">verbose_print</span><span class="p">(</span>
<span class="s2">"Error, if you want to run an ensemble in a population, the output needs to be deferred"</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span>
@@ -2801,7 +2824,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html b/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
index f812032ac62baafb6ad6c0ed6e71b0e52a48421b..22629f991899b712cf6771625fe6db1273d928a8 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
@@ -786,7 +786,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/hpc_functions.html b/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
index 0d35b38e58a165917fbeab56e0a5917b52602287..24338e44ea77f361e3e82b567f41d1808bd0f93c 100644
--- a/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
@@ -315,7 +315,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/plot_functions.html b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
index bf1fc894bf9cc255c3529a9eb7f303b39332dbe6..acfd39c1545acf75e6282c54bd8822bd16ac93e3 100644
--- a/docs/build/html/_modules/binarycpython/utils/plot_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
@@ -792,7 +792,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
index 1d2d038dc9c39bd6ca9e15c9315dda4896a5da59..fb0db0ee1323d8e88e7a47ddcaab1432a356dfd2 100644
--- a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
+++ b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
@@ -271,7 +271,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
index 5f3c4b1a426f8e1c10215f302c7a239833de6104..87fe236fcbaca9f967067e6f03644d11a4c7c662 100644
--- a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
@@ -191,7 +191,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
index 225645e2b3b040f57b45cf10f9bccdfce0a4c4d4..31738128bd2382cd7026c887d8b4c18fdb9b771c 100644
--- a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
+++ b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
@@ -169,12 +169,76 @@
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">re</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">create_arg_string</span>
+
<span class="n">AURSUN</span> <span class="o">=</span> <span class="mf">2.150445198804013386961742071435e02</span>
<span class="n">YEARDY</span> <span class="o">=</span> <span class="mf">3.651995478818308811241877265275e02</span>
+
+
+<div class="viewcode-block" id="minimum_period_for_RLOF"><a class="viewcode-back" href="../../../useful_funcs.html#binarycpython.utils.useful_funcs.minimum_period_for_RLOF">[docs]</a><span class="k">def</span> <span class="nf">minimum_period_for_RLOF</span><span class="p">(</span><span class="n">M1</span><span class="p">,</span> <span class="n">M2</span><span class="p">,</span> <span class="n">metallicity</span><span class="p">,</span> <span class="n">store_memaddr</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</span>
+
+<span class="sd"> Handles the output and returns the minimum orbital period at which RLOF just does not occur at zams</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> M1: Primary mass in solar mass</span>
+<span class="sd"> M2: Secondary mass in solar mass</span>
+<span class="sd"> metallicity: metallicity</span>
+<span class="sd"> store_memaddr (optional): store memory adress</span>
+<span class="sd"> Returns:</span>
+<span class="sd"> minimum orbital_period that just does not cause a RLOF at ZAMS</span>
+
+<span class="sd"> """</span>
+
+ <span class="n">bse_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="n">M1</span><span class="p">,</span> <span class="s2">"M_2"</span><span class="p">:</span> <span class="n">M2</span><span class="p">,</span> <span class="s2">"metallicity"</span><span class="p">:</span> <span class="n">metallicity</span><span class="p">,</span> <span class="s2">"minimum_orbital_period_for_instant_RLOF"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s2">"minimum_separation_for_instant_RLOF"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+
+ <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c "</span> <span class="o">+</span> <span class="n">create_arg_string</span><span class="p">(</span><span class="n">bse_dict</span><span class="p">)</span>
+
+ <span class="n">output</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_minimum_orbit_for_RLOF</span><span class="p">(</span><span class="n">argstring</span><span class="p">,</span> <span class="n">store_memaddr</span><span class="p">)</span>
+
+ <span class="n">minimum_period</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="s1">'MINIMUM PERIOD (.*)'</span><span class="p">,</span> <span class="n">output</span><span class="p">)</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
+
+ <span class="k">return</span> <span class="n">minimum_period</span></div>
+
+<span class="c1"># print(minimum_period_for_RLOF(10, 5, 0.02))</span>
+<span class="c1"># print(minimum_period_for_RLOF(10, 2, 0.02))</span>
+
+<div class="viewcode-block" id="minimum_separation_for_RLOF"><a class="viewcode-back" href="../../../useful_funcs.html#binarycpython.utils.useful_funcs.minimum_separation_for_RLOF">[docs]</a><span class="k">def</span> <span class="nf">minimum_separation_for_RLOF</span><span class="p">(</span><span class="n">M1</span><span class="p">,</span> <span class="n">M2</span><span class="p">,</span> <span class="n">metallicity</span><span class="p">,</span> <span class="n">store_memaddr</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</span>
+
+<span class="sd"> Handles the output and returns the minimum separation at which RLOF just does not occur at ZAMS</span>
+
+<span class="sd"> Args:</span>
+<span class="sd"> M1: Primary mass in solar mass</span>
+<span class="sd"> M2: Secondary mass in solar mass</span>
+<span class="sd"> metallicity: metallicity</span>
+<span class="sd"> store_memaddr (optional): store memory adress</span>
+<span class="sd"> Returns:</span>
+<span class="sd"> minimum separation that just does not cause a RLOF at ZAMS</span>
+
+<span class="sd"> """</span>
+
+ <span class="n">bse_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="n">M1</span><span class="p">,</span> <span class="s2">"M_2"</span><span class="p">:</span> <span class="n">M2</span><span class="p">,</span> <span class="s2">"metallicity"</span><span class="p">:</span> <span class="n">metallicity</span><span class="p">,</span> <span class="s2">"minimum_orbital_period_for_instant_RLOF"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s2">"minimum_separation_for_instant_RLOF"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+
+ <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c "</span> <span class="o">+</span> <span class="n">create_arg_string</span><span class="p">(</span><span class="n">bse_dict</span><span class="p">)</span>
+
+ <span class="n">output</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_minimum_orbit_for_RLOF</span><span class="p">(</span><span class="n">argstring</span><span class="p">,</span> <span class="n">store_memaddr</span><span class="p">)</span>
+
+ <span class="n">minimum_separation</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="s1">'MINIMUM SEPARATION (.*)'</span><span class="p">,</span> <span class="n">output</span><span class="p">)</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
+
+ <span class="k">return</span> <span class="n">minimum_separation</span></div>
+
+<span class="c1"># print(minimum_separation_for_RLOF(0.08, 0.08, 0.00002))</span>
+<span class="c1"># print(minimum_separation_for_RLOF(10, 2, 0.02))</span>
+
<div class="viewcode-block" id="calc_period_from_sep"><a class="viewcode-back" href="../../../useful_funcs.html#binarycpython.utils.useful_funcs.calc_period_from_sep">[docs]</a><span class="k">def</span> <span class="nf">calc_period_from_sep</span><span class="p">(</span>
<span class="n">M1</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">M2</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span> <span class="n">sep</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span>
<span class="p">)</span> <span class="o">-></span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
@@ -420,7 +484,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index af315ee0873cc4d1f11110798fdc42ffefe966f2..a789af0843b21968bf2fb91f5c7fea80bd15f39f 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -172,7 +172,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/_sources/binary_c_parameters.rst.txt b/docs/build/html/_sources/binary_c_parameters.rst.txt
index 56de8181e1e5404f7c0e5b2c6ec273f278045544..4fe498e19b7be769db2dba6961d758d454815b8e 100644
--- a/docs/build/html/_sources/binary_c_parameters.rst.txt
+++ b/docs/build/html/_sources/binary_c_parameters.rst.txt
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: branch_david **binary_c git revision**: 5479:20210111:463f148ec **Built on**: Jan 28 2021 20:10:20
+ **binary_c git branch**: branch_david **binary_c git revision**: 5542:20210311:f3401ead4 **Built on**: Mar 22 2021 12:07:51
Section: stars
diff --git a/docs/build/html/_sources/examples.rst.txt b/docs/build/html/_sources/examples.rst.txt
index 281bfaa659e3e775f75243f608c963bde50b7049..ab58720d9b5a670eb13d8468daa687e72ab86e52 100644
--- a/docs/build/html/_sources/examples.rst.txt
+++ b/docs/build/html/_sources/examples.rst.txt
@@ -5,4 +5,5 @@ This chapter contains the source code of example scripts which show the way of u
.. toctree::
:hidden:
- general_examples
\ No newline at end of file
+ general_examples
+ population_example
\ No newline at end of file
diff --git a/docs/build/html/_sources/general_examples.rst.txt b/docs/build/html/_sources/general_examples.rst.txt
index 4a070790a2c7ef4fa05a5c5d76026750ff9bfae4..8509de5b72faf82bc026ed2b785b2d72b4ccc702 100644
--- a/docs/build/html/_sources/general_examples.rst.txt
+++ b/docs/build/html/_sources/general_examples.rst.txt
@@ -3,5 +3,5 @@ Examples
The source code of the general examples.
.. literalinclude:: ../../examples/examples.py
- :language: ruby
+ :language: python
:linenos:
\ No newline at end of file
diff --git a/docs/build/html/_sources/population_example.rst.txt b/docs/build/html/_sources/population_example.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..192372d019133d818c4ba6ad207c5dc09989de62
--- /dev/null
+++ b/docs/build/html/_sources/population_example.rst.txt
@@ -0,0 +1,7 @@
+Example of population script
+============================
+The source code of a script to run a population of stars.
+
+.. literalinclude:: ../../examples/example_population.py
+ :language: python
+ :linenos:
\ No newline at end of file
diff --git a/docs/build/html/binary_c_parameters.html b/docs/build/html/binary_c_parameters.html
index 99a345af06ce15fe613878668bb7d17ed7636987..fadee75952a70b28799dfa0b17b5cf3f5f0e92a7 100644
--- a/docs/build/html/binary_c_parameters.html
+++ b/docs/build/html/binary_c_parameters.html
@@ -37,7 +37,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Population grid code options" href="grid_options_descriptions.html" />
- <link rel="prev" title="Examples" href="general_examples.html" />
+ <link rel="prev" title="Example of population script" href="population_example.html" />
</head>
<body class="wy-body-for-nav">
@@ -168,7 +168,7 @@
<h1>Binary_c parameters<a class="headerlink" href="#binary-c-parameters" title="Permalink to this headline">¶</a></h1>
<p>The following chapter contains all the parameters that the current version of binary_c can handle, along with their descriptions and other properties.</p>
<dl class="simple">
-<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: branch_david <strong>binary_c git revision</strong>: 5479:20210111:463f148ec <strong>Built on</strong>: Jan 28 2021 20:10:20</p>
+<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: branch_david <strong>binary_c git revision</strong>: 5542:20210311:f3401ead4 <strong>Built on</strong>: Mar 22 2021 12:07:51</p>
</dd>
</dl>
<div class="section" id="section-stars">
@@ -2991,7 +2991,7 @@
<a href="grid_options_descriptions.html" class="btn btn-neutral float-right" title="Population grid code options" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="general_examples.html" class="btn btn-neutral float-left" title="Examples" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="population_example.html" class="btn btn-neutral float-left" title="Example of population script" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
@@ -3001,7 +3001,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/custom_logging_functions.html b/docs/build/html/custom_logging_functions.html
index 53417465e84684402abed0de6593660837bb75fa..24fb7ce334b87a930af40a6f711c21984b294e47 100644
--- a/docs/build/html/custom_logging_functions.html
+++ b/docs/build/html/custom_logging_functions.html
@@ -378,7 +378,7 @@ I recommend using this in function in combination with a function that generates
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/distribution_functions.html b/docs/build/html/distribution_functions.html
index d4b19ea9955384606852a0ecf28fbf863d854e3c..24ab3090a372707eb5a272e075eed19bc3f6482a 100644
--- a/docs/build/html/distribution_functions.html
+++ b/docs/build/html/distribution_functions.html
@@ -754,7 +754,7 @@ and is be given by dp/dlogP ~ (logP)^p for all other binary configurations (defa
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/examples.html b/docs/build/html/examples.html
index 0e441813cfc862c84b2b9a11f606515b200d7300..d94fdbd349546254cb6e17e9e8e0263c1eae4db4 100644
--- a/docs/build/html/examples.html
+++ b/docs/build/html/examples.html
@@ -88,6 +88,7 @@
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="general_examples.html">Examples</a></li>
+<li class="toctree-l2"><a class="reference internal" href="population_example.html">Example of population script</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="binary_c_parameters.html">Binary_c parameters</a></li>
@@ -185,7 +186,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/functions.html b/docs/build/html/functions.html
index e836d5b3d8b15003855f57e5e1bf716cc1063825..0b8698f3ef325ed40849dde447ef053806177b72 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -709,7 +709,7 @@ Writes the results to a .rst file that can be included in the docs.</p>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/general_examples.html b/docs/build/html/general_examples.html
index 204c52761359e88622ad8c52c2afafd8ce944a34..82aecdc2b570ec7d37f37139303bbb9ae38d0386 100644
--- a/docs/build/html/general_examples.html
+++ b/docs/build/html/general_examples.html
@@ -36,7 +36,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Binary_c parameters" href="binary_c_parameters.html" />
+ <link rel="next" title="Example of population script" href="population_example.html" />
<link rel="prev" title="Examples" href="examples.html" />
</head>
@@ -88,6 +88,7 @@
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="examples.html">Examples</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Examples</a></li>
+<li class="toctree-l2"><a class="reference internal" href="population_example.html">Example of population script</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="binary_c_parameters.html">Binary_c parameters</a></li>
@@ -162,7 +163,7 @@
<div class="section" id="examples">
<h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
<p>The source code of the general examples.</p>
-<div class="highlight-ruby notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<div class="highlight-python notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
4
@@ -391,43 +392,43 @@
227
228
229</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/python3</span>
-<span class="n">import</span> <span class="n">os</span>
-<span class="n">import</span> <span class="n">sys</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
-<span class="n">from</span> <span class="n">binarycpython</span> <span class="n">import</span> <span class="n">_binary_c_bindings</span>
+<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
-<span class="n">from</span> <span class="n">binarycpython</span><span class="o">.</span><span class="n">utils</span><span class="o">.</span><span class="n">functions</span> <span class="n">import</span> <span class="n">example_parse_output</span>
-<span class="n">from</span> <span class="n">binarycpython</span><span class="o">.</span><span class="n">utils</span><span class="o">.</span><span class="n">custom_logging_functions</span> <span class="n">import</span> <span class="p">(</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">example_parse_output</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">autogen_C_logging_code</span><span class="p">,</span>
<span class="n">binary_c_log_code</span><span class="p">,</span>
<span class="n">create_and_load_logging_function</span><span class="p">,</span>
<span class="p">)</span>
-<span class="n">from</span> <span class="n">binarycpython</span><span class="o">.</span><span class="n">utils</span><span class="o">.</span><span class="n">run_system_wrapper</span> <span class="n">import</span> <span class="n">run_system</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.run_system_wrapper</span> <span class="kn">import</span> <span class="n">run_system</span>
-<span class="s2">"""</span>
-<span class="s2">Very basic scripts to run a binary system and print the output.</span>
+<span class="sd">"""</span>
+<span class="sd">Very basic scripts to run a binary system and print the output.</span>
-<span class="s2">Use these as inspiration/base.</span>
-<span class="s2">"""</span>
+<span class="sd">Use these as inspiration/base.</span>
+<span class="sd">"""</span>
<span class="k">def</span> <span class="nf">run_example_binary</span><span class="p">():</span>
- <span class="s2">"""</span>
-<span class="s2"> Function to run a binary system. Very basic approach which directly adresses the run_system(..) python-c wrapper function.</span>
-<span class="s2"> """</span>
+ <span class="sd">"""</span>
+<span class="sd"> Function to run a binary system. Very basic approach which directly adresses the run_system(..) python-c wrapper function.</span>
+<span class="sd"> """</span>
- <span class="n">m1</span> <span class="o">=</span> <span class="mi">15</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># Msun</span>
- <span class="n">m2</span> <span class="o">=</span> <span class="mi">14</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># Msun</span>
+ <span class="n">m1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="mf">14.0</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># 0 = ignored, use period</span>
- <span class="n">orbital_period</span> <span class="o">=</span> <span class="mi">4530</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># days</span>
- <span class="n">eccentricity</span> <span class="o">=</span> <span class="mi">0</span><span class="o">.</span><span class="mi">0</span>
- <span class="n">metallicity</span> <span class="o">=</span> <span class="mi">0</span><span class="o">.</span><span class="mo">02</span>
+ <span class="n">orbital_period</span> <span class="o">=</span> <span class="mf">4530.0</span> <span class="c1"># days</span>
+ <span class="n">eccentricity</span> <span class="o">=</span> <span class="mf">0.0</span>
+ <span class="n">metallicity</span> <span class="o">=</span> <span class="mf">0.02</span>
<span class="n">max_evolution_time</span> <span class="o">=</span> <span class="mi">15000</span> <span class="c1"># Myr. You need to include this argument.</span>
<span class="c1">#</span>
- <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c M_1 {m1} M_2 {m2} separation {separation} orbital_period {orbital_period} \</span>
-<span class="s2"> eccentricity {eccentricity} metallicity {metallicity} \</span>
-<span class="s2"> max_evolution_time {max_evolution_time}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c M_1 </span><span class="si">{m1}</span><span class="s2"> M_2 </span><span class="si">{m2}</span><span class="s2"> separation </span><span class="si">{separation}</span><span class="s2"> orbital_period </span><span class="si">{orbital_period}</span><span class="s2"> </span><span class="se">\</span>
+<span class="s2"> eccentricity </span><span class="si">{eccentricity}</span><span class="s2"> metallicity </span><span class="si">{metallicity}</span><span class="s2"> </span><span class="se">\</span>
+<span class="s2"> max_evolution_time </span><span class="si">{max_evolution_time}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">m1</span><span class="o">=</span><span class="n">m1</span><span class="p">,</span>
<span class="n">m2</span><span class="o">=</span><span class="n">m2</span><span class="p">,</span>
<span class="n">separation</span><span class="o">=</span><span class="n">separation</span><span class="p">,</span>
@@ -444,24 +445,24 @@
<span class="k">def</span> <span class="nf">run_example_binary_with_run_system</span><span class="p">():</span>
- <span class="s2">"""</span>
-<span class="s2"> This function serves as an example on the function run_system and parse_output.</span>
-<span class="s2"> There is more functionality with this method and several tasks are done behind the scene.</span>
+ <span class="sd">"""</span>
+<span class="sd"> This function serves as an example on the function run_system and parse_output.</span>
+<span class="sd"> There is more functionality with this method and several tasks are done behind the scene.</span>
-<span class="s2"> Requires pandas, numpy to run.</span>
+<span class="sd"> Requires pandas, numpy to run.</span>
-<span class="s2"> run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background</span>
-<span class="s2"> parse_output: Takes the raw output of binary_c and selects those lines that start with the given header.</span>
-<span class="s2"> Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header</span>
+<span class="sd"> run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background</span>
+<span class="sd"> parse_output: Takes the raw output of binary_c and selects those lines that start with the given header.</span>
+<span class="sd"> Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header</span>
-<span class="s2"> The parsing of the output only works correctly if either all of the values are described inline like `mass=<number>' or none of them are.</span>
-<span class="s2"> """</span>
+<span class="sd"> The parsing of the output only works correctly if either all of the values are described inline like `mass=<number>' or none of them are.</span>
+<span class="sd"> """</span>
- <span class="n">import</span> <span class="n">pandas</span> <span class="n">as</span> <span class="n">pd</span>
- <span class="n">import</span> <span class="n">numpy</span> <span class="n">as</span> <span class="n">np</span>
+ <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+ <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="c1"># Run system. all arguments can be given as optional arguments.</span>
- <span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="no">M_1</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="no">M_2</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">separation</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">orbital_period</span><span class="o">=</span><span class="mi">100000000000</span><span class="p">)</span>
+ <span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">M_2</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">separation</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">orbital_period</span><span class="o">=</span><span class="mi">100000000000</span><span class="p">)</span>
<span class="c1"># print(output)</span>
@@ -490,7 +491,7 @@
<span class="c1"># This example has column headers which are numbered, but we can override that with custom headers.</span>
<span class="n">df2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">result_example_header_2</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
- <span class="n">df2</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="o">[</span><span class="s2">"time"</span><span class="p">,</span> <span class="s2">"mass_1"</span><span class="p">,</span> <span class="s2">"mass_2"</span><span class="p">,</span> <span class="s2">"st1"</span><span class="p">,</span> <span class="s2">"st2"</span><span class="p">,</span> <span class="s2">"sep"</span><span class="p">,</span> <span class="s2">"ecc"</span><span class="o">]</span>
+ <span class="n">df2</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"time"</span><span class="p">,</span> <span class="s2">"mass_1"</span><span class="p">,</span> <span class="s2">"mass_2"</span><span class="p">,</span> <span class="s2">"st1"</span><span class="p">,</span> <span class="s2">"st2"</span><span class="p">,</span> <span class="s2">"sep"</span><span class="p">,</span> <span class="s2">"ecc"</span><span class="p">]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">df2</span><span class="p">)</span>
<span class="c1"># print(df)</span>
@@ -504,15 +505,15 @@
<span class="k">def</span> <span class="nf">run_example_custom_logging_autogenerated</span><span class="p">():</span>
- <span class="s2">"""</span>
-<span class="s2"> This is an example function for the autogeneration of logging codes that binary_c uses.</span>
-<span class="s2"> """</span>
+ <span class="sd">"""</span>
+<span class="sd"> This is an example function for the autogeneration of logging codes that binary_c uses.</span>
+<span class="sd"> """</span>
<span class="c1"># generate logging lines</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">autogen_C_logging_code</span><span class="p">(</span>
<span class="p">{</span>
- <span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span> <span class="o">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[0].mass"</span><span class="o">]</span><span class="p">,</span>
- <span class="s2">"my_sss2"</span><span class="p">:</span> <span class="o">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[1].mass"</span><span class="o">]</span><span class="p">,</span>
+ <span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span> <span class="p">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[0].mass"</span><span class="p">],</span>
+ <span class="s2">"my_sss2"</span><span class="p">:</span> <span class="p">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[1].mass"</span><span class="p">],</span>
<span class="p">}</span>
<span class="p">)</span>
@@ -525,14 +526,14 @@
<span class="p">)</span>
<span class="c1">#</span>
- <span class="n">m1</span> <span class="o">=</span> <span class="mi">15</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># Msun</span>
- <span class="n">m2</span> <span class="o">=</span> <span class="mi">14</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># Msun</span>
+ <span class="n">m1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="mf">14.0</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># 0 = ignored, use period</span>
- <span class="n">orbital_period</span> <span class="o">=</span> <span class="mi">4530</span><span class="o">.</span><span class="mi">0</span> <span class="c1"># days</span>
- <span class="n">eccentricity</span> <span class="o">=</span> <span class="mi">0</span><span class="o">.</span><span class="mi">0</span>
- <span class="n">metallicity</span> <span class="o">=</span> <span class="mi">0</span><span class="o">.</span><span class="mo">02</span>
+ <span class="n">orbital_period</span> <span class="o">=</span> <span class="mf">4530.0</span> <span class="c1"># days</span>
+ <span class="n">eccentricity</span> <span class="o">=</span> <span class="mf">0.0</span>
+ <span class="n">metallicity</span> <span class="o">=</span> <span class="mf">0.02</span>
<span class="n">max_evolution_time</span> <span class="o">=</span> <span class="mi">15000</span>
- <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">argstring</span> <span class="o">=</span> <span class="s2">"binary_c M_1 </span><span class="si">{0:g}</span><span class="s2"> M_2 </span><span class="si">{1:g}</span><span class="s2"> separation </span><span class="si">{2:g}</span><span class="s2"> orbital_period </span><span class="si">{3:g}</span><span class="s2"> eccentricity </span><span class="si">{4:g}</span><span class="s2"> metallicity </span><span class="si">{5:g}</span><span class="s2"> max_evolution_time </span><span class="si">{6:g}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">m1</span><span class="p">,</span>
<span class="n">m2</span><span class="p">,</span>
<span class="n">separation</span><span class="p">,</span>
@@ -551,33 +552,33 @@
<span class="k">def</span> <span class="nf">run_example_binary_with_custom_logging</span><span class="p">():</span>
- <span class="s2">"""</span>
-<span class="s2"> Function that will use a automatically generated piece of logging code. Compile it, load it</span>
-<span class="s2"> into memory and run a binary system. See run_system on how several things are done in the background here.</span>
-<span class="s2"> """</span>
+ <span class="sd">"""</span>
+<span class="sd"> Function that will use a automatically generated piece of logging code. Compile it, load it</span>
+<span class="sd"> into memory and run a binary system. See run_system on how several things are done in the background here.</span>
+<span class="sd"> """</span>
- <span class="n">import</span> <span class="n">pandas</span> <span class="n">as</span> <span class="n">pd</span>
- <span class="n">import</span> <span class="n">numpy</span> <span class="n">as</span> <span class="n">np</span>
+ <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+ <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="c1"># generate logging lines. Here you can choose whatever you want to have logged, and with what header</span>
<span class="c1"># this generates working print statements</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">autogen_C_logging_code</span><span class="p">(</span>
<span class="p">{</span>
- <span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span> <span class="o">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[0].mass"</span><span class="o">]</span><span class="p">,</span>
+ <span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span> <span class="p">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[0].mass"</span><span class="p">],</span>
<span class="p">}</span>
<span class="p">)</span>
<span class="c1"># OR</span>
<span class="c1"># You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals.</span>
- <span class="n">logging_line</span> <span class="o">=</span> <span class="s1">'Printf("MY_STELLAR_DATA time=%g mass=%g</span><span class="se">\\</span><span class="s1">n", stardata->model.time, stardata->star[0].mass)'</span>
+ <span class="n">logging_line</span> <span class="o">=</span> <span class="s1">'Printf("MY_STELLAR_DATA time=</span><span class="si">%g</span><span class="s1"> mass=</span><span class="si">%g</span><span class="se">\\</span><span class="s1">n", stardata->model.time, stardata->star[0].mass)'</span>
<span class="c1"># Generate entire shared lib code around logging lines</span>
<span class="n">custom_logging_code</span> <span class="o">=</span> <span class="n">binary_c_log_code</span><span class="p">(</span><span class="n">logging_line</span><span class="p">)</span>
<span class="c1"># Run system. all arguments can be given as optional arguments. the custom_logging_code is one of them and will be processed automatically.</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span>
- <span class="no">M_1</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
- <span class="n">metallicity</span><span class="o">=</span><span class="mi">0</span><span class="o">.</span><span class="mo">002</span><span class="p">,</span>
- <span class="no">M_2</span><span class="o">=</span><span class="mi">0</span><span class="o">.</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">M_1</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">metallicity</span><span class="o">=</span><span class="mf">0.002</span><span class="p">,</span>
+ <span class="n">M_2</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span>
<span class="n">separation</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">orbital_period</span><span class="o">=</span><span class="mi">100000000000</span><span class="p">,</span>
<span class="n">custom_logging_code</span><span class="o">=</span><span class="n">custom_logging_code</span><span class="p">,</span>
@@ -600,18 +601,18 @@
<span class="k">def</span> <span class="nf">run_example_binary_with_writing_logfile</span><span class="p">():</span>
- <span class="s2">"""</span>
-<span class="s2"> Same as above but when giving the log_filename argument the log filename will be written</span>
-<span class="s2"> """</span>
+ <span class="sd">"""</span>
+<span class="sd"> Same as above but when giving the log_filename argument the log filename will be written</span>
+<span class="sd"> """</span>
- <span class="n">import</span> <span class="n">pandas</span> <span class="n">as</span> <span class="n">pd</span>
- <span class="n">import</span> <span class="n">numpy</span> <span class="n">as</span> <span class="n">np</span>
- <span class="n">import</span> <span class="n">tempfile</span>
+ <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</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">tempfile</span>
<span class="c1"># Run system. all arguments can be given as optional arguments.</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span>
- <span class="no">M_1</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
- <span class="no">M_2</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span>
+ <span class="n">M_1</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
+ <span class="n">M_2</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span>
<span class="n">separation</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">orbital_period</span><span class="o">=</span><span class="mi">100000000000</span><span class="p">,</span>
<span class="n">log_filename</span><span class="o">=</span><span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">()</span> <span class="o">+</span> <span class="s2">"/test_log.txt"</span><span class="p">,</span>
@@ -631,7 +632,7 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="binary_c_parameters.html" class="btn btn-neutral float-right" title="Binary_c parameters" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="population_example.html" class="btn btn-neutral float-right" title="Example of population script" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="examples.html" class="btn btn-neutral float-left" title="Examples" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
@@ -644,7 +645,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index fd3fd4fdab9e7ceff7ba3521a0e18521a47943e9..e9954b899a4e96fef83e739dab6e87ecd7338ace 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -454,6 +454,10 @@
<li><a href="functions.html#binarycpython.utils.functions.make_build_text">make_build_text() (in module binarycpython.utils.functions)</a>
</li>
<li><a href="functions.html#binarycpython.utils.functions.merge_dicts">merge_dicts() (in module binarycpython.utils.functions)</a>
+</li>
+ <li><a href="useful_funcs.html#binarycpython.utils.useful_funcs.minimum_period_for_RLOF">minimum_period_for_RLOF() (in module binarycpython.utils.useful_funcs)</a>
+</li>
+ <li><a href="useful_funcs.html#binarycpython.utils.useful_funcs.minimum_separation_for_RLOF">minimum_separation_for_RLOF() (in module binarycpython.utils.useful_funcs)</a>
</li>
<li>
module
@@ -632,7 +636,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/grid.html b/docs/build/html/grid.html
index 18bc400ab69c1b897716ff3f98233ee19ab4fde8..8ced97503a8ddaf708ab2e314b78d9bb496091c7 100644
--- a/docs/build/html/grid.html
+++ b/docs/build/html/grid.html
@@ -191,6 +191,7 @@ but copying functionality isn’t recommended except if you know what you are do
<li><p>TODO: uncomment and implement the HPC functionality</p></li>
<li><p>TODO: think of a clean and nice way to unload and remove the custom_logging_info library from memory (and from disk)</p></li>
<li><p>TODO: think of a nice way to remove the loaded grid_code/ generator from memory.</p></li>
+<li><p>TODO: Create a designated dict for results</p></li>
</ul>
</dd>
</dl>
@@ -465,7 +466,7 @@ like m1,m2,sep, orb-per, ecc, probability etc.</p>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/grid_options_defaults.html b/docs/build/html/grid_options_defaults.html
index ea357ce8c92d814935585deef60e15fa0c6870b8..148ec390eb8387bb28eb85d726280d263da07bf8 100644
--- a/docs/build/html/grid_options_defaults.html
+++ b/docs/build/html/grid_options_defaults.html
@@ -261,7 +261,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/grid_options_descriptions.html b/docs/build/html/grid_options_descriptions.html
index 7e45825ec62aff7dd211a245b56e88f6acd6d864..aef7e1c0c4f0583822bf0908c65a64d8a89b4417 100644
--- a/docs/build/html/grid_options_descriptions.html
+++ b/docs/build/html/grid_options_descriptions.html
@@ -326,7 +326,7 @@ There are 1 options that are not described yet.</p>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/hpc_functions.html b/docs/build/html/hpc_functions.html
index b4e2a376d570255f5247bbc112bbb216d08aa08a..627876c8f96a6fefdb5c1d5adcbf856a5b594d01 100644
--- a/docs/build/html/hpc_functions.html
+++ b/docs/build/html/hpc_functions.html
@@ -197,7 +197,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index f596f5792a19d1579dab3700d3a603e7aef802d3..7937e04943dba6d1afc70ff513cad7227b1a15d3 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -228,7 +228,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index 9abe42379b70b37661b55aa5b1dcb593eac43ab2..aa5eb5e26efd91d79e10b479834dcd6295957375 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -208,7 +208,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index ac4ccb7b8e572b34ae35f77d6aafe34954e41522..f64b02e86059822786cc5d39fb155ab3016694d5 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/plot_functions.html b/docs/build/html/plot_functions.html
index 48bcfe1bca30e4c312c3aa8c75843b64cf94ba2d..308c870e7fc6e6eb40b16a5eb880c7e713b37bb4 100644
--- a/docs/build/html/plot_functions.html
+++ b/docs/build/html/plot_functions.html
@@ -430,7 +430,7 @@ This is not included in all the plotting routines.</p></li>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/population_example.html b/docs/build/html/population_example.html
new file mode 100644
index 0000000000000000000000000000000000000000..3452450151bbf54692a145e148d5afeb399690a5
--- /dev/null
+++ b/docs/build/html/population_example.html
@@ -0,0 +1,633 @@
+
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+<li class="toctree-l2"><a class="reference internal" href="general_examples.html">Examples</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Example of population script</a></li>
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+
+ <div class="section" id="example-of-population-script">
+<h1>Example of population script<a class="headerlink" href="#example-of-population-script" title="Permalink to this headline">¶</a></h1>
+<p>The source code of a script to run a population of stars.</p>
+<div class="highlight-python notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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+204</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
+
+<span class="c1"># import json</span>
+<span class="c1"># import time</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">get_help_all</span><span class="p">,</span> <span class="n">get_help</span><span class="p">,</span> <span class="n">create_hdf5</span><span class="p">,</span> <span class="n">output_lines</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
+
+<span class="c1">#########################################################</span>
+<span class="c1"># This file serves as an example for running a population.</span>
+<span class="c1"># The use of help(<function>) is a good way to inspect what parameters are there to use</span>
+<span class="c1">#########################################################</span>
+
+<span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+ <span class="c1"># EXAMPLE PARSE_FUNCTION</span>
+
+ <span class="c1"># extract info from the population instance</span>
+
+ <span class="c1"># Get some information from the</span>
+ <span class="n">data_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"data_dir"</span><span class="p">]</span>
+ <span class="n">base_filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"base_filename"</span><span class="p">]</span>
+
+ <span class="c1"># Check directory, make if necessary</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">data_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="n">seperator</span> <span class="o">=</span> <span class="s2">" "</span>
+
+ <span class="c1"># Create filename</span>
+ <span class="n">outfilename</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">data_dir</span><span class="p">,</span> <span class="n">base_filename</span><span class="p">)</span>
+
+ <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"time"</span><span class="p">,</span> <span class="s2">"mass"</span><span class="p">,</span> <span class="s2">"zams_mass"</span><span class="p">,</span> <span class="s2">"probability"</span><span class="p">,</span> <span class="s2">"radius"</span><span class="p">,</span> <span class="s2">"stellar_type"</span><span class="p">]</span>
+
+ <span class="c1"># Go over the output.</span>
+ <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="n">output_lines</span><span class="p">(</span><span class="n">output</span><span class="p">):</span>
+ <span class="n">headerline</span> <span class="o">=</span> <span class="n">el</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># CHeck the header and act accordingly</span>
+ <span class="k">if</span> <span class="n">headerline</span> <span class="o">==</span> <span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="n">el</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">:]</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span><span class="o">==</span><span class="nb">len</span><span class="p">(</span><span class="n">values</span><span class="p">):</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Amount of column names isnt equal to amount of columns"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</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="n">outfilename</span><span class="p">):</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfilename</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">seperator</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfilename</span><span class="p">,</span> <span class="s2">"a"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">seperator</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">values</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+<span class="c1"># Create population object</span>
+<span class="n">example_pop</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
+
+<span class="c1"># If you want verbosity, set this before other things</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+
+<span class="c1"># Setting values can be done via .set(<parameter_name>=<value>)</span>
+<span class="c1"># Values that are known to be binary_c_parameters are loaded into bse_options.</span>
+<span class="c1"># Those that are present in the default grid_options are set in grid_options</span>
+<span class="c1"># All other values that you set are put in a custom_options dict</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+ <span class="c1"># binary_c physics options</span>
+ <span class="n">M_1</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="c1"># bse_options</span>
+ <span class="n">separation</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="c1"># bse_options</span>
+ <span class="n">orbital_period</span><span class="o">=</span><span class="mi">45000000080</span><span class="p">,</span> <span class="c1"># bse_options</span>
+ <span class="n">max_evolution_time</span><span class="o">=</span><span class="mi">15000</span><span class="p">,</span> <span class="c1"># bse_options</span>
+ <span class="n">eccentricity</span><span class="o">=</span><span class="mf">0.02</span><span class="p">,</span> <span class="c1"># bse_options</span>
+
+ <span class="c1"># Set companion to low mass</span>
+ <span class="n">M_2</span><span class="o">=</span><span class="mf">0.08</span><span class="p">,</span> <span class="c1"># Since in the example we run a single system, we should set the companion mass here. If we donm't do this, the code will complain. </span>
+
+ <span class="c1"># grid_options</span>
+ <span class="n">amt_cores</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="c1"># grid_options</span>
+ <span class="n">verbose</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="c1"># verbosity. Not fully configured correctly yet but having it value of 1 prints alot of stuff</span>
+
+ <span class="c1"># Custom options # TODO: need to be set in grid_options probably</span>
+ <span class="n">data_dir</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">temp_dir</span><span class="p">(),</span> <span class="s2">"example_python_population_result"</span>
+ <span class="p">),</span> <span class="c1"># custom_options</span>
+ <span class="n">base_filename</span><span class="o">=</span><span class="s2">"example_pop.dat"</span><span class="p">,</span> <span class="c1"># custom_options</span>
+<span class="p">)</span>
+
+<span class="c1"># Creating a parsing function</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+ <span class="n">parse_function</span><span class="o">=</span><span class="n">parse_function</span><span class="p">,</span> <span class="c1"># Setting the parse function thats used in the evolve_population</span>
+<span class="p">)</span>
+
+<span class="c1">### Custom logging</span>
+
+<span class="c1">## Below example requires changing the parse function</span>
+<span class="c1">## very simple example of custom logging. Will work but need to change the parse function to handle that nicely.</span>
+<span class="c1"># example_pop.set(</span>
+<span class="c1"># C_auto_logging={</span>
+<span class="c1"># "MY_HEADER_LINE": ["star[0].mass", "star[1].mass", "model.probability"]</span>
+<span class="c1"># }</span>
+<span class="c1"># )</span>
+
+
+<span class="c1"># Log the moment when the star turns into neutron</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+ <span class="n">C_logging_code</span><span class="o">=</span><span class="s2">"""</span>
+<span class="s2">if(stardata->star[0].stellar_type >= 13) </span>
+<span class="s2">{</span>
+<span class="s2"> if (stardata->model.time < stardata->model.max_evolution_time)</span>
+<span class="s2"> {</span>
+<span class="s2"> Printf("MY_STELLAR_DATA </span><span class="si">%30.12e</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%d</span><span class="se">\\</span><span class="s2">n",</span>
+<span class="s2"> // </span>
+<span class="s2"> stardata->model.time, // 1</span>
+<span class="s2"> stardata->star[0].mass, // 2</span>
+<span class="s2"> stardata->common.zero_age.mass[0], // 4</span>
+<span class="s2"> stardata->model.probability, // 5</span>
+<span class="s2"> stardata->star[0].radius, // 6</span>
+<span class="s2"> stardata->star[0].stellar_type // 7</span>
+<span class="s2"> );</span>
+<span class="s2"> };</span>
+<span class="s2"> /* Kill the simulation to save time */</span>
+<span class="s2"> stardata->model.max_evolution_time = stardata->model.time - stardata->model.dtm;</span>
+<span class="s2">};</span>
+<span class="s2">"""</span>
+<span class="p">)</span>
+
+<span class="c1"># Add grid variables</span>
+<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">20</span><span class="p">,</span>
+ <span class="s1">'q'</span><span class="p">:</span> <span class="mi">20</span><span class="p">,</span>
+ <span class="s1">'per'</span><span class="p">:</span> <span class="mi">40</span>
+<span class="p">}</span>
+
+<span class="c1"># Mass</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">(</span>
+ <span class="n">name</span><span class="o">=</span><span class="s2">"lnm1"</span><span class="p">,</span>
+ <span class="n">longname</span><span class="o">=</span><span class="s2">"Primary mass"</span><span class="p">,</span>
+ <span class="n">valuerange</span><span class="o">=</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">150</span><span class="p">],</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="s2">"</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">resolution</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]),</span>
+ <span class="n">spacingfunc</span><span class="o">=</span><span class="s2">"const(math.log(2), math.log(150), </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">resolution</span><span class="p">[</span><span class="s2">"M_1"</span><span class="p">]),</span>
+ <span class="n">precode</span><span class="o">=</span><span class="s2">"M_1=math.exp(lnm1)"</span><span class="p">,</span>
+ <span class="n">probdist</span><span class="o">=</span><span class="s2">"three_part_powerlaw(M_1, 0.1, 0.5, 1.0, 150, -1.3, -2.3, -2.3)*M_1"</span><span class="p">,</span>
+ <span class="n">dphasevol</span><span class="o">=</span><span class="s2">"dlnm1"</span><span class="p">,</span>
+ <span class="n">parameter_name</span><span class="o">=</span><span class="s2">"M_1"</span><span class="p">,</span>
+ <span class="n">condition</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="c1"># Impose a condition on this grid variable. Mostly for a check for yourself</span>
+<span class="p">)</span>
+
+<span class="c1"># # Mass ratio</span>
+<span class="c1"># test_pop.add_grid_variable(</span>
+<span class="c1"># name="q",</span>
+<span class="c1"># longname="Mass ratio",</span>
+<span class="c1"># valuerange=["0.1/M_1", 1],</span>
+<span class="c1"># resolution="{}".format(resolution['q']),</span>
+<span class="c1"># spacingfunc="const(0.1/M_1, 1, {})".format(resolution['q']),</span>
+<span class="c1"># probdist="flatsections(q, [{'min': 0.1/M_1, 'max': 1.0, 'height': 1}])",</span>
+<span class="c1"># dphasevol="dq",</span>
+<span class="c1"># precode="M_2 = q * M_1",</span>
+<span class="c1"># parameter_name="M_2",</span>
+<span class="c1"># condition="", # Impose a condition on this grid variable. Mostly for a check for yourself </span>
+<span class="c1"># )</span>
+
+<span class="c1"># # </span>
+<span class="c1"># test_pop.add_grid_variable(</span>
+<span class="c1"># name="log10per", # in days</span>
+<span class="c1"># longname="log10(Orbital_Period)", </span>
+<span class="c1"># valuerange=[0.15, 5.5],</span>
+<span class="c1"># resolution="{}".format(resolution["per"]),</span>
+<span class="c1"># spacingfunc="const(0.15, 5.5, {})".format(resolution["per"]),</span>
+<span class="c1"># precode="""orbital_period = 10** log10per</span>
+<span class="c1"># sep = calc_sep_from_period(M_1, M_2, orbital_period)</span>
+<span class="c1"># sep_min = calc_sep_from_period(M_1, M_2, 10**0.15)</span>
+<span class="c1"># sep_max = calc_sep_from_period(M_1, M_2, 10**5.5)""", </span>
+<span class="c1"># probdist="sana12(M_1, M_2, sep, orbital_period, sep_min, sep_max, math.log10(10**0.15), math.log10(10**5.5), -0.55)",</span>
+<span class="c1"># parameter_name="orbital_period",</span>
+<span class="c1"># dphasevol="dlog10per",</span>
+<span class="c1"># )</span>
+
+
+
+<span class="c1"># Exporting of all the settings can be done with .export_all_info()</span>
+<span class="c1"># on default it exports everything, but can be supressed by turning it off:</span>
+<span class="c1"># population settings (bse_options, grid_options, custom_options), turn off with include_population</span>
+<span class="c1"># settings=False</span>
+<span class="c1"># binary_c_defaults (all the commandline arguments that binary c accepts, and their defaults).</span>
+<span class="c1"># turn off with include_binary_c_defaults=False</span>
+<span class="c1"># include_binary_c_version_info (all the compilation info, and information about the compiled</span>
+<span class="c1"># parameters), turn off with include_binary_c_version_info=False</span>
+<span class="c1"># include_binary_c_help_all (all the help information for all the binary_c parameters),</span>
+<span class="c1"># turn off with include_binary_c_help_all=Fase</span>
+<span class="c1"># On default it will write this to the custom_options['data_dir'], but that can be overriden by</span>
+<span class="c1"># setting use_datadir=False and providing an outfile=<></span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">export_all_info</span><span class="p">()</span>
+
+<span class="c1">## Executing a single system</span>
+<span class="c1">## This uses the M_1 orbital period etc set with the set function</span>
+<span class="c1"># output = example_pop.evolve_single()</span>
+<span class="c1"># print(output)</span>
+
+<span class="c1">## Executing a population</span>
+<span class="c1">## This uses the values generated by the grid_variables</span>
+<span class="n">example_pop</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span> <span class="c1"># TODO: update this function call</span>
+
+<span class="c1"># Wrapping up the results to an hdf5 file can be done by using the create_hdf5</span>
+<span class="c1"># (<directory containing data and settings>) This function takes the settings file</span>
+<span class="c1"># (ending in _settings.json) and the data files (ending in .dat) from the data_dir</span>
+<span class="c1"># and packing them into an hdf5 file, which is then written into the same data_dir directory</span>
+<span class="n">create_hdf5</span><span class="p">(</span><span class="n">data_dir</span><span class="o">=</span><span class="n">example_pop</span><span class="o">.</span><span class="n">custom_options</span><span class="p">[</span><span class="s2">"data_dir"</span><span class="p">],</span> <span class="n">name</span><span class="o">=</span><span class="s2">"example_pop.hdf5"</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+</div>
+
+
+ </div>
+
+ </div>
+ <footer>
+
+ <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+
+ <a href="binary_c_parameters.html" class="btn btn-neutral float-right" title="Binary_c parameters" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+
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+ <a href="general_examples.html" class="btn btn-neutral float-left" title="Examples" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+
+ </div>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+
+ © Copyright 2021, David Hendriks, Robert Izzard
+
+ </p>
+ </div>
+
+
+
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+
+ <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+
+ provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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\ No newline at end of file
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 9440b93e90b774c2e6ed1298bb4416769982db0b..3a44ccaf316334b0c2cba68c95f003caf0842bff 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -237,7 +237,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/readme_link.html b/docs/build/html/readme_link.html
index 5f3f9f89d8c77c13ce95b175553eb2f7750d94ee..0d318532938c6888bb3eeb3861f4d942b9478ae7 100644
--- a/docs/build/html/readme_link.html
+++ b/docs/build/html/readme_link.html
@@ -260,7 +260,7 @@ export PYTHONPATH=<full path to root dir of repo>:$PYTHONPATH
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/run_system_wrapper.html b/docs/build/html/run_system_wrapper.html
index 6130498febeb635fa4a54d547da182d59a1253bf..6a55ea25c60438e298258e2e7fc71285ea652c80 100644
--- a/docs/build/html/run_system_wrapper.html
+++ b/docs/build/html/run_system_wrapper.html
@@ -244,7 +244,7 @@ and returns what the parse_function returns</p>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index a715353036ae243b42b9147a90a7fad5893a037f..611aafb8d84bd3b75951ff9d0288a405cf408aee 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -176,7 +176,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index e67d016e379708e1b1c1510bb8dff2433973af2e..18e10d8649e817ea96646ad84173d62364080160 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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module"],titleterms:{"function":4,"public":8,algorithm:0,binari:0,binary_c:[0,10,14],binarycpython:11,build:14,code:[8,11],custom_logging_funct:1,descript:7,distribution_funct:2,document:10,environ:14,exampl:[3,5,13],faq:14,grid:[7,8],grid_class:6,hpc_function:9,indic:10,input:0,instruct:14,misc:0,modul:[1,2,4,6,9,12,14,15,16,17,18],note:14,nucsyn:0,option:[7,8],output:0,paramet:0,plot_funct:12,popul:[8,13],privat:8,python:[10,14],requir:14,run_system_wrapp:15,script:13,section:0,spacing_funct:16,star:0,stellar_typ:17,tabl:10,usag:14,useful_func:18,variabl:14,welcom:10}})
\ No newline at end of file
diff --git a/docs/build/html/spacing_functions.html b/docs/build/html/spacing_functions.html
index d4b59005d5a57829dc989483d19dd56946a30742..0aac247b138c0368c4ff7667efd99fc3f94224d1 100644
--- a/docs/build/html/spacing_functions.html
+++ b/docs/build/html/spacing_functions.html
@@ -220,7 +220,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/stellar_types.html b/docs/build/html/stellar_types.html
index 967fdfa76f3c6dce190010969a3ef60303e0d6e2..51edae1c16d4afbf8d91ea328e5351ee23e0a1bb 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -201,7 +201,7 @@
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/build/html/useful_funcs.html b/docs/build/html/useful_funcs.html
index 386b9cb822c46b320fcbb2c168e6805fd50b62f4..aca941bd7dd59de07727620ec3a2e58f9a6b2787 100644
--- a/docs/build/html/useful_funcs.html
+++ b/docs/build/html/useful_funcs.html
@@ -230,6 +230,46 @@
</dl>
</dd></dl>
+<dl class="py function">
+<dt id="binarycpython.utils.useful_funcs.minimum_period_for_RLOF">
+<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">minimum_period_for_RLOF</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">metallicity</span></em>, <em class="sig-param"><span class="n">store_memaddr</span><span class="o">=</span><span class="default_value">- 1</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_period_for_RLOF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_period_for_RLOF" title="Permalink to this definition">¶</a></dt>
+<dd><p>Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</p>
+<p>Handles the output and returns the minimum orbital period at which RLOF just does not occur at zams</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>M1</strong> – Primary mass in solar mass</p></li>
+<li><p><strong>M2</strong> – Secondary mass in solar mass</p></li>
+<li><p><strong>metallicity</strong> – metallicity</p></li>
+<li><p><strong>store_memaddr</strong> (<em>optional</em>) – store memory adress</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>minimum orbital_period that just does not cause a RLOF at ZAMS</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt id="binarycpython.utils.useful_funcs.minimum_separation_for_RLOF">
+<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">minimum_separation_for_RLOF</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">M1</span></em>, <em class="sig-param"><span class="n">M2</span></em>, <em class="sig-param"><span class="n">metallicity</span></em>, <em class="sig-param"><span class="n">store_memaddr</span><span class="o">=</span><span class="default_value">- 1</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#minimum_separation_for_RLOF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.minimum_separation_for_RLOF" title="Permalink to this definition">¶</a></dt>
+<dd><p>Wrapper function for _binary_c_bindings.return_minimum_orbit_for_RLOF</p>
+<p>Handles the output and returns the minimum separation at which RLOF just does not occur at ZAMS</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>M1</strong> – Primary mass in solar mass</p></li>
+<li><p><strong>M2</strong> – Secondary mass in solar mass</p></li>
+<li><p><strong>metallicity</strong> – metallicity</p></li>
+<li><p><strong>store_memaddr</strong> (<em>optional</em>) – store memory adress</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>minimum separation that just does not cause a RLOF at ZAMS</p>
+</dd>
+</dl>
+</dd></dl>
+
<dl class="py function">
<dt id="binarycpython.utils.useful_funcs.ragb">
<code class="sig-prename descclassname">binarycpython.utils.useful_funcs.</code><code class="sig-name descname">ragb</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">m</span></em>, <em class="sig-param"><span class="n">z</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/useful_funcs.html#ragb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#binarycpython.utils.useful_funcs.ragb" title="Permalink to this definition">¶</a></dt>
@@ -335,7 +375,7 @@ determine if two stars collide on the ZAMS</p>
<div role="contentinfo">
<p>
- © Copyright 2020, David Hendriks, Robert Izzard
+ © Copyright 2021, David Hendriks, Robert Izzard
</p>
</div>
diff --git a/docs/source/binary_c_parameters.rst b/docs/source/binary_c_parameters.rst
index 56de8181e1e5404f7c0e5b2c6ec273f278045544..4fe498e19b7be769db2dba6961d758d454815b8e 100644
--- a/docs/source/binary_c_parameters.rst
+++ b/docs/source/binary_c_parameters.rst
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: branch_david **binary_c git revision**: 5479:20210111:463f148ec **Built on**: Jan 28 2021 20:10:20
+ **binary_c git branch**: branch_david **binary_c git revision**: 5542:20210311:f3401ead4 **Built on**: Mar 22 2021 12:07:51
Section: stars
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8f5768736b981db76340efd880517048c0373585..dc821f72be00f3d8a8731413cfb35ea9a4a02709 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -31,7 +31,7 @@ cautodoc_root = os.path.abspath("../../")
# -- Project information -----------------------------------------------------
project = "binary_c-python"
-copyright = "2020, David Hendriks, Robert Izzard"
+copyright = "2021, David Hendriks, Robert Izzard"
author = "David Hendriks, Robert Izzard"
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
index 281bfaa659e3e775f75243f608c963bde50b7049..ab58720d9b5a670eb13d8468daa687e72ab86e52 100644
--- a/docs/source/examples.rst
+++ b/docs/source/examples.rst
@@ -5,4 +5,5 @@ This chapter contains the source code of example scripts which show the way of u
.. toctree::
:hidden:
- general_examples
\ No newline at end of file
+ general_examples
+ population_example
\ No newline at end of file
diff --git a/docs/source/general_examples.rst b/docs/source/general_examples.rst
index 4a070790a2c7ef4fa05a5c5d76026750ff9bfae4..8509de5b72faf82bc026ed2b785b2d72b4ccc702 100644
--- a/docs/source/general_examples.rst
+++ b/docs/source/general_examples.rst
@@ -3,5 +3,5 @@ Examples
The source code of the general examples.
.. literalinclude:: ../../examples/examples.py
- :language: ruby
+ :language: python
:linenos:
\ No newline at end of file
diff --git a/docs/source/population_example.rst b/docs/source/population_example.rst
new file mode 100644
index 0000000000000000000000000000000000000000..192372d019133d818c4ba6ad207c5dc09989de62
--- /dev/null
+++ b/docs/source/population_example.rst
@@ -0,0 +1,7 @@
+Example of population script
+============================
+The source code of a script to run a population of stars.
+
+.. literalinclude:: ../../examples/example_population.py
+ :language: python
+ :linenos:
\ No newline at end of file