doc update (#287)

rinikerlab · Apr 6, 2022 · 53767f5 · 53767f5
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diff --git a/docs/Examples/developer_examples/dev_example_PyGromosPP.html b/docs/Examples/developer_examples/dev_example_PyGromosPP.html
diff --git a/docs/Examples/developer_examples/dev_example_PyGromosPP.ipynb b/docs/Examples/developer_examples/dev_example_PyGromosPP.ipynb
diff --git a/docs/Examples/developer_examples/dev_example_gromos_files.html b/docs/Examples/developer_examples/dev_example_gromos_files.html
diff --git a/docs/Examples/developer_examples/dev_example_gromos_files.ipynb b/docs/Examples/developer_examples/dev_example_gromos_files.ipynb
diff --git a/docs/Examples/developer_examples/dev_example_gromos_simulation.html b/docs/Examples/developer_examples/dev_example_gromos_simulation.html
diff --git a/docs/Examples/developer_examples/dev_example_gromos_simulation.ipynb b/docs/Examples/developer_examples/dev_example_gromos_simulation.ipynb
diff --git a/docs/Examples/developer_examples/dev_example_gromos_tutorial_on_low_level.html b/docs/Examples/developer_examples/dev_example_gromos_tutorial_on_low_level.html
diff --git a/docs/Examples/developer_examples/dev_example_gromos_tutorial_on_low_level.ipynb b/docs/Examples/developer_examples/dev_example_gromos_tutorial_on_low_level.ipynb
diff --git a/docs/Examples/developer_examples/dev_example_submission_systems.html b/docs/Examples/developer_examples/dev_example_submission_systems.html
@@ -599,7 +599,7 @@ <h3>Queue Checking:<a class="headerlink" href="#Queue-Checking:" title="Permalin
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/3507705770.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/3507705770.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-fg">----&gt; 1</span><span class="ansi-red-fg"> </span>sub_lsf<span class="ansi-blue-fg">.</span>get_queued_jobs<span class="ansi-blue-fg">(</span><span class="ansi-blue-fg">)</span>
 <span class="ansi-green-intense-fg ansi-bold">      2</span> sub_lsf<span class="ansi-blue-fg">.</span>job_queue_list
 
@@ -677,7 +677,7 @@ <h3>Submission:<a class="headerlink" href="#Submission:" title="Permalink to thi
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/3188711362.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/3188711362.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-intense-fg ansi-bold">      2</span> job_name <span class="ansi-blue-fg">=</span> <span class="ansi-blue-fg">&#34;Test1&#34;</span>
 <span class="ansi-green-intense-fg ansi-bold">      3</span>
 <span class="ansi-green-fg">----&gt; 4</span><span class="ansi-red-fg"> </span>job_id <span class="ansi-blue-fg">=</span> sub_lsf<span class="ansi-blue-fg">.</span>submit_to_queue<span class="ansi-blue-fg">(</span>Submission_job<span class="ansi-blue-fg">(</span>bash_command<span class="ansi-blue-fg">,</span> job_name<span class="ansi-blue-fg">)</span><span class="ansi-blue-fg">)</span>
@@ -756,7 +756,7 @@ <h3>Submission:<a class="headerlink" href="#Submission:" title="Permalink to thi
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/1706125824.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/1706125824.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-intense-fg ansi-bold">      1</span> <span class="ansi-red-fg">#search for the just submitted job in the queue</span>
 <span class="ansi-green-fg">----&gt; 2</span><span class="ansi-red-fg"> </span>sub_lsf<span class="ansi-blue-fg">.</span>search_queue_for_jobid<span class="ansi-blue-fg">(</span>job_id<span class="ansi-blue-fg">)</span>
 
@@ -826,7 +826,7 @@ <h3>Submission:<a class="headerlink" href="#Submission:" title="Permalink to thi
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/1654124141.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/1654124141.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-fg">----&gt; 1</span><span class="ansi-red-fg"> </span>sub_lsf<span class="ansi-blue-fg">.</span>search_queue_for_jobname<span class="ansi-blue-fg">(</span><span class="ansi-blue-fg">&#34;Test1&#34;</span><span class="ansi-blue-fg">)</span>
 
 <span class="ansi-green-fg">~/PyGromosTools/pygromos/simulations/hpc_queuing/submission_systems/lsf.py</span> in <span class="ansi-cyan-fg">search_queue_for_jobname</span><span class="ansi-blue-fg">(self, job_name, regex)</span>
@@ -912,7 +912,7 @@ <h3>Submitting multiple jobs<a class="headerlink" href="#Submitting-multiple-job
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/422912753.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/422912753.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-intense-fg ansi-bold">      4</span>     job_name <span class="ansi-blue-fg">=</span> <span class="ansi-blue-fg">&#34;Test&#34;</span><span class="ansi-blue-fg">+</span>str<span class="ansi-blue-fg">(</span>test<span class="ansi-blue-fg">)</span>
 <span class="ansi-green-intense-fg ansi-bold">      5</span>
 <span class="ansi-green-fg">----&gt; 6</span><span class="ansi-red-fg">     </span>job_id <span class="ansi-blue-fg">=</span> sub_lsf<span class="ansi-blue-fg">.</span>submit_to_queue<span class="ansi-blue-fg">(</span>Submission_job<span class="ansi-blue-fg">(</span>bash_command<span class="ansi-blue-fg">,</span> job_name<span class="ansi-blue-fg">)</span><span class="ansi-blue-fg">)</span>
@@ -991,7 +991,7 @@ <h3>Submitting multiple jobs<a class="headerlink" href="#Submitting-multiple-job
 During handling of the above exception, another exception occurred:
 
 <span class="ansi-red-fg">Exception</span>                                 Traceback (most recent call last)
-<span class="ansi-green-fg">/tmp/ipykernel_31485/722442852.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
+<span class="ansi-green-fg">/tmp/ipykernel_4765/722442852.py</span> in <span class="ansi-cyan-fg">&lt;module&gt;</span>
 <span class="ansi-green-fg">----&gt; 1</span><span class="ansi-red-fg"> </span>sub_lsf<span class="ansi-blue-fg">.</span>search_queue_for_jobname<span class="ansi-blue-fg">(</span><span class="ansi-blue-fg">&#34;Te&#34;</span><span class="ansi-blue-fg">,</span> regex<span class="ansi-blue-fg">=</span><span class="ansi-green-fg">True</span><span class="ansi-blue-fg">)</span>
 
 <span class="ansi-green-fg">~/PyGromosTools/pygromos/simulations/hpc_queuing/submission_systems/lsf.py</span> in <span class="ansi-cyan-fg">search_queue_for_jobname</span><span class="ansi-blue-fg">(self, job_name, regex)</span>