Commit e27196e9 authored by Steve Plimpton's avatar Steve Plimpton
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parent 268fdab7

doc/html/Section_start.html

+11 −9
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@@ -1769,15 +1769,17 @@ computation. These thread timings are taking from the first MPI rank 
only and and thus, as the breakdown for MPI tasks can change from MPI

rank to MPI rank, this breakdown can be very different for individual

ranks. Here is an example output for this section:</p>

<p>Thread timings breakdown (MPI rank 0):

Total threaded time 0.6846 / 90.6%

Section |  min time  |  avg time  |  max time  <a href="#id37"><span class="problematic" id="id38">|%varavg|</span></a> %total

&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;

Pair    | 0.5127     | 0.5147     | 0.5167     |   0.3 | 75.18

Bond    | 0.0043139  | 0.0046779  | 0.0050418  |   0.5 |  0.68

Kspace  | 0.070572   | 0.074541   | 0.07851    |   1.5 | 10.89

Neigh   | 0.084778   | 0.086969   | 0.089161   |   0.7 | 12.70

Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Thread</span> <span class="n">timings</span> <span class="n">breakdown</span> <span class="p">(</span><span class="n">MPI</span> <span class="n">rank</span> <span class="mi">0</span><span class="p">):</span>

<span class="n">Total</span> <span class="n">threaded</span> <span class="n">time</span> <span class="mf">0.6846</span> <span class="o">/</span> <span class="mf">90.6</span><span class="o">%</span>

<span class="n">Section</span> <span class="o">|</span>  <span class="nb">min</span> <span class="n">time</span>  <span class="o">|</span>  <span class="n">avg</span> <span class="n">time</span>  <span class="o">|</span>  <span class="nb">max</span> <span class="n">time</span>  <span class="o">|%</span><span class="n">varavg</span><span class="o">|</span> <span class="o">%</span><span class="n">total</span>

<span class="o">---------------------------------------------------------------</span>

<span class="n">Pair</span>    <span class="o">|</span> <span class="mf">0.5127</span>     <span class="o">|</span> <span class="mf">0.5147</span>     <span class="o">|</span> <span class="mf">0.5167</span>     <span class="o">|</span>   <span class="mf">0.3</span> <span class="o">|</span> <span class="mf">75.18</span>

<span class="n">Bond</span>    <span class="o">|</span> <span class="mf">0.0043139</span>  <span class="o">|</span> <span class="mf">0.0046779</span>  <span class="o">|</span> <span class="mf">0.0050418</span>  <span class="o">|</span>   <span class="mf">0.5</span> <span class="o">|</span>  <span class="mf">0.68</span>

<span class="n">Kspace</span>  <span class="o">|</span> <span class="mf">0.070572</span>   <span class="o">|</span> <span class="mf">0.074541</span>   <span class="o">|</span> <span class="mf">0.07851</span>    <span class="o">|</span>   <span class="mf">1.5</span> <span class="o">|</span> <span class="mf">10.89</span>

<span class="n">Neigh</span>   <span class="o">|</span> <span class="mf">0.084778</span>   <span class="o">|</span> <span class="mf">0.086969</span>   <span class="o">|</span> <span class="mf">0.089161</span>   <span class="o">|</span>   <span class="mf">0.7</span> <span class="o">|</span> <span class="mf">12.70</span>

<span class="n">Reduce</span>  <span class="o">|</span> <span class="mf">0.0036485</span>  <span class="o">|</span> <span class="mf">0.003737</span>   <span class="o">|</span> <span class="mf">0.0038254</span>  <span class="o">|</span>   <span class="mf">0.1</span> <span class="o">|</span>  <span class="mf">0.55</span>

</pre></div>

</div>

<p>The third section lists the number of owned atoms (Nlocal), ghost atoms

(Nghost), and pair-wise neighbors stored per processor.  The max and min

values give the spread of these values across processors with a 10-bin

doc/html/_sources/Section_start.txt

+11 −9
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@@ -1978,6 +1978,8 @@ only and and thus, as the breakdown for MPI tasks can change from MPI 
rank to MPI rank, this breakdown can be very different for individual

ranks. Here is an example output for this section:



.. parsed-literal::



   Thread timings breakdown (MPI rank 0):

   Total threaded time 0.6846 / 90.6%

   Section |  min time  |  avg time  |  max time  |%varavg| %total

doc/html/_sources/compute_sna_atom.txt

+4 −4
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@@ -196,18 +196,18 @@ described by the following piece of python code: 


   for j1 in range(0,twojmax+1):

       if(diagonal==2): 

           print j1/2,j1/2,j1/2

           print j1/2.,j1/2.,j1/2.

       elif(diagonal==1):

           for j in range(0,min(twojmax,2*j1)+1,2): 

               print j1/2,j1/2,j/2

               print j1/2.,j1/2.,j/2.

       elif(diagonal==0):

           for j2 in range(0,j1+1):

               for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 

                   print j1/2,j2/2,j/2

                   print j1/2.,j2/2.,j/2.

       elif(diagonal==3):

           for j2 in range(0,j1+1):

               for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 

                   if (j>=j1): print j1/2,j2/2,j/2

                   if (j>=j1): print j1/2.,j2/2.,j/2.



Compute *snad/atom* evaluates a per-atom array. The columns are

arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each

doc/html/compute_sna_atom.html

+4 −4
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@@ -278,18 +278,18 @@ each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as 
described by the following piece of python code:</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>

    <span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span>

        <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span>

        <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span>

    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>

        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>

            <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>

            <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>

    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>

        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>

            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>

                <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>

                <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>

    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span>

        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>

            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>

                <span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>

                <span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>

</pre></div>

</div>

<p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are

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