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| Offset 193, 23 lines modified | Offset 193, 23 lines modified | ||
| 193 | <span·class="gh">Out[16]:·</span><span·class="go">5</span> | 193 | <span·class="gh">Out[16]:·</span><span·class="go">5</span> |
| 194 | <span·class="gp">In·[17]:·</span><span·class="n">snap</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">N</span> | 194 | <span·class="gp">In·[17]:·</span><span·class="n">snap</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">N</span> |
| 195 | <span·class="gh">Out[17]:·</span><span·class="go">9</span> | 195 | <span·class="gh">Out[17]:·</span><span·class="go">9</span> |
| 196 | <span·class="gp">In·[18]:·</span><span·class="n">snap</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">position</span> | 196 | <span·class="gp">In·[18]:·</span><span·class="n">snap</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">position</span> |
| 197 | <span·class="gh">Out[18]:·</span> | 197 | <span·class="gh">Out[18]:·</span> |
| 198 | <span·class="go">array([[0.31649902,·0.930899··,·0.6207448·],</span> | ||
| 198 | <span·class="go">array([[0.04864376,·0.6388678·,·0.47861114],</span> | ||
| 199 | <span·class="go">·······[0.51105905,·0.02546922,·0.39761963],</span> | ||
| 200 | <span·class="go">·······[0.05343684,·0.2479186·,·0.43118024],</span> | ||
| 201 | <span·class="go">·······[0.78773755,·0.7398912·,·0.33950448],</span> | ||
| 202 | <span·class="go">·······[0.69232833,·0.7173891·,·0.32247263],</span> | ||
| 203 | <span·class="go">·······[0.1 | 199 | <span·class="go">·······[0.11056859,·0.62811136,·0.20228414],</span> |
| 200 | <span·class="go">·······[0.94560254,·0.85934305,·0.0717991·],</span> | ||
| 201 | <span·class="go">·······[0.24312589,·0.6255072·,·0.8853982·],</span> | ||
| 202 | <span·class="go">·······[0.9675033·,·0.35954842,·0.36298457],</span> | ||
| 203 | <span·class="go">·······[0.79735494,·0.62377787,·0.34841114],</span> | ||
| 204 | <span·class="go">·······[0.5 | 204 | <span·class="go">·······[0.5194623·,·0.19607814,·0.7781965·],</span> |
| 205 | <span·class="go">·······[0. | 205 | <span·class="go">·······[0.7472676·,·0.80175644,·0.10671829],</span> |
| 206 | <span·class="go">·······[0.6 | 206 | <span·class="go">·······[0.6548015·,·0.93369675,·0.04346667]],·dtype=float32)</span> |
| 207 | </pre></div> | 207 | </pre></div> |
| 208 | </div> | 208 | </div> |
| 209 | <p><a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory"·title="gsd.hoomd.HOOMDTrajectory"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>·supports·random·indexing·of·frames·in·the·file. | 209 | <p><a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory"·title="gsd.hoomd.HOOMDTrajectory"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>·supports·random·indexing·of·frames·in·the·file. |
| 210 | Indexing·into·a·trajectory·returns·a·<a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.Snapshot"·title="gsd.hoomd.Snapshot"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.Snapshot</span></code></a>.</p> | 210 | Indexing·into·a·trajectory·returns·a·<a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.Snapshot"·title="gsd.hoomd.Snapshot"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.Snapshot</span></code></a>.</p> |
| 211 | </section> | 211 | </section> |
| 212 | <section·id="slicing-and-selection"> | 212 | <section·id="slicing-and-selection"> |
| 213 | <h2>Slicing·and·selection<a·class="headerlink"·href="#slicing-and-selection"·title="Permalink·to·this·heading"></a></h2> | 213 | <h2>Slicing·and·selection<a·class="headerlink"·href="#slicing-and-selection"·title="Permalink·to·this·heading"></a></h2> |
| Offset 236, 21 lines modified | Offset 236, 21 lines modified | ||
| 236 | <h2>Pure·python·reader<a·class="headerlink"·href="#pure-python-reader"·title="Permalink·to·this·heading"></a></h2> | 236 | <h2>Pure·python·reader<a·class="headerlink"·href="#pure-python-reader"·title="Permalink·to·this·heading"></a></h2> |
| 237 | <div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">In·[23]:·</span><span·class="n">f</span>·<span·class="o">=</span>·<span·class="n">gsd</span><span·class="o">.</span><span·class="n">pygsd</span><span·class="o">.</span><span·class="n">GSDFile</span><span·class="p">(</span><span·class="nb">open</span><span·class="p">(</span><span·class="s1">'test.gsd'</span><span·class="p">,</span>·<span·class="s1">'rb'</span><span·class="p">))</span> | 237 | <div·class="highlight-ipython·notranslate"><div·class="highlight"><pre><span></span><span·class="gp">In·[23]:·</span><span·class="n">f</span>·<span·class="o">=</span>·<span·class="n">gsd</span><span·class="o">.</span><span·class="n">pygsd</span><span·class="o">.</span><span·class="n">GSDFile</span><span·class="p">(</span><span·class="nb">open</span><span·class="p">(</span><span·class="s1">'test.gsd'</span><span·class="p">,</span>·<span·class="s1">'rb'</span><span·class="p">))</span> |
| 238 | <span·class="gp">In·[24]:·</span><span·class="n">t</span>·<span·class="o">=</span>·<span·class="n">gsd</span><span·class="o">.</span><span·class="n">hoomd</span><span·class="o">.</span><span·class="n">HOOMDTrajectory</span><span·class="p">(</span><span·class="n">f</span><span·class="p">);</span> | 238 | <span·class="gp">In·[24]:·</span><span·class="n">t</span>·<span·class="o">=</span>·<span·class="n">gsd</span><span·class="o">.</span><span·class="n">hoomd</span><span·class="o">.</span><span·class="n">HOOMDTrajectory</span><span·class="p">(</span><span·class="n">f</span><span·class="p">);</span> |
| 239 | <span·class="gp">In·[25]:·</span><span·class="n">t</span><span·class="p">[</span><span·class="mi">3</span><span·class="p">]</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">position</span> | 239 | <span·class="gp">In·[25]:·</span><span·class="n">t</span><span·class="p">[</span><span·class="mi">3</span><span·class="p">]</span><span·class="o">.</span><span·class="n">particles</span><span·class="o">.</span><span·class="n">position</span> |
| 240 | <span·class="gh">Out[25]:·</span> | 240 | <span·class="gh">Out[25]:·</span> |
| 241 | <span·class="go">array([[0.8549712·,·0.8540309·,·0.88189095],</span> | ||
| 241 | <span·class="go">array([[0.7596063·,·0.35071316,·0.44357768],</span> | ||
| 242 | <span·class="go">·······[0.9681369·,·0.2930677·,·0.7252575·],</span> | ||
| 243 | <span·class="go">·······[0. | 242 | <span·class="go">·······[0.9028438·,·0.2554103·,·0.2721972·],</span> |
| 243 | <span·class="go">·······[0.9459284·,·0.6330105·,·0.4404471·],</span> | ||
| 244 | <span·class="go">·······[0. | 244 | <span·class="go">·······[0.8604843·,·0.3100594·,·0.21919934],</span> |
| 245 | <span·class="go">·······[0.20218222,·0.10614425,·0.4902229·],</span> | ||
| 245 | <span·class="go">·······[0. | 246 | <span·class="go">·······[0.7367657·,·0.9544418·,·0.47768393],</span> |
| 246 | <span·class="go">·······[0.7138911·,·0.75650555,·0.12414929],</span> | ||
| 247 | <span·class="go">·······[0. | 247 | <span·class="go">·······[0.66016376,·0.37475777,·0.17023604]],·dtype=float32)</span> |
| 248 | </pre></div> | 248 | </pre></div> |
| 249 | </div> | 249 | </div> |
| 250 | <p>You·can·use·<strong>GSD</strong>·without·needing·to·compile·C·code·to·read·<strong>GSD</strong>·files | 250 | <p>You·can·use·<strong>GSD</strong>·without·needing·to·compile·C·code·to·read·<strong>GSD</strong>·files |
| 251 | using·<a·class="reference·internal"·href="python-module-gsd.pygsd.html#gsd.pygsd.GSDFile"·title="gsd.pygsd.GSDFile"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.pygsd.GSDFile</span></code></a>·in·combination·with·<a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory"·title="gsd.hoomd.HOOMDTrajectory"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>.·It | 251 | using·<a·class="reference·internal"·href="python-module-gsd.pygsd.html#gsd.pygsd.GSDFile"·title="gsd.pygsd.GSDFile"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.pygsd.GSDFile</span></code></a>·in·combination·with·<a·class="reference·internal"·href="python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory"·title="gsd.hoomd.HOOMDTrajectory"><code·class="xref·any·py·py-class·docutils·literal·notranslate"><span·class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>.·It |
| 252 | only·supports·the·<code·class="docutils·literal·notranslate"><span·class="pre">rb</span></code>·mode·and·does·not·read·files·as·fast·as·the·C | 252 | only·supports·the·<code·class="docutils·literal·notranslate"><span·class="pre">rb</span></code>·mode·and·does·not·read·files·as·fast·as·the·C |
| 253 | implementation.·It·takes·in·a·python·file-like·object,·so·it·can·be·used·with | 253 | implementation.·It·takes·in·a·python·file-like·object,·so·it·can·be·used·with |
| 254 | in-memory·IO·classes,·and·grid·file·classes·that·access·data·over·the·internet.</p> | 254 | in-memory·IO·classes,·and·grid·file·classes·that·access·data·over·the·internet.</p> |
| Offset 105, 23 lines modified | Offset 105, 23 lines modified | ||
| 105 | Out[16]:·5 | 105 | Out[16]:·5 |
| 106 | In·[17]:·snap.particles.N | 106 | In·[17]:·snap.particles.N |
| 107 | Out[17]:·9 | 107 | Out[17]:·9 |
| 108 | In·[18]:·snap.particles.position | 108 | In·[18]:·snap.particles.position |
| 109 | Out[18]: | 109 | Out[18]: |
| 110 | array([[0.04864376,·0.6388678·,·0.47861114], | ||
| 111 | ·······[0.51105905,·0.02546922,·0.39761963], | ||
| 112 | ·······[0.05343684,·0.2479186·,·0.43118024], | ||
| 113 | ·······[0.78773755,·0.7398912·,·0.33950448], | ||
| 114 | ·······[0.69232833,·0.7173891·,·0.32247263], | ||
| 115 | ·······[0.1698959·,·0.881418··,·0.521817··], | ||
| 116 | ·······[0.5025626·,·0.2316291·,·0.69645876], | ||
| 117 | ·······[0.11591081,·0.18207751,·0.44569942], | ||
| 118 | 110 | array([[0.31649902,·0.930899··,·0.6207448·], | |
| 111 | ·······[0.11056859,·0.62811136,·0.20228414], | ||
| 112 | ·······[0.94560254,·0.85934305,·0.0717991·], | ||
| 113 | ·······[0.24312589,·0.6255072·,·0.8853982·], | ||
| 114 | ·······[0.9675033·,·0.35954842,·0.36298457], | ||
| 115 | ·······[0.79735494,·0.62377787,·0.34841114], | ||
| 116 | ·······[0.5194623·,·0.19607814,·0.7781965·], | ||
| 117 | ·······[0.7472676·,·0.80175644,·0.10671829], | ||
| 118 | ·······[0.6548015·,·0.93369675,·0.04346667]],·dtype=float32) | ||
| 119 | gsd.hoomd.HOOMDTrajectory·supports·random·indexing·of·frames·in·the·file. | 119 | gsd.hoomd.HOOMDTrajectory·supports·random·indexing·of·frames·in·the·file. |
| 120 | Indexing·into·a·trajectory·returns·a·gsd.hoomd.Snapshot. | 120 | Indexing·into·a·trajectory·returns·a·gsd.hoomd.Snapshot. |
| 121 | *****·Slicing·and·selectionï·***** | 121 | *****·Slicing·and·selectionï·***** |
| 122 | Use·the·slicing·operator·to·select·individual·frames·or·a·subset·of·a | 122 | Use·the·slicing·operator·to·select·individual·frames·or·a·subset·of·a |
| 123 | trajectory. | 123 | trajectory. |
| 124 | In·[19]:·f·=·gsd.hoomd.open(name='test.gsd',·mode='rb') | 124 | In·[19]:·f·=·gsd.hoomd.open(name='test.gsd',·mode='rb') |
| Offset 142, 21 lines modified | Offset 142, 21 lines modified | ||
| 142 | *****·Pure·python·readerï·***** | 142 | *****·Pure·python·readerï·***** |
| 143 | In·[23]:·f·=·gsd.pygsd.GSDFile(open('test.gsd',·'rb')) | 143 | In·[23]:·f·=·gsd.pygsd.GSDFile(open('test.gsd',·'rb')) |
| 144 | In·[24]:·t·=·gsd.hoomd.HOOMDTrajectory(f); | 144 | In·[24]:·t·=·gsd.hoomd.HOOMDTrajectory(f); |
| 145 | In·[25]:·t[3].particles.position | 145 | In·[25]:·t[3].particles.position |
| 146 | Out[25]: | 146 | Out[25]: |
| 147 | array([[0.7596063·,·0.35071316,·0.44357768], | ||
| 148 | ·······[0.9681369·,·0.2930677·,·0.7252575·], | ||
| 149 | ·······[0.6025038·,·0.48719928,·0.28194723], | ||
| 150 | ·······[0.9904632·,·0.5146152·,·0.821801··], | ||
| 151 | ·······[0.16287279,·0.9844114·,·0.13382909], | ||
| 152 | ·······[0.7138911·,·0.75650555,·0.12414929], | ||
| 153 | 147 | array([[0.8549712·,·0.8540309·,·0.88189095], | |
| 148 | ·······[0.9028438·,·0.2554103·,·0.2721972·], | ||
| 149 | ·······[0.9459284·,·0.6330105·,·0.4404471·], | ||
| 150 | ·······[0.8604843·,·0.3100594·,·0.21919934], | ||
| 151 | ·······[0.20218222,·0.10614425,·0.4902229·], | ||
| 152 | ·······[0.7367657·,·0.9544418·,·0.47768393], | ||
| 153 | ·······[0.66016376,·0.37475777,·0.17023604]],·dtype=float32) | ||
| 154 | You·can·use·GSD·without·needing·to·compile·C·code·to·read·GSD·files·using | 154 | You·can·use·GSD·without·needing·to·compile·C·code·to·read·GSD·files·using |
| 155 | gsd.pygsd.GSDFile·in·combination·with·gsd.hoomd.HOOMDTrajectory.·It·only | 155 | gsd.pygsd.GSDFile·in·combination·with·gsd.hoomd.HOOMDTrajectory.·It·only |
| 156 | supports·the·rb·mode·and·does·not·read·files·as·fast·as·the·C·implementation. | 156 | supports·the·rb·mode·and·does·not·read·files·as·fast·as·the·C·implementation. |
| 157 | It·takes·in·a·python·file-like·object,·so·it·can·be·used·with·in-memory·IO | 157 | It·takes·in·a·python·file-like·object,·so·it·can·be·used·with·in-memory·IO |
| 158 | classes,·and·grid·file·classes·that·access·data·over·the·internet. | 158 | classes,·and·grid·file·classes·that·access·data·over·the·internet. |
| 159 | Warning | 159 | Warning |
| 160 | gsd.pygsd·is·slow.·Use·gsd.hoomd.open·whenever·possible. | 160 | gsd.pygsd·is·slow.·Use·gsd.hoomd.open·whenever·possible. |
| Offset 809, 66 lines modified | Offset 809, 66 lines modified | ||
| 809 | ········"step":·[8,·11,·13,·15,·17], | 809 | ········"step":·[8,·11,·13,·15,·17], |
| 810 | ········"random":·[8,·9], | 810 | ········"random":·[8,·9], |
| 811 | ········"extend":·[8,·13,·15], | 811 | ········"extend":·[8,·13,·15], |
| 812 | ········"rang":·[8,·14], | 812 | ········"rang":·[8,·14], |
| 813 | ········"similar":·8, | 813 | ········"similar":·8, |
| 814 | ········"express":·[8,·12], | 814 | ········"express":·[8,·12], |
| 815 | ········"snap":·8, | 815 | ········"snap":·8, |
| 816 | ········"31649902":·8, | ||
| 817 | ········"930899":·8, | ||
| 816 | ········" | 818 | ········"6207448":·8, |
| 819 | ········"11056859":·8, | ||
| 820 | ········"62811136":·8, | ||
| 821 | ········"20228414":·8, | ||
| 822 | ········"94560254":·8, | ||
| 823 | ········"85934305":·8, | ||
| 824 | ········"0717991":·8, | ||
| 825 | ········"24312589":·8, | ||
| 826 | ········"6255072":·8, | ||
| 827 | ········"8853982":·8, | ||
| 828 | ········"9675033":·8, | ||
| 829 | ········"35954842":·8, | ||
| 830 | ········"36298457":·8, | ||
| 831 | ········"79735494":·8, | ||
| 817 | ········"6 | 832 | ········"62377787":·8, |
| 818 | ········" | 833 | ········"34841114":·8, |
| 819 | ········"51105905":·8, | ||
| 820 | ········" | 834 | ········"5194623":·8, |
| 821 | ········"39761963":·8, | ||
| 822 | ········"05343684":·8, | ||
| 823 | ········"2479186":·8, | ||
| 824 | ········"43118024":·8, | ||
| 825 | ········"78773755":·8, | ||
| 826 | ········"7398912":·8, | ||
| 827 | ········"33950448":·8, | ||
| 828 | ········"69232833":·8, | ||
| 829 | ········"7173891":·8, | ||
| 830 | ········"32247263":·8, | ||
| 831 | ········"1698959":·8, | ||
| 832 | ········"881418":·8, | ||
| 833 | ········"521817":·8, | ||
| 834 | ········"5025626":·8, | ||
| 835 | ········"2316291":·8, | ||
| 836 | ········"69645876":·8, | ||
| 837 | ········"1 | 835 | ········"19607814":·8, |
| 838 | ········" | 836 | ········"7781965":·8, |
| 839 | ········"44569942":·8, | ||
| 840 | ········" | 837 | ········"7472676":·8, |
| 838 | ········"80175644":·8, | ||
| 839 | ········"10671829":·8, | ||
| 841 | ········" | 840 | ········"6548015":·8, |
| 841 | ········"93369675":·8, | ||
| 842 | ········" | 842 | ········"04346667":·8, |
| 843 | ········"individu":·8, | 843 | ········"individu":·8, |
| 844 | ········"print":·[8,·16], | 844 | ········"print":·[8,·16], |
| 845 | ········"every_2nd_fram":·8, | 845 | ········"every_2nd_fram":·8, |
| 846 | ········"t":·[8,·11,·16], | 846 | ········"t":·[8,·11,·16], |
| 847 | ········"7596063":·8, | ||
| 848 | ········" | 847 | ········"8549712":·8, |
| 849 | ········"44357768":·8, | ||
| 850 | ········" | 848 | ········"8540309":·8, |
| 849 | ········"88189095":·8, | ||
| 851 | ········"2930677":·8, | ||
| 852 | ········"7252575":·8, | ||
| 853 | ········" | 850 | ········"9028438":·8, |
| 854 | ········" | 851 | ········"2554103":·8, |
| 855 | ········"2 | 852 | ········"2721972":·8, |
| 856 | ········"9 | 853 | ········"9459284":·8, |
| 854 | ········"6330105":·8, | ||
| 855 | ········"4404471":·8, | ||
| 856 | ········"8604843":·8, | ||
| 857 | ········" | 857 | ········"3100594":·8, |
| 858 | ········" | 858 | ········"21919934":·8, |
| 859 | ········"20218222":·8, | ||
| 860 | ········"10614425":·8, | ||
| 859 | ········" | 861 | ········"4902229":·8, |
| 862 | ········"7367657":·8, | ||
| 860 | ········"9 | 863 | ········"9544418":·8, |
| 861 | ········"13382909":·8, | ||
| 862 | ········"7 | 864 | ········"47768393":·8, |
| 863 | ········"75650555":·8, | ||
| 864 | ········"12414929":·8, | ||
| 865 | ········"8925799":·8, | ||
| 866 | ········"5341969":·8, | ||
| 867 | ········" | 865 | ········"66016376":·8, |
| 866 | ········"37475777":·8, | ||
| 867 | ········"17023604":·8, | ||
| 868 | ········"It":·[8,·13,·16,·17], | 868 | ········"It":·[8,·13,·16,·17], |
| 869 | ········"like":·[8,·14,·16], | 869 | ········"like":·[8,·14,·16], |
| 870 | ········"grid":·[8,·16], | 870 | ········"grid":·[8,·16], |
| 871 | ········"over":·[8,·15], | 871 | ········"over":·[8,·15], |
| 872 | ········"internet":·[8,·11], | 872 | ········"internet":·[8,·11], |
| 873 | ········"slow":·8, | 873 | ········"slow":·8, |
| 874 | ········"whenev":·8, | 874 | ········"whenev":·8, |